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  • 1. Adam, GIR
    et al.
    Cui, HM
    Miller, SJ
    Flam, F
    Ohlsson, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Allele-specific in situ hybridization (ASISH) analysis: A novel technique which resolves differential allelic usage of H19 within the same cell lineage during human placental development1996In: DEVELOPMENT, ISSN 0950-1991, Vol. 122, no 3, p. 839-847Article in journal (Refereed)
    Abstract [en]

    Precursory studies of H19 transcription during human foetal development have demonstrated maternally derived monoallelic expression, Analyses in extra-embryonic tissues, however, have been more equivocal, with discernible levels of expression of the pater

  • 2. Adewumi, Oluseun
    et al.
    Aflatoonian, Behrouz
    Ahrlund-Richter, Lars
    Amit, Michal
    Andrews, Peter W.
    Beighton, Gemma
    Bello, Paul A.
    Benvenisty, Nissim
    Berry, Lorraine S.
    Bevan, Simon
    Blum, Barak
    Brooking, Justin
    Chen, Kevin G.
    Choo, Andre B. H.
    Churchill, Gary A.
    Corbel, Marie
    Damjanov, Ivan
    Draper, Jon S.
    Dvorak, Petr
    Emanuelsson, Katarina
    Fleck, Roland A.
    Ford, Angela
    Gertow, Karin
    Gertsenstein, Marina
    Gokhale, Paul J.
    Hamilton, Rebecca S.
    Hampl, Ales
    Healy, Lyn E.
    Hovatta, Outi
    Hyllner, Johan
    Imreh, Marta P.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Itskovitz-Eldor, Joseph
    Jackson, Jamie
    Johnson, Jacqueline L.
    Jones, Mark
    Kee, Kehkooi
    King, Benjamin L.
    Knowles, Barbara B.
    Lako, Majlinda
    Lebrin, Franck
    Mallon, Barbara S.
    Manning, Daisy
    Mayshar, Yoav
    Mckay, Ronald D. G.
    Michalska, Anna E.
    Mikkola, Milla
    Mileikovsky, Masha
    Minger, Stephen L.
    Moore, Harry D.
    Mummery, Christine L.
    Nagy, Andras
    Nakatsuji, Norio
    O'Brien, Carmel M.
    Oh, Steve K. W.
    Olsson, Cia
    Otonkoski, Timo
    Park, Kye-Yoon
    Passier, Robert
    Patel, Hema
    Patel, Minal
    Pedersen, Roger
    Pera, Martin F.
    Piekarczyk, Marian S.
    Pera, Renee A. Reijo
    Reubinoff, Benjamin E.
    Robins, Allan J.
    Rossant, Janet
    Rugg-Gunn, Peter
    Schulz, Thomas C.
    Semb, Henrik
    Sherrer, Eric S.
    Siemen, Henrike
    Stacey, Glyn N.
    Stojkovic, Miodrag
    Suemori, Hirofumi
    Szatkiewicz, Jin
    Turetsky, Tikva
    Tuuri, Timo
    van den Brink, Steineke
    Vintersten, Kristina
    Vuoristo, Sanna
    Ward, Dorien
    Weaver, Thomas A.
    Young, Lesley A.
    Zhang, Weidong
    Characterization of human embryonic stem cell lines by the International Stem Cell Initiative2007In: Nature Biotechnology, ISSN 1087-0156, E-ISSN 1546-1696, Vol. 25, no 7, p. 803-816Article in journal (Refereed)
    Abstract [en]

    The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue- nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.

  • 3. Aucott, Rebecca
    et al.
    Bullwinkel, Joern
    Yu, Yang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Billur, Mustafa
    Brown, Jeremy P.
    Menzel, Ursula
    Kioussis, Dimitris
    Wang, Guozheng
    Reisert, Ingrid
    Weimer, Joerg
    Pandita, Raj K.
    Sharma, Girdhar G.
    Pandita, Tej K.
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Singh, Prim B.
    HP1-beta is required for development of the cerebral neocortex and neuromuscular junctions2008In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 183, no 4, p. 597-606Article in journal (Refereed)
    Abstract [en]

    HP1 proteins are thought to be modulators of chromatin organization in all mammals, yet their exact physiological function remains unknown. In a first attempt to elucidate the function of these proteins in vivo, we disrupted the murine Cbx1 gene, which encodes the HP1-beta isotype, and show that the Cbx1(-/-) null mutation leads to perinatal lethality. The newborn mice succumbed to acute respiratory failure, whose likely cause is the defective development of neuromuscular junctions within the endplate of the diaphragm. We also observe aberrant cerebral cortex development in Cbx1(-/-) mutant brains, which have reduced proliferation of neuronal precursors, widespread cell death, and edema. In vitro cultures of neurospheres from Cbx1(-/-) mutant brains reveal a dramatic genomic instability. Our results demonstrate that HP1 proteins are not functionally redundant and that they are likely to regulate lineage-specific changes in heterochromatin organization.

