uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Publications (10 of 36) Show all publications
Li, J., Davis, B. W., Jern, P., Dorshorst, B. J., Siegel, P. B. & Andersson, L. (2019). Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken. Mobile DNA, 10(1), Article ID 38.
Open this publication in new window or tab >>Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken
Show others...
2019 (English)In: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 10, no 1, article id 38Article in journal (Refereed) Published
Abstract [en]

Background

Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of CYP19A1 encoding aromatase that converts androgens to estrogen and thereby inhibits the development of male-specific plumage. A long terminal repeat (LTR) from an uncharacterized endogenous retrovirus (ERV) insertion was found in an isoform of the CYP19A1 transcript from henny feathering chicken. However, the complete sequence and the genomic position of the insertion were not determined.

Results

We used publicly available whole genome sequence data to determine the flanking sequences of the ERV, and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region, was detected partially in an aromatase transcript, which present a plausible explanation for ectopic expression of aromatase in non-ovarian tissues underlying the henny feathering phenotype.

Conclusions

We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5’end of CYP19A1. The presence of this ERV showed complete concordance with the henny feathering phenotype both within a pedigree segregating for this phenotype and across breeds.

Keywords
Chicken, Henny feather, Aromatase, Endogenous retrovirus, ERV, LTR
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-392029 (URN)10.1186/s13100-019-0181-4 (DOI)000483302300001 ()31467598 (PubMedID)
Available from: 2019-08-28 Created: 2019-08-28 Last updated: 2019-10-18Bibliographically approved
Medstrand, P. & Jern, P. (2019). Obituary: Jonas Blomberg (1944–2019).
Open this publication in new window or tab >>Obituary: Jonas Blomberg (1944–2019)
2019 (English)Other (Other (popular science, discussion, etc.))
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-379310 (URN)10.1186/s12977-019-0469-y (DOI)000461307600001 ()30871570 (PubMedID)
Note

Minnesord (Obituary)

Available from: 2019-03-15 Created: 2019-03-15 Last updated: 2019-04-12Bibliographically approved
Pettersson, M. E. & Jern, P. (2019). Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups. Genes, 10(2), Article ID 162.
Open this publication in new window or tab >>Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups
2019 (English)In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 2, article id 162Article in journal (Refereed) Published
Abstract [en]

Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-377511 (URN)10.3390/genes10020162 (DOI)000460742800091 ()30791656 (PubMedID)
Funder
Swedish Research Council Formas, 2010-474Swedish Research Council Formas, 2018-01008Swedish Research Council, 2015-02429Swedish Research Council, 2018-03017
Available from: 2019-02-21 Created: 2019-02-21 Last updated: 2019-04-04Bibliographically approved
Kutter, C., Jern, P. & Suh, A. (2018). Bridging gaps in transposable element research with single-molecule and single-cell technologies. Mobile DNA, 9, Article ID 34.
Open this publication in new window or tab >>Bridging gaps in transposable element research with single-molecule and single-cell technologies
2018 (English)In: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 9, article id 34Article in journal (Refereed) Published
Abstract [en]

More than half of the genomic landscape in humans and many other organisms is composed of repetitive DNA, which mostly derives from transposable elements (TEs) and viruses. Recent technological advances permit improved assessment of the repetitive content across genomes and newly developed molecular assays have revealed important roles of TEs and viruses in host genome evolution and organization. To update on our current understanding of TE biology and to promote new interdisciplinary strategies for the TE research community, leading experts gathered for the 2nd Uppsala Transposon Symposium on October 4–5, 2018 in Uppsala, Sweden. Using cutting-edge single-molecule and single-cell approaches, research on TEs and other repeats has entered a new era in biological and biomedical research.

