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Pettersson, M., Rochus, C. M., Han, F., Chen, J., Hill, J., Wallerman, O., . . . Andersson, L. (2019). A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection. Genome Research, 29(11), 1919-1928
Open this publication in new window or tab >>A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
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2019 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 29, no 11, p. 1919-1928Article in journal (Refereed) Published
Abstract [en]

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.

Place, publisher, year, edition, pages
Cold Spring Harbor Laboratory Press (CSHL), 2019
Keywords
Atlantic herring, assembly, ecological adaptation, supergene
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-396775 (URN)10.1101/gr.253435.119 (DOI)000493952800015 ()31649060 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Research Council of Norway, 254774Wellcome trust, WT108749/Z/15/Z
Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28Bibliographically approved
Cavalli, M., Baltzer, N., Umer, H. M., Grau, J., Lemnian, I., Pan, G., . . . Wadelius, C. (2019). Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases. Scientific Reports, 9, Article ID 2695.
Open this publication in new window or tab >>Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 2695Article in journal (Refereed) Published
Abstract [en]

Several Genome Wide Association Studies (GWAS) have reported variants associated to immune diseases. However, the identified variants are rarely the drivers of the associations and the molecular mechanisms behind the genetic contributions remain poorly understood. ChIP-seq data for TFs and histone modifications provide snapshots of protein-DNA interactions allowing the identification of heterozygous SNPs showing significant allele specific signals (AS-SNPs). AS-SNPs can change a TF binding site resulting in altered gene regulation and are primary candidates to explain associations observed in GWAS and expression studies. We identified 17,293 unique AS-SNPs across 7 lymphoblastoid cell lines. In this set of cell lines we interrogated 85% of common genetic variants in the population for potential regulatory effect and we identified 237 AS-SNPs associated to immune GWAS traits and 714 to gene expression in B cells. To elucidate possible regulatory mechanisms we integrated long-range 3D interactions data to identify putative target genes and motif predictions to identify TFs whose binding may be affected by AS-SNPs yielding a collection of 173 AS-SNPs associated to gene expression and 60 to B cell related traits. We present a systems strategy to find functional gene regulatory variants, the TFs that bind differentially between alleles and novel strategies to detect the regulated genes.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-379258 (URN)10.1038/s41598-019-39633-0 (DOI)000459571100059 ()30804403 (PubMedID)
Funder
Swedish Research Council, 78081Swedish National Infrastructure for Computing (SNIC)EXODIAB - Excellence of Diabetes Research in SwedenSwedish Diabetes AssociationErnfors FoundationSwedish Cancer Society, 160518German Research Foundation (DFG), GR-3526/1German Research Foundation (DFG), GR-3526/2
Available from: 2019-03-15 Created: 2019-03-15 Last updated: 2019-10-07Bibliographically approved
Christmas, M. J., Wallberg, A., Bunikis, I., Olsson, A., Wallerman, O. & Webster, M. T. (2019). Chromosomal inversions associated with environmental adaptation in honeybees. Molecular Ecology, 28(6), 1358-1374
Open this publication in new window or tab >>Chromosomal inversions associated with environmental adaptation in honeybees
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2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 6, p. 1358-1374Article in journal (Refereed) Published
Abstract [en]

Chromosomal inversions can facilitate local adaptation in the presence of gene flow by suppressing recombination between well-adapted native haplotypes and poorly adapted migrant haplotypes. East African mountain populations of the honeybee Apis mellifera are highly divergent from neighbouring lowland populations at two extended regions in the genome, despite high similarity in the rest of the genome, suggesting that these genomic regions harbour inversions governing local adaptation. Here, we utilize a new highly contiguous assembly of the honeybee genome to characterize these regions. Using whole-genome sequencing data from 55 highland and lowland bees, we find that the highland haplotypes at both regions are present at high frequencies in three independent highland populations but extremely rare elsewhere. The boundaries of both divergent regions are characterized by regions of high homology with each other positioned in opposite orientations and contain highly repetitive, long inverted repeats with homology to transposable elements. These regions are likely to represent inversion breakpoints that participate in nonallelic homologous recombination. Using long-read data, we confirm that the lowland samples are contiguous across breakpoint regions. We do not find evidence for disruption of functional sequence by these breakpoints, which suggests that the inversions are likely maintained due to their allelic content conferring local adaptation in highland environments. Finally, we identify a third divergent genomic region, which contains highly divergent segregating haplotypes that also may contain inversion variants under selection. The results add to a growing body of evidence indicating the importance of chromosomal inversions in local adaptation.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
chromosomal inversion, honeybee, local adaptation, long-read sequencing, nonallelic homologous recombination, structural variation
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-383207 (URN)10.1111/mec.14944 (DOI)000465219200012 ()30431193 (PubMedID)
Funder
Swedish Research Council Formas, 2013-722Swedish Research Council, 2014-5096
Available from: 2019-05-23 Created: 2019-05-23 Last updated: 2019-08-12Bibliographically approved
Hiltunen, M., Grudzinska-Sterno, M., Wallerman, O., Ryberg, M. & Johannesson, H. (2019). Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades. Current Biology, 29(16), 2758-2765
Open this publication in new window or tab >>Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades
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2019 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 16, p. 2758-2765Article in journal (Refereed) Published
Abstract [en]

Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and resequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 x 10(-12) mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.

Place, publisher, year, edition, pages
CELL PRESS, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-393895 (URN)10.1016/j.cub.2019.07.025 (DOI)000481587900033 ()31402298 (PubMedID)
Available from: 2019-10-18 Created: 2019-10-18 Last updated: 2019-10-18Bibliographically approved
Andrade, P., Pinho, C., Perez i de lanuza, G., Afonso, S., Brejcha, J., Rubin, C.-J., . . . Carneiro, M. (2019). Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proceedings of the National Academy of Sciences of the United States of America, 116(12), 5633-5642
Open this publication in new window or tab >>Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
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2019 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 12, p. 5633-5642Article in journal (Refereed) Published
Abstract [en]

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

Keywords
Podarcis muralis, carotenoid pigmentation, pterin pigmentation, balanced polymorphism, introgression
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-381075 (URN)10.1073/pnas.1820320116 (DOI)000461679000067 ()30819892 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2017-02907Swedish Research Council, E0446501EU, Horizon 2020, PTDC/BIA-EVL/30288/2017 -NORTE -01-0145-FEDER-30288EU, Horizon 2020, PTDC/BIA-EVL/30288/2017 -NORTE -01-0145-FEDER-30288EU, FP7, Seventh Framework Programme, 286431Swedish Research Council
Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-23Bibliographically approved
Cavalli, M., Pan, G., Nord, H., Wallén Arzt, E., Wallerman, O. & Wadelius, C. (2017). Genetic prevention of hepatitis C virus-induced liver fibrosis by allele-specific downregulation of MERTK. Hepatology Research, 47(8), 826-830
Open this publication in new window or tab >>Genetic prevention of hepatitis C virus-induced liver fibrosis by allele-specific downregulation of MERTK
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2017 (English)In: Hepatology Research, ISSN 1386-6346, E-ISSN 1872-034X, Vol. 47, no 8, p. 826-830Article in journal (Refereed) Published
Abstract [en]

AIM: Infection by hepatitis C virus (HCV) can result in the development of liver fibrosis and may eventually progress into cirrhosis and hepatocellular carcinoma. However, the molecular mechanisms for this process are not fully known. Several genome-wide association studies have been carried out to pinpoint causative variants in HCV-infected patient cohorts, but these variants are usually not the functional ones. The aim of this study was to identify the regulatory single nucleotide polymorphism associated with the risk of HCV-induced liver fibrosis and elucidate its molecular mechanism.

METHODS: We utilized a bioinformatics approach to identify a non-coding regulatory variant, located in an intron of the MERTK gene, based on differential transcription factor binding between the alleles. We validated the results using expression reporter assays and electrophoresis mobility shift assays.

RESULTS: Chromatin immunoprecipitation sequencing indicated that transcription factor(s) bind stronger to the A allele of rs6726639. Electrophoresis mobility shift assays supported these findings and suggested that the transcription factor is interferon regulatory factor 1 (IRF1). Luciferase report assays showed lower enhancer activity from the A allele and that IRF1 may act as a repressor.

CONCLUSIONS: Treatment of hepatitis C with interferon-α results in increased IRF1 levels and our data suggest that this leads to an allele-specific downregulation of MERTK mediated by an allelic effect on the regulatory element containing the functional rs6726639. This variant also shows the hallmarks for being the driver of the genome-wide association studies for reduced risk of liver fibrosis and non-alcoholic fatty liver disease at MERTK.