  • 4. Barton, S C
    et al.
    Arney, K L
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Niveleau, A
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Surani, M A
    Haaf, T
    Genome-wide methylation patterns in normal and uniparental early mouse embryos2001In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 10, no 26, p. 2983-7Article in journal (Refereed)
  • 5.
    Bergström, Rosita
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utveckling.
    Epigenetic Regulation of Replication Timing and Signal Transduction2006Licentiate thesis, monograph (Other scientific)
  • 6. Bergström, Rosita
    et al.
    Lezcano, Magda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Sjölinder, Mikael
    Mukhopadhyay, Rituparna
    Whitehead, Joanne
    Tiwari, Vijay Kumar
    Kurukuti, Sreenivasulu
    Mattsson, Anita
    Ohlsson, Rolf
    The Chromatin Insulator Protein CTCF delays DNA Replication TimingArticle in journal (Refereed)
  • 7. Bertilsson, G
    et al.
    Heidrich, J
    Svensson, K
    Asman, M
    Jendeberg, L
    Sydow-Backman, M
    Ohlsson, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Postlind, H
    Blomquist, P
    Berkenstam, A
    Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction1998In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, ISSN 0027-8424, Vol. 95, no 21, p. 12208-12213Article in journal (Other scientific)
    Abstract [en]

    Nuclear receptors regulate metabolic pathways in response to changes in the environment by appropriate alterations in gene expression of key metabolic enzymes, Here, a computational search approach based on iteratively built hidden Markov models of nuclea

  • 8. Brunner, Sandra
    et al.
    Colman, Dvora
    Travis, Alexander J.
    Luhmann, Ulrich F. O.
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Feil, Silke
    Imsand, Coni
    Nelson, Jacquelyn
    Grimm, Christian
    Ruelicke, Thomas
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Neidhardt, John
    Berger, Wolfgang
    Overexpression of RPGR leads to male infertility in mice due to defects in flagellar assembly2008In: Biology of Reproduction, ISSN 0006-3363, E-ISSN 1529-7268, Vol. 79, no 4, p. 608-617Article in journal (Refereed)
    Abstract [en]

    Male infertility is one possible consequence of a group of disorders arising from dysfunction of cilia. Ciliopathies include primary ciliary dyskinesia, polycystic kidney disease, Usher syndrome, nephronophthisis, Bardet-Biedl syndrome, Alstrom syndrome, and Meckel-Gruber syndrome as well as some forms of retinal degenerations. Mutations in the retinitis pigmentosa GTPase regulator gene (RPGR) are best known for leading to retinal degeneration but have also been associated with ciliary dysfunctions affecting other tissues. To further study the involvement of RPGR in ciliopathies, transgenic mouse lines overexpressing RPGR were generated. Animals carrying the transgene in varying copy numbers were investigated. We found that infertility due to aberrant spermatozoa correlated with increased copy numbers. In animals with moderately increased gene copies of Rpgr, structural disorganization in the flagellar midpiece, outer dense fibers, and fibrous sheath was apparent. In contrast, in animals with high copy numbers, condensed sperm heads were present, but the flagellum was absent in the vast majority of spermatozoa, although early steps of flagellar biogenesis were observed. This complexity of defects in flagellar assembly suggests a role of RPGR in intraflagellar transport processes.

  • 9. Bugge, Anne
    et al.
    Siersbaek, Majken
    Madsen, Maria S.
    Göndör, Anita
    Rougier, Carole
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Mandrup, Susanne
    A Novel Intronic Peroxisome Proliferator-activated Receptor gamma Enhancer in the Uncoupling Protein (UCP) 3 Gene as a Regulator of Both UCP2 and-3 Expression in Adipocytes2010In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 285, no 23, p. 17310-17317Article in journal (Refereed)
    Abstract [en]

    Uncoupling Proteins (UCPs) are integral ion channels residing in the inner mitochondrial membrane. UCP2 is ubiquitously expressed, while UCP3 is found primarily in muscles and adipose tissue. Although the exact molecular mechanism of action is controversial, it is generally agreed that both homologues function to facilitate mitochondrial fatty acid oxidation. UCP2 and -3 expression is activated by the peroxisome proliferator-activated receptors (PPARs), but so far no PPAR response element has been reported in the vicinity of the Ucp2 and Ucp3 genes. Using genome-wide profiling of PPAR gamma occupancy in 3T3-L1 adipocytes we demonstrate that PPAR gamma associates with three chromosomal regions in the vicinity of the Ucp3 locus and weakly with a site in intron 1 of the Ucp2 gene. These sites are isolated from the nearest neighboring sites by >900 kb. The most prominent PPAR gamma binding site in the Ucp2 and Ucp3 loci is located in intron 1 of the Ucp3 gene and is the only site that facilitates PPAR gamma transactivation of a heterologous promoter. This site furthermore transactivates the endogenous Ucp3 promoter, and using chromatin conformation capture we show that it loops out to specifically interact with the Ucp2 promoter and intron 1. Our data indicate that PPAR gamma transactivation of both UCP2 and -3 is mediated through this novel enhancer in Ucp3 intron 1.