National Category
Biological Sciences
Research subject
Biology
Identifiers
urn:nbn:se:uu:diva-368657 (URN)10.1186/s13100-018-0140-5 (DOI)000452516700001 ()
Funder
Swedish Research Council, 2018-00767Wenner-Gren Foundations, ESv2018-0014
Available from: 2018-12-06 Created: 2018-12-06 Last updated: 2019-01-21Bibliographically approved
Rivas-Carrillo, S. D., Pettersson, M., Rubin, C.-J. & Jern, P. (2018). Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations. Proceedings of the National Academy of Sciences of the United States of America, 115(43), 11012-11017, Article ID 201815056.
Open this publication in new window or tab >>Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations
2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 43, p. 11012-11017, article id 201815056Article in journal (Refereed) Published
Abstract [en]

Although recent advances in sequencing and computational analyses have facilitated use of endogenous retroviruses (ERVs) for deciphering coevolution among retroviruses and their hosts, sampling effects from different host populations present major challenges. Here we utilize available whole-genome data from wild and domesticated European rabbit (Oryctolagus cuniculus sp.) populations, sequenced as DNA pools by paired-end Illumina technology, for identifying segregating reference as well as nonreference ERV loci, to reveal their variation along the host phylogeny and domestication history. To produce new viruses, retroviruses must insert a proviral DNA copy into the host nuclear DNA. Occasional proviral insertions into the host germline have been passed down through generations as inherited ERVs during millions of years. These ERVs represent retroviruses that were active at the time of infection and thus present a remarkable record of historical virus–host associations. To examine segregating ERVs in host populations, we apply a reference library search strategy for anchoring ERV-associated short-sequence read pairs from pooled whole-genome sequences to reference genome assembly positions. We show that most ERVs segregate along host phylogeny but also uncover radiation of some ERVs, identified as segregating loci among wild and domestic rabbits. The study targets pertinent issues regarding genome sampling when examining virus–host evolution from the genomic ERV record and offers improved scope regarding common strategies for single-nucleotide variant analyses in host population comparative genomics.

Keywords
endogenous, retrovirus, host population, segregation, comparative genomics, evolution
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-362814 (URN)10.1073/pnas.1815056115 (DOI)000448040500066 ()30297425 (PubMedID)
Funder
Swedish Research Council, VR-M 2015-02429
Note

Correction in: PNAS, vol. 115, issue 52, pages E12465. DOI: 10.1073/pnas.1820237116

Available from: 2018-10-10 Created: 2018-10-10 Last updated: 2019-01-14Bibliographically approved
Brattås, P. L., Jönsson, M. E., Fasching, L., Nelander Wahlestedt, J., Shahsavani, M., Falk, R., . . . Jakobsson, J. (2017). TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells. Cell reports, 18(1), 1-11
Open this publication in new window or tab >>TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells
Show others...
2017 (English)In: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 18, no 1, p. 1-11Article in journal (Refereed) Published
Abstract [en]

Endogenous retroviruses (ERVs), which make up 8% of the human genome, have been proposed to participate in the control of gene regulatory networks. In this study, we find a region- and developmental stage-specific expression pattern of ERVs in the developing human brain, which is linked to a transcriptional network based on ERVs. We demonstrate that almost 10,000, primarily primate-specific, ERVs act as docking platforms for the co-repressor protein TRIM28 in human neural progenitor cells, which results in the establishment of local heterochromatin. Thereby, TRIM28 represses ERVs and consequently regulates the expression of neighboring genes. These results uncover a gene regulatory network based on ERVs that participates in control of gene expression of protein-coding transcripts important for brain development.

Place, publisher, year, edition, pages
Elsevier, 2017
National Category
Neurosciences Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-311976 (URN)10.1016/j.celrep.2016.12.010 (DOI)000396465300001 ()28052240 (PubMedID)
Funder
Swedish Research Council, K2014-62X-22527-01-3 2015-02429Swedish Foundation for Strategic Research , FFL12-0074The Swedish Brain Foundation, FO2015-0040Swedish Cancer Society, 150279
Available from: 2017-01-04 Created: 2017-01-04 Last updated: 2018-01-13Bibliographically approved
Martínez Barrio, Á., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., . . . Andersson, L. (2016). The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLIFE, 5, Article ID e12081.
Open this publication in new window or tab >>The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Show others...
2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed) Published
Abstract [en]

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

National Category
Genetics and Breeding Evolutionary Biology Genetics Fish and Aquacultural Science
Identifiers
urn:nbn:se:uu:diva-279967 (URN)10.7554/eLife.12081 (DOI)000387459700001 ()27138043 (PubMedID)
Funder
EU, European Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg Foundation
Note

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan and Nima Rafati contributed equally to this work.

Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2017-11-29Bibliographically approved
Kierczak, M., Jablonska, J., Forsberg, S. K., Bianchi, M., Tengvall, K., Pettersson, M., . . . Lindblad-Toh, K. (2015). cgmisc: Enhanced Genome-wide Association Analyses and Visualisation. Bioinformatics, 31(23), 3830-3831
Open this publication in new window or tab >>cgmisc: Enhanced Genome-wide Association Analyses and Visualisation
Show others...
2015 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 31, no 23, p. 3830-3831Article in journal (Refereed) Published
Abstract [en]

SUMMARY:

High-throughput genotyping and sequencing technologies facilitate studies of complex genetic traits and provide new research opportunities. The increasing popularity of genome-wide association studies (GWAS) leads to the discovery of new associated loci and a better understanding of the genetic architecture underlying not only diseases, but also other monogenic and complex phenotypes. Several softwares are available for performing GWAS analyses, R environment being one of them.

RESULTS: We present cgmisc, an R package that enables enhanced data analysis and visualisation of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of the existing software. It also provides several tools for advanced visualisation of genomic data and utilises the power of the R language to aid in preparation of publication-quality figures. Some of the package functions are specific for the domestic dog (Canis familiaris) data.

AVAILABILITY: The package is operating system-independent and is available from: https://github.com/cgmisc-team/cgmisc CONTACT: cgmisc@imbim.uu.se.

National Category
Bioinformatics and Systems Biology Medical Genetics
Identifiers
urn:nbn:se:uu:diva-259684 (URN)10.1093/bioinformatics/btv426 (DOI)000366378400016 ()6249815 (PubMedID)
Funder
Swedish Foundation for Strategic Research Swedish Research Council FormasSwedish Research CouncilEU, European Research CouncilEU, European Research Council
Available from: 2015-08-10 Created: 2015-08-10 Last updated: 2018-01-11Bibliographically approved
Hayward, A., Cornwallis, C. K. & Jern, P. (2015). Pan-vertebrate comparative genomics unmasks retrovirus macroevolution. Proceedings of the National Academy of Sciences of the United States of America, 112(2), 464-469
Open this publication in new window or tab >>Pan-vertebrate comparative genomics unmasks retrovirus macroevolution
2015 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 2, p. 464-469Article in journal (Refereed) Published
Abstract [en]

Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host-retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host-virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host-viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host-virus coevolution better.

National Category
Bioinformatics and Systems Biology Evolutionary Biology Microbiology
Identifiers
urn:nbn:se:uu:diva-239481 (URN)10.1073/pnas.1414980112 (DOI)000347732300054 ()1091-6490 (Electronic) 0027-8424 (Linking) (ISBN)
Available from: 2014-12-28 Created: 2014-12-28 Last updated: 2017-12-05Bibliographically approved
Delhomme, N., Sundström, G., Zamani, N., Lantz, H., Lin, Y. C., Hvidsten, T. R., . . . Street, N. R. (2015). Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLoS ONE, 10(9), Article ID e0139080.
Open this publication in new window or tab >>Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
Show others...
2015 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 9, article id e0139080Article in journal (Refereed) Published
Abstract [en]

After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.

National Category
Agricultural Science, Forestry and Fisheries Natural Sciences
Identifiers
urn:nbn:se:uu:diva-263259 (URN)10.1371/journal.pone.0139080 (DOI)000362170700039 ()26413905 (PubMedID)1932-6203 (Electronic) 1932-6203 (Linking) (ISBN)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilVINNOVASwedish Research Council FormasSwedish Foundation for Strategic Research
Available from: 2015-09-29 Created: 2015-09-29 Last updated: 2017-12-01Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3393-5825

Search in DiVA

Show all publications