Keywords
MERTK, hepatitis C virus, liver fibrosis, single nucleotide polymorphism
National Category
Basic Medicine
Identifiers
urn:nbn:se:uu:diva-318340 (URN)10.1111/hepr.12810 (DOI)000404794000012 ()27577861 (PubMedID)
Funder
Swedish Cancer Society, 15 0878Swedish Research Council, A0350501Swedish Diabetes Association, 2015-064
Available from: 2017-03-24 Created: 2017-03-24 Last updated: 2018-01-13Bibliographically approved
Melo, F. R., Wallerman, O., Paivandy, A., Calounova, G., Gustafson, A.-M., Sabari, B. R., . . . Pejler, G. (2017). Tryptase-catalyzed core histone truncation: A novel epigenetic regulatory mechanism in mast cells. Journal of Allergy and Clinical Immunology, 140(2), 474-485
Open this publication in new window or tab >>Tryptase-catalyzed core histone truncation: A novel epigenetic regulatory mechanism in mast cells
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2017 (English)In: Journal of Allergy and Clinical Immunology, ISSN 0091-6749, E-ISSN 1097-6825, Vol. 140, no 2, p. 474-485Article in journal (Refereed) Published
Abstract [en]

Background: Mast cells are key effector cells in allergic reactions. When activated to degranulate, they release a plethora of bioactive compounds from their secretory granules, including mast cell-restricted proteases such as tryptase. In a previous study, we showed that tryptase, in addition to its intragranular location, can be found within the nuclei of mast cells where it truncates core histones at their N-terminal ends. Objective: Considering that the N-terminal portions of the core histones constitute sites for posttranslational modifications of major epigenetic impact, we evaluated whether histone truncation by tryptase could have an impact on epigenetic events in mast cells. Methods: Mast cells were cultured from wild-type and tryptase null mice, followed by an assessment of their profile of epigenetic histone modifications and their phenotypic characteristics. Results: We show that tryptase truncates nucleosomal histone 3 and histone 2B (H2B) and that its absence results in accumulation of the epigenetic mark, lysine 5-acetylated H2B. Intriguingly, the accumulation of lysine 5-acetylated H2B was cell age-dependent and was associated with a profound upregulation of markers of non-mast cell lineages, loss of proliferative control, chromatin remodeling as well as extensive morphological alterations. Conclusions: These findings introduce tryptase-catalyzed histone clipping as a novel epigenetic regulatory mechanism, which in the mast cell context may be crucial for maintaining cellular identity.

Place, publisher, year, edition, pages
MOSBY-ELSEVIER, 2017
Keywords
Mast cells, epigenetics, core histones, histone acetylation, tryptase, mMCP6, secretory granules, serglycin, serglycin proteoglycan, H2B, H2BK5ac
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-335673 (URN)10.1016/j.jaci.2016.11.044 (DOI)000406855500020 ()28108335 (PubMedID)
Funder
Swedish Research Council, K2014-68X-0913-23-4Swedish Cancer Society, CAN 2013/423Swedish Heart Lung Foundation, 20150290Swedish Research Council Formas, 221-2012-1098Torsten Söderbergs stiftelse, M80/14NIH (National Institute of Health), R01-GM40922
Available from: 2017-12-20 Created: 2017-12-20 Last updated: 2017-12-20Bibliographically approved
Cavalli, M., Pan, G., Nord, H., Arzt, E. W., Wallerman, O. & Wadelius, C. (2016). Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals. Genomics, 107(6), 248-254
Open this publication in new window or tab >>Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals
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2016 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 107, no 6, p. 248-254Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies (GWAS) point to regions with associated genetic variants but rarely to a specific gene and therefore detailed knowledge regarding the genes contributing to complex traits and diseases remains elusive. The functional role of GWAS-SNPs is also affected by linkage disequilibrium with many variants on the same haplotype and sometimes in the same regulatory element almost equally likely to mediate the effect. Using ChIP-seq data on many transcription factors, we pinpointed genetic variants in HepG2 and HeLa-S3 cell lines which show a genome-wide significant difference in binding between alleles. We identified a collection of 3713 candidate functional regulatory variants many of which are likely drivers of GWAS signals or genetic difference in expression. A recent study investigated many variants before finding the functional ones at the GALNT2 locus, which we found in our genome-wide screen in HepG2. This illustrates the efficiency of our approach.