  • 10. Burke, Les J
    et al.
    Zhang, Ru
    Bartkuhn, Marek
    Tiwari, Vijay K
    Tavoosidana, Gholamreza
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Kurukuti, Sreenivasulu
    Weth, Christine
    Leers, Joerg
    Galjart, Niels
    Ohlsson, Rolf
    CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin2005In: European Molecular Biology Organization, ISSN 0261 - 4189, Vol. 24, no 18, p. 10-Article in journal (Refereed)
  • 11. Burke, Les J
    et al.
    Zhang, Ru
    Bartkuhn, Marek
    Tiwari, Vijay K
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Tavoosidana, Gholamreza
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbioloig.
    Kurukuti, Sreenivasulu
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Weth, Christine
    Leers, Joerg
    Galjart, Niels
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Renkawitz, Rainer
    CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin.2005In: EMBO J, ISSN 0261-4189, Vol. 24, no 18, p. 3291-300Article in journal (Refereed)
  • 12. Burke, Les J
    et al.
    Zhang, Ru
    Bartkuhn, Marek
    Tiwari, Vijay Kumar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Tavosidana, Gholamreza
    Kurukuti, Sreenivasulu
    Weth, Christine
    Leers, Joerg
    Galjart, Niels
    Ohlsson, Rolf
    CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin2005In: EMBO journal, ISSN 0261-4189, Vol. 24, no 18, p. 3291-3300Article in journal (Refereed)
  • 13. Chernukhin, Igor
    et al.
    Shamsuddin, Shaharum
    Bergstrom, Rosita
    Yu, WenQiang
    Whitehead, Joanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Mukhopadhyay, Rituparna
    Docquier, France
    Kang, Sung Yun
    Vigneron, Marc
    Wu, Shwu-Yuan
    CTCF complexes with the largest subunit of RNA polymerase II are recruited to CTCF target sites genome-wide: implications for the mechanism of chromatin insulator function and origin of noncoding transcriptsArticle in journal (Refereed)
  • 14. Chernukhin, Igor
    et al.
    Shamsuddin, Shaharum
    Kang, Sung Yun
    Bergström, Rosita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Kwon, Yoo-Wook
    Yu, WenQiang
    Whitehead, Joanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Mukhopadhyay, Rituparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Docquier, France
    Farrar, Dawn
    Morrison, Ian
    Vigneron, Marc
    Wu, Shwu-Yuan
    Chiang, Sheng-Ming
    Loukinov, Dimitri
    Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Klenova, Elena
    CTCF Interacts with and Recruits the Largest Subunit of RNA Polymerase II to CTCF Target Sites Genome-Wide2007In: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 27, no 5, p. 1631-1648Article in journal (Refereed)
    Abstract [en]

    CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. "Serial" chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the β-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.

  • 15. Constância, Miguel
    et al.
    Hemberger, Myriam
    Hughes, Jennifer
    Dean, Wendy
    Ferguson-Smith, Anne
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Stewart, Francesca
    Kelsey, Gavin
    Fowden, Abigail
    Sibley, Colin
    Reik, Wolf
    Placental-specific IGF-II is a major modulator of placental and fetal growth2002In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 417, no 6892, p. 945-8Article in journal (Refereed)
  • 16. Cowell, Ian G.
    et al.
    Aucott, Rebecca
    Mahadevaiah, Shantha K.
    Burgoyne, Paul S.
    Huskisson, Neville
    Bongiorni, Silvia
    Prantera, Giorgio
    Fanti, Laura
    Pimpinelli, Sergio
    Wu, Rong
    Gilbert, David M.
    Shi, Wei
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Morrison, Harris
    Jeppesen, Peter
    Singh, Prim B.
    Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals2002In: Chromosoma, ISSN 0009-5915, E-ISSN 1432-0886, Vol. 111, no 1, p. 22-36Article in journal (Refereed)
  • 17. Cross, JC
    et al.
    Coan, PM
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Hemberger, M
    Kibschull, M
    Ferguson-Smith, AC
    Genes and development: a workshop report2004In: Placenta Supplement A, Trophoblast Research, ISSN 0143-4004, Vol. 18, p. S39-S41Article in journal (Refereed)
  • 18. Cui, H
    et al.
    Hedborg, F
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Women's and Children's Health. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    He, L
    Nordenskjold, A
    Pfeifer, S
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Women's and Children's Health. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Ohlsson, R
    Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Inactivation of H19, an imprinted and putative tumor repressor gene, is a preneoplastic event during Wilms' tumorigenesis1997In: Cancer Research, Vol. 57, p. 4469-Article in journal (Refereed)
    Abstract [en]

    Genetic evidence shows that the parent of origin-dependent expression patterns of the Igf2 and H19 genes is coordinated in mouse, such that H19 controls the activity of Igf2 in cis. Equally compelling evidence for a similar situation in humans is absent, although the frequently observed activation of the maternal IGF2 allele (ie., loss of imprinting) in Wilms' tumors has been attributed to the silencing of the maternal H19 locus. We show here that loss of H19 activity is generally a preneoplastic event, which may be linked with an overgrowth lesion that has been proposed to be permissive for tumor formation. Although our results document one instance in which a postneoplastic loss of H19 activity correlates with loss of IGF2 imprinting at the cellular level, it appears that inactivation of H19 is more generally independent of loss of imprinting of IGF2, at least in our specimens. Our results imply that inactivation of H19 correlates with blastema overgrowth and can be independent of a regulatory role with respect to IGF2 imprinting status in cis.

  • 19. EKSTROM, TJ
    et al.
    CUI, HM
    OHLSSON, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    PROMOTER-SPECIFIC IGF2 IMPRINTING STATUS AND ITS PLASTICITY DURING HUMAN LIVER DEVELOPMENT1995In: DEVELOPMENT, ISSN 0950-1991, Vol. 121, no 2, p. 309-316Article in journal (Refereed)
    Abstract [en]

    IGF2 has been shown to be expressed preferentially from the paternally derived allele, although the maternal allele can be found active during both prenatal and postnatal development as well as in neoplastic tumours in humans. We addressed here whether or not the biallelic expression patterns that can be seen during postnatal human liver development reflected a coordinated change in the activities of the four promoters of human IGF2. We show here that the P2, P3 and P4 promoters, but not the P1 promoter, display monoallelic activity in embryonic, neonatal and younger infant liver specimens. The P2, P3 and P4 promoters can, however, be found active either monoallelically or biallelically or even monoallelically on opposite parental alleles in older infant and adult liver specimens. In contrast, H19, which is closely linked to IGF2, is monoallelically expressed in all postnatal liver samples analysed. We conclude that the functional imprinting status of IGF2 during postnatal liver development appears to be promoter/enhancer-specific and either partly or completely independent of H19.

  • 20.
    Emilsson, Lina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Alzheimer’s disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signalling2006In: Neurobiology of Disease, ISSN 0969-9961, E-ISSN 1095-953X, Vol. 21, no 3, p. 618-625Article in journal (Refereed)
    Abstract [en]

    We combined global and high-resolution strategies to find genes with altered mRNA expression levels in one of the largest collection of brain autopsies from Alzheimer's patients and controls ever studied. Our global analysis involved microarray hybridizations of large pools of samples obtained from 114 individuals, using two independent sets of microarrays. Ten genes selected from the microarray experiments were quantified on each individual separately using real-time RT-PCR. This high-resolution analysis accounted for systematic differences in age, postmortem interval, brain pH, and reference gene expression, and it estimated the effect of disease on mRNA levels, on top of the effect of all other variables. Differential expression was confirmed for eight out of ten genes. Among them, Type B inositol 1,4,5-trisphosphate 3-kinase (ITPKB), and regulator of G protein signaling 4 (RGS4) showed highly altered expression levels in patients (P values < 0.0001). Our results point towards increased inositol triphospate (IP3)-mediated calcium signaling in Alzheimer's disease.

  • 21.
    Emilsson, Lina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Low mRNA levels of RGS4 splice variants in Alzheimer’s disease and association between a rare haplotype and decreased mRNA expression2006In: Synapse, ISSN 0887-4476, E-ISSN 1098-2396, Vol. 59, no 3, p. 173-176Article in journal (Refereed)
    Abstract [en]

    Regulator of G-protein signaling 4 (RGS4) showed decreased mRNAlevels in Alzheimer’s disease in a large collection of human brain autopsies from prefrontalcortex. The expression levels of three RGS4 splice variants were examined inthe same samples, and the association between RGS4 gene expression and/or the diseasewith single nucleotide polymorphisms located in this gene was explored. We showthat all splice variants are down-regulated in patients. We also demonstrate that onerare haplotype (ATAG) is associated with decreased mRNA levels in both cases andcontrols. Our results suggest that an altered regulation in transcription initiation maybe an important mechanism for low RGS4 protein levels in Alzeimer’s disease.

  • 22. Feinberg, Andrew P
    et al.
    Cui, Hengmi
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    DNA methylation and genomic imprinting: insights from cancer into epigenetic mechanisms.2002In: Semin Cancer Biol, ISSN 1044-579X, Vol. 12, no 5, p. 389-98Article in journal (Refereed)
  • 23. Feinberg, Andrew P
    et al.
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Henikoff, Steven
    The epigenetic progenitor origin of human cancer.2006In: Nat Rev Genet, ISSN 1471-0056, Vol. 7, no 1, p. 21-33Article in journal (Refereed)
  • 24. Frank, D
    et al.
    Mendelsohn, C L
    Ciccone, E
    Svensson, K
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Ohlsson, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Tycko, B
    A novel pleckstrin homology-related gene family defined by Ipl/Tssc3, TDAG51, and Tih1: tissue-specific expression, chromosomal location, and parental imprinting.1999In: Mamm Genome, ISSN 0938-8990, Vol. 10, no 12, p. 1150-9Article in journal (Refereed)
    Abstract [en]

    We previously described a gene, Ipl (Tssc3), that is expressed selectively from the maternal allele in placenta, yolk sac, and fetal liver and that maps within the imprinted domain of mouse distal Chromosome (Chr) 7/human Chr 11p15.5 (Hum Mol Genet 6, 2021, 1997). Ipl is similar to TDAG51, a gene that is involved in FAS/CD95 expression. Here we describe another gene, Tih1 (TDAG/Ipl homologue 1), with equivalent sequence similarity to Ipl. Structural prediction indicates that the products of these three genes share a central motif resembling a pleckstrin-homology (PH) domain, and TIH1 protein has weak sequence similarity to the PH-domain protein SEC7/CYTOHESIN. Like Ipl, Tih1 is a small gene with a single small intron. Tih1 maps to distal mouse Chr 1 and human Chr 1q31, chromosomal regions that have not shown evidence for imprinting and, in contrast to Ipl, Tih1 is expressed equally from both parental alleles. Ipl, Tih1, and TDAG51 have overlapping but distinct patterns of expression. Tih1 and TDAG51 are expressed in multiple fetal and adult tissues. In contrast, during early mouse development Ipl mRNA and protein are highly specific for two tissues involved in maternal/fetal exchange: visceral endoderm of the yolk sac and labyrinthine trophoblast of the placenta. These findings highlight the dominance of chromosomal context over gene structure in some examples of parental imprinting and extend previous evidence for placenta-specific expression of imprinted genes. The data also define a new subfamily of PH domain genes.