Keywords
Allele-specific regulation, Association to GWAS/eQTLs, Functional variants
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-299903 (URN)10.1016/j.ygeno.2016.04.006 (DOI)000378623700004 ()27126307 (PubMedID)
Funder
Swedish Research Council, 2010-3505Swedish Diabetes Association, 2015-064
Available from: 2016-07-29 Created: 2016-07-29 Last updated: 2018-01-10Bibliographically approved
Cavalli, M., Pan, G., Nord, H., Wallerman, O., Arzt, E. W., Berggren, O., . . . Wadelius, C. (2016). Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression. Human Genetics, 135(5), 485-497
Open this publication in new window or tab >>Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression
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2016 (English)In: Human Genetics, ISSN 0340-6717, E-ISSN 1432-1203, Vol. 135, no 5, p. 485-497Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies (GWAS) have identified a large number of disease-associated SNPs, but in few cases the functional variant and the gene it controls have been identified. To systematically identify candidate regulatory variants, we sequenced ENCODE cell lines and used public ChIP-seq data to look for transcription factors binding preferentially to one allele. We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones. Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability. The majority of allele-specific variants (96 %) were specific to a cell type. Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types. Functionally validated SNPs support identification of an SNP in SYNGR1 which may expose to the risk of rheumatoid arthritis and primary biliary cirrhosis, as well as an SNP in the last intron of COG6 exposing to the risk of psoriasis. We propose that by repeating the ChIP-seq experiments of 20 selected transcription factors in three to ten people, the most common polymorphisms can be interrogated for allele-specific binding. Our strategy may help to remove the current bottleneck in functional annotation of the genome.

National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-297809 (URN)10.1007/s00439-016-1654-x (DOI)000374459200004 ()26993500 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), b2010003Swedish National Infrastructure for Computing (SNIC), b2011107Swedish Research Council, 541-2013-8161Swedish Diabetes AssociationKnut and Alice Wallenberg Foundation
Available from: 2016-06-28 Created: 2016-06-28 Last updated: 2018-01-10Bibliographically approved
Wang, X., Xie, B., Qi, Y., Wallerman, O., Vasylovska, S., Andersson, L., . . . Welsh, N. (2016). Knock-down of ZBED6 in insulin-producing cells promotes N-cadherin junctions between beta-cells and neural crest stem cells in vitro. Scientific Reports, 6, Article ID 19006.
Open this publication in new window or tab >>Knock-down of ZBED6 in insulin-producing cells promotes N-cadherin junctions between beta-cells and neural crest stem cells in vitro
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2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 19006Article in journal (Refereed) Published
Abstract [en]

The role of the novel transcription factor ZBED6 for the adhesion/clustering of insulin-producing mouse MIN6 and βTC6 cells was investigated. Zbed6-silencing in the insulin producing cells resulted in increased three-dimensional cell-cell clustering and decreased adhesion to mouse laminin and human laminin 511. This was paralleled by a weaker focal adhesion kinase phosphorylation at laminin binding sites. Zbed6-silenced cells expressed less E-cadherin and more N-cadherin at cell-to-cell junctions. A strong ZBED6-binding site close to the N-cadherin gene transcription start site was observed. Three-dimensional clustering in Zbed6-silenced cells was prevented by an N-cadherin neutralizing antibody and by N-cadherin knockdown. Co-culture of neural crest stem cells (NCSCs) with Zbed6-silenced cells, but not with control cells, stimulated the outgrowth of NCSC processes. The cell-to-cell junctions between NCSCs and βTC6 cells stained more intensely for N-cadherin when Zbed6-silenced cells were co-cultured with NCSCs. We conclude that ZBED6 decreases the ratio between N- and E-cadherin. A lower N- to E-cadherin ratio may hamper the formation of three-dimensional beta-cell clusters and cell-to-cell junctions with NCSC, and instead promote efficient attachment to a laminin support and monolayer growth. Thus, by controlling beta-cell adhesion and cell-to-cell junctions, ZBED6 might play an important role in beta-cell differentiation, proliferation and survival.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-223614 (URN)10.1038/srep19006 (DOI)000368128900001 ()26750727 (PubMedID)
Funder
Swedish Diabetes AssociationSwedish Child Diabetes FoundationNovo NordiskSwedish Research Council, 20716Stiftelsen Olle Engkvist Byggmästare
Available from: 2014-04-22 Created: 2014-04-22 Last updated: 2018-01-11Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1037-7904

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