  • 25. Franklin, Gary C.
    et al.
    Adam, Gail I.R.
    Miller, Stephen J.
    Moncrieff, Colin L.
    Ullerås, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    An Inr-containing sequence flanking the TATA box of the human c-sis (PDGF-B) proto-oncogene promoter functions in cis as a co-activator for its intronic enhancer1995In: Oncogene, ISSN 0950-9232, E-ISSN 1476-5594, Vol. 11, no 9, p. 1873-1884Article in journal (Other academic)
    Abstract [en]

    High-level activity of the human PDGF-B promoter in choriocarcinoma cell lines depends upon an atypical, intronic enhancer-like element which does not function with heterologous promoters tested. An extensive series of mutant PDGF-B promoter-driven constructs identified a sequence flanking the TATA box which is required specifically for enhancer-mediated transcription in human choriocarcinoma cell lines. This element, which we here term an enhancer-dependent cis co-activator (EDC) contains an Inr (initiator) consensus sequence upstream of the TATA box which is required, but not sufficient for its function. Requirement for the EDC is cell type-specific, since it was dispensable for enhancer-mediated transcription in a human breast cancer cell line. Although it lies within the region defined, the TATA box itself is not required for EDC function, or for basal promoter function which may derive from a second Inr-like sequence situated at the transcriptional start site. These observations indicate that interactions between some promoter and enhancer elements may be more complex than that generally described for 'classical' enhancer systems and may suggest an additional function for the initiator motif.

  • 26.
    Guibert, Sylvain
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Zhao, Zhihu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Sjölinder, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Göndör, Anita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Fernandez, Alejandro
    Pant, Vinod
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    CTCF-binding sites within the H19 ICR differentially regulate local chromatin structures and cis-acting functions2012In: Epigenetics, ISSN 1559-2294, E-ISSN 1559-2308, Vol. 7, no 4, p. 361-369Article in journal (Refereed)
    Abstract [en]

    It is generally assumed that CTCF-binding sites are synonymous with the demarcation of expression domains by promoting the formation of chromatin loops. We have proposed earlier, however, that such features may be context-dependent. In support of this notion, we show here that chromatin loop structures, impinging on CTCF-binding sites 1/2 and 3/4 at the 5' and 3'-ends, respectively, within the maternal allele of the H19 imprinting control region (ICR), differ significantly. Although abrogation of CTCF binding to the maternal H19 ICR allele results in loss of chromatin loops in the 3'-region, there is a dramatic gain of long-range chromatin loops impinging on the 5'-region. As the degree of occupancy of its four CTCF-binding sites discriminates between the chromatin insulator and replication timing functions, we submit that the CTCF-binding sites within the H19 ICR are functionally diverse and organize context-dependent higher order chromatin conformations.

  • 27.
    Göndör, Anita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Epigenetic Regulation of Higher Order Chromatin Conformations and Gene Transcription2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Epigenetic states constitute heritable features of the chromatin to regulate when, where and how genes are expressed in the developing conceptus. A special case of epigenetic regulation, genomic imprinting, is defined as parent of origin-dependent monoallelic expression. The Igf2-H19 locus is considered as paradigm of genomic imprinting with a growth-promoting gene, Igf2, expressed paternally and a growth antagonist, H19 encoding a non-coding transcript, expressed only from the maternal allele. The monoallelic expression patterns are regulated by the epigenetic status at an imprinting control region (ICR) in the 5´-flank of the H19 gene. The chromatin insulator protein CTCF interacts with only the maternal H19 ICR allele to prevent downstream enhancers to communicate with the Igf2 promoters. Mutations of these CTCF binding sites lead to biallelic Igf2 expression, increased size of the conceptus and predisposition for cancer.

    Reasoning that these effects cannot be explained by the regulation of Igf2 expression alone, a technique was invented to examine long-range chromatin interactions without prior knowledge of the interacting partners. Applying the circular chromosomal conformation capture (4C) technique to mouse neonatal liver cells, it was observed that 114 unique sequences interacted with the H19 ICR. A majority of these interactors was in complex with only the maternal H19 ICR allele and depended on the presence of functional CTCF binding sites. The functional consequence of chromosomal networks was demonstrated by the observation that the maternal H19 ICR allele regulated the transcription of two genes on another chromosome. As the chromosomal networks underwent reprogramming during the maturation of embryonic stem cells, attention was turned to human cancer cells, displaying features common with mouse embryonic stem cells. Subsequently, chromatin folding at the human H19 ICR suggested that stable chromatin loops were organized by synergistic interactions within and between baits and interactors. The presence of these interactions was linked to DNA methylation patterns involving repeat elements. A "flower" model of chromatin networks was formulated to explain these observations.

    This thesis has unravealed a novel feature of the epigenome and its functions to regulate gene expression in trans. The identified roles for CTCF as an architectural factor in the organization of higher order chromatin conformations may be of importance in understanding development and disease ontogeny from novel perspectives.

    List of papers
    1. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
    Open this publication in new window or tab >>Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
    Show others...
    2006 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 38, no 11, p. 1341-1347Article in journal (Refereed) Published
    Abstract [en]

    Accumulating evidence converges on the possibility that chromosomes interact with each other to regulate transcription in trans. To systematically explore the epigenetic dimension of such interactions, we devised a strategy termed circular chromosome conformation capture (4C). This approach involves a circularization step that enables high-throughput screening of physical interactions between chromosomes without a preconceived idea of the interacting partners. Here we identify 114 unique sequences from all autosomes, several of which interact primarily with the maternally inherited H19 imprinting control region. Imprinted domains were strongly overrepresented in the library of 4C sequences, further highlighting the epigenetic nature of these interactions. Moreover, we found that the direct interaction between differentially methylated regions was linked to epigenetic regulation of transcription in trans. Finally, the patterns of interactions specific to the maternal H19 imprinting control region underwent reprogramming during in vitro maturation of embryonic stem cells. These observations shed new light on development, cancer epigenetics and the evolution of imprinting.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96389 (URN)10.1038/ng1891 (DOI)000241592700025 ()17033624 (PubMedID)
    Available from: 2007-10-31 Created: 2007-10-31 Last updated: 2017-12-14Bibliographically approved
    2. A high-resolution map of chromatin loops impinging on the human H19 imprinting control region in cis uncovers a re-peat element-based higher order chromatin structure
    Open this publication in new window or tab >>A high-resolution map of chromatin loops impinging on the human H19 imprinting control region in cis uncovers a re-peat element-based higher order chromatin structure
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-96390 (URN)
    Available from: 2007-10-31 Created: 2007-10-31 Last updated: 2010-01-14Bibliographically approved
    3. High-resolution circular chromosomal conformation cap-ture (4C) assay
    Open this publication in new window or tab >>High-resolution circular chromosomal conformation cap-ture (4C) assay
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-96391 (URN)
    Available from: 2007-10-31 Created: 2007-10-31 Last updated: 2010-01-14Bibliographically approved
    4. The 4C technique: the ‘Rosetta stone’ for genome biology in 3D?
    Open this publication in new window or tab >>The 4C technique: the ‘Rosetta stone’ for genome biology in 3D?
    2007 (English)In: Current Opinion in Cell Biology, ISSN 0955-0674, E-ISSN 1879-0410, Vol. 19, no 3, p. 321-325Article in journal (Refereed) Published
    Abstract [en]

    Despite considerable efforts, the spatial link between the nuclear architecture and the genome remains enigmatic. The 4C method, independently innovated in four different laboratories, might in combination with other methods change that. As this method is based on the unbiased identification of sequences interacting with specific baits, there are unique opportunities for unravelling the secrets of how the genome functions in 3D.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96392 (URN)10.1016/j.ceb.2007.04.008 (DOI)000247775200012 ()
    Available from: 2007-10-31 Created: 2007-10-31 Last updated: 2017-12-14Bibliographically approved
  • 28.
    Göndör, Anita
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Transcription in the loop.2006In: Nat Genet, ISSN 1061-4036, Vol. 38, no 11, p. 1229-30Article in journal (Refereed)
  • 29.
    Göndör, Anita
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Rougier, Carole
    Ohlsson, Rolf
    High-resolution circular chromosomal conformation cap-ture (4C) assayManuscript (Other (popular science, discussion, etc.))
  • 30.
    Göndör, Anita
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Rougier, Carole
    Singh Sandhu, Kuljeet
    Sumida, Noriyuki
    Holodnuk, Irina
    Wang, Sha
    Ohlsson, Rolf
    A high-resolution map of chromatin loops impinging on the human H19 imprinting control region in cis uncovers a re-peat element-based higher order chromatin structureManuscript (Other (popular science, discussion, etc.))
  • 31. Haaf, Thomas
    et al.
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Arney, Katharine L.
    Surani, M. Azim
    Barton, Sheila C.
    Differential dementhylation of paternal and maternal genomes in the preimplantation mouse embryo: implications for mammalian development2004In: Chromosomes today / [ed] Schmid, Michael, Nanda, Indrajit, Dordrecht: Kluwer , 2004, Vol. 14, p. 207-214Chapter in book (Other academic)
  • 32. Hancock, Anne L
    et al.
    Brown, Keith W
    Moorwood, Kim
    Moon, Hanlim
    Holmgren, Claes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Mardikar, Sudhanshu H
    Dallosso, Anthony R
    Klenova, Elena
    Loukinov, Dmitri
    Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Lobanenkov, Victor V
    Malik, Karim
    A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and exhibits sequential epigenetic defects during Wilms' tumourigenesis2007In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 16, no 3, p. 343-354Article in journal (Refereed)
    Abstract [en]

    We have shown previously that AWT1 and WT1-AS are functionally imprinted in human kidney. In the adult kidney, expression of both transcripts is restricted to the paternal allele, with the silent maternal allele retaining methylation at the WT1 antisense regulatory region (WT1 ARR). Here, we report characterization of the WT1 ARR differentially methylated region and show that it contains a transcriptional silencer element acting on both the AWT1 and WT1-AS promoters. DNA methylation of the silencer results in increased transcriptional repression, and the silencer is also shown to be an in vitro and in vivo target site for the imprinting regulator protein CTCF. Binding of CTCF is methylation-sensitive and limited to the unmethylated silencer. Potentiation of the silencer activity is demonstrated after CTCF protein is knocked down, suggesting a novel silencer-blocking activity for CTCF. We also report assessment of WT1 ARR methylation in developmental and tumour tissues, including the first analysis of Wilms' tumour precursor lesions, nephrogenic rests. Nephrogenic rests show increases in methylation levels relative to foetal kidney and reductions relative to the adult kidney, together with biallelic expression of AWT1 and WT1-AS. Notably, the methylation status of CpG residues within the CTCF target site appears to distinguish monoallelic and biallelic expression states. Our data suggest that failure of methylation spreading at the WT1 ARR early in renal development, followed by imprint erasure, occurs during Wilms' tumourigenesis. We propose a model wherein imprinting defects at chromosome 11p13 may contribute to Wilms' tumourigenesis.

  • 33.
    Hedborg, Fredrik
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Ohlsson, Rolf
    Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Sandstedt, Bengt
    Grimelius, Lars
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Hoehner, Jeff
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Pahlman, Sven
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    IGF2 expression is a marker for paraganglionic/SIF cell differentiation in neuroblastoma1995In: Am J Pathol, Vol. 146, p. 833-Article in journal (Refereed)
  • 34. Horsthemke, B
    et al.
    Surani, A
    James, T
    Ohlsson, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    The mechanisms of genomic imprinting.1999In: Results Probl Cell Differ, ISSN 0080-1844, Vol. 25, p. 91-118Article in journal (Refereed)
  • 35. Ishikawa, Hitoshi
    et al.
    Rattigan, Aine
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Burgoyne, Paul S.
    Effects of sex chromosome dosage on placental size in mice2003In: Biology of Reproduction, ISSN 0006-3363, E-ISSN 1529-7268, Vol. 69, no 2, p. 483-8Article in journal (Refereed)
  • 36. Janson, Peter C. J.
    et al.
    Winerdal, Malin E.
    Marits, Per
    Thorn, Magnus
    Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Winqvist, Ola
    FOXP3 Promoter Demethylation Reveals the Committed Treg Population in Humans2008In: PLoS ONE, ISSN 1932-6203, Vol. 3, no 2, p. e1612-Article in journal (Refereed)
    Abstract [en]

    Background: Naturally occurring thymus derived regulatory T cells (Tregs) are central in the maintenance of self-tolerance. The transcription factor FOXP3 is crucial for the suppressive activity of Tregs and is considered the most specific marker for this population. However, human non regulatory T cells upregulate FOXP3 transiently upon activation which calls for other means to identify the Treg population. Since epigenetic mechanisms are involved in the establishment of stable gene expression patterns during cell differentiation, we hypothesized that the methylation profile of the FOXP3 promoter would allow the distinction of truly committed Tregs. Methodology/Principal Findings: Human CD4(+) CD25(hi) Tregs displayed a demethylated FOXP3 promoter (1.4%+/-0.95% SEM methylated) in contrast to CD4(+) CD25(lo) T cells which were partially methylated (27.9%+/-7.1%). Furthermore, stimulated CD4(+)CD25(lo) T cells transiently expressed FOXP3 but remained partially methylated, suggesting promoter methylation as a mechanism for regulation of stable FOXP3 expression and Treg commitment. In addition, transient FOXP3 expressing cells exhibited suppressive abilities that correlate to the methylation status of the FOXP3 promoter. As an alternative to bisulphite sequencing, we present a restriction enzyme based screening method for the identification of committed Tregs and apply this method to evaluate the effect of various culturing conditions. We show that a partial demethylation occurs in long-term cultures after activation, whereas the addition of TGF-beta and/or IL-10 does not induce any additional change in methylation level. Conclusions/Significance: The unique FOXP3 promoter methylation profile in Tregs suggests that a demethylated pattern is a prerequisite for stable FOXP3 expression and suppressive phenotype. Presently, FOXP3 is used to identify Tregs in several human diseases and there are future implications for adoptive Treg transfer in immunotherapy. In these settings there is a need to distinguish true Tregs from transiently FOXP3(+) activated T cells. The screening method we present allows this distinction and enables the identification of cells suitable for in vitro expansions and clinical use.

  • 37.
    Kanduri, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Restriction enzyme BstZ17I is sensitive to cytosine methylation.2001In: FEMS Microbiol Lett, ISSN 0378-1097, Vol. 200, no 2, p. 191-3Article in journal (Refereed)
  • 38.
    Kanduri, C
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Pant, V
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Loukinov, D
    Pugacheva, E
    Qi, C F
    Wolffe, A
    Ohlsson, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Lobanenkov, V V
    Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive.2000In: Curr Biol, ISSN 0960-9822, Vol. 10, no 14, p. 853-6Article in journal (Refereed)
  • 39.
    KANDURI, C
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    PFEIFER, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    YIMING, L
    OHLSSON, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    GENES WITHOUT PROTEIN PRODUCTS : IS H19 THE NORM OR THE EXCEPTION?1999In: Current science, ISSN 0011-3891, Vol. 77, no 4, p. 539-544Article in journal (Other (popular scientific, debate etc.))
    Abstract [en]

    The increasing number of RNA polymease II transcripts without any apparent open reading frame has increased our awareness that gene functions can be selected for without involving a protein product.

    By using the H19 gene as a point of reference, we highlight here several common features among non-coding genes, such as their antisense position in subchromosomal expression domains which are often genomically imprinted. We also discuss the need to critically examine the translatability of transcripts which are considered non-coding. Finally, we present a model to explain the origin of non-coding genes.

  • 40.
    Kanduri, C
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Raman, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Characterisation of developmentally regulated chromatin structure in the coding region of the proto-oncogene, c-fos, in the male laboratory mouse1999In: INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY, ISSN 0214-6282, Vol. 43, no 3, p. 279-282Article in journal (Other scientific)
    Abstract [en]

    In mouse, tissue-specific developmental de novo methylation of the proto-oncogene c-fos, which is abundantly expressed during embryonic stages, occurs perinatally (between the day of birth to 20 dpp) and is maintained in the adult. In liver, where c-fos i

  • 41.
    Kanduri, C
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Raman, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Tissue-specific characterisation of DNA methylation in the gonad-specific proto-oncogene, c-mos, in the male laboratory mouse1999In: INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY, ISSN 0214-6282, Vol. 43, no 1, p. 91-94Article in journal (Other scientific)
    Abstract [en]

    The proto-oncogene, c-mos, which is expressed only in the germ cells of both testis and ovary, plays an important role in meiotic maturation of these cells. In this research, the methylation status of several CpG sites, present both upstream and within th

  • 42.
    Kanduri, Chandrasekhar
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Fitzpatrick, Galina
    Mukhopadhyay, Rituparna
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Kanduri, Meena
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Lobanenkov, Victor
    Higgins, Michael
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    A differentially methylated imprinting control region within the Kcnq1 locus harbors a methylation-sensitive chromatin insulator.2002In: J Biol Chem, ISSN 0021-9258, Vol. 277, no 20, p. 18106-10Article in journal (Refereed)
  • 43.
    Kanduri, Chandrasekhar
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Kanduri, Meena
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Liu, Liang
    Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Thakur, Noopur
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Pfeifer, Susan
    Department of Women's and Children's Health. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Ohlsson, Rolf
    Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    The kinetics of deregulation of expression by de novo methylation of the h19 imprinting control region in cancer cells.2002In: Cancer Res, ISSN 0008-5472, Vol. 62, no 16, p. 4545-8Article in journal (Refereed)
  • 44. Kanduri, Chandrasekhar
    et al.
    Meena, Kanduri
    Liu, Liang
    Thakur, Noopur
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Pfeifer, Susan
    Ohlsson, Rolf
    The kinetics of deregulation of expression by de novo methylation of the H19 imprinting control region in cancer cells2002In: Cancer Research, Vol. 16, no 62, p. 4545-4548Article in journal (Refereed)
  • 45.
    Kanduri, Chandrasekhar
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Thakur, Noopur
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Pandey, Radha Raman
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    The length of the transcript encoded from the Kcnq1ot1 antisense promoter determines the degree of silencing.2006In: EMBO J, ISSN 0261-4189, Vol. 25, no 10, p. 2096-106Article in journal (Refereed)
  • 46.
    Kanduri, Meena
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Kanduri, Chandrasekhar
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Mariano, Piero
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Vostrov, Alexander A
    Quitschke, Wolfgang
    Lobanenkov, Victor
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. zoologisk utvecklingsbiologi. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Multiple nucleosome positioning sites regulate the CTCF-mediated insulator function of the H19 imprinting control region.2002In: Mol Cell Biol, ISSN 0270-7306, Vol. 22, no 10, p. 3339-44Article in journal (Refereed)
  • 47. Klenova, E
    et al.
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. Zoologisk utvecklingsbiologi.
    Poly(ADP-ribosyl)ation and epigenetics. Is CTCF PARt of the plot?2005In: Cell Cycle, Vol. 4, no 1, p. 96-101Article in journal (Other (popular scientific, debate etc.))
  • 48. Klenova, Elena M
    et al.
    Morse, Herbert C
    Ohlsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics. zoologisk utvecklingsbiologi.
    Lobanenkov, Victor V
    The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer.2002In: Semin Cancer Biol, ISSN 1044-579X, Vol. 12, no 5, p. 399-414Article in journal (Refereed)
  • 49. Kourmouli, Niki
    et al.
    Jeppesen, Peter
    Mahadevhaiah, Shantha
    Burgoyne, Paul
    Wu, Rong
    Gilbert, David M.
    Bongiorni, Silvia
    Prantera, Giorgio
    Fanti, Laura
    Pimpinelli, Sergio
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Singh, Prim B.
    Heterochromatin and tri-methylated lysine 20 of histone H4 in animals2004In: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 117, no 14, p. 2491-2501Article in journal (Refereed)
  • 50. Kurth, Thomas
    et al.
    Berger, Juergen
    Wilsch-Braeuninger, Michaela
    Kretschmar, Susanne
    Cerny, Robert
    Schwarz, Heinz
    Löfberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Piendl, Thomas
    Epperlein, Hans H.
    Electron Microscopy of the Amphibian Model Systems Xenopus laevis and Ambystoma mexicanum2010In: Methods in Cell Biology, ISSN 0091-679X, Vol. 96, p. 395-423Article, review/survey (Refereed)
    Abstract [en]

    In this chapter we provide a set of different protocols for the ultrastructural analysis of amphibian (Xenopus, axolotl) tissues, mostly of embryonic origin. For Xenopus these methods include: (1) embedding gastrulae and tailbud embryos into Spurr's resin for TEM, (2) post-embedding labeling of methacrylate (K4M) and cryosections through adult and embryonic epithelia for correlative LM and TEM, and (3) pre-embedding labeling of embryonic tissues with silver-enhanced nanogold. For the axolotl (Ambystoma mexicanum) we present the following methods: (1) SEM of migrating neural crest (NC) cells; (2) SEM and TEM of extracellular matrix (ECM) material; (3) Cryo-SEM of extracellular matrix (ECM) material after cryoimmobilization; and (4) TEM analysis of hyaluronan using high-pressure freezing and HABP labeling. These methods provide exemplary approaches for a variety of questions in the field of amphibian development and regeneration, and focus on cell biological issues that can only be answered with fine structural imaging methods, such as electron microscopy.