Roos, Christian

[["dc.bibliographiccitation.firstpage","1188"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Epigenetics"],["dc.bibliographiccitation.lastpage","1199"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Bell, Christopher G."],["dc.contributor.author","Wilson, Gareth A."],["dc.contributor.author","Butcher, Lee M."],["dc.contributor.author","Roos, Christian"],["dc.contributor.author","Walter, Lutz"],["dc.contributor.author","Beck, Stephan"],["dc.date.accessioned","2019-07-09T11:40:05Z"],["dc.date.available","2019-07-09T11:40:05Z"],["dc.date.issued","2012-10-01"],["dc.description.abstract","Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variability via DNA methylation, and this epigenetic mark functions as a regulatory mechanism. Therefore, species-specific CpGs may influence species-specific regulation. We report non-polymorphic species-specific CpG dinucleotides (termed \"CpG beacons\") as a distinct genomic feature associated with CpG island (CGI) evolution, human traits and disease. Using an inter-primate comparison, we identified 21 extreme CpG beacon clusters (≥ 20/kb peaks, empirical p < 1.0 × 10(-3)) in humans, which include associations with four monogenic developmental and neurological disease related genes (Benjamini-Hochberg corrected p = 6.03 × 10(-3)). We also demonstrate that beacon-mediated CpG density gain in CGIs correlates with reduced methylation in these species in orthologous CGIs over time, via human, chimpanzee and macaque MeDIP-seq. Therefore mapping into both the genomic and epigenomic space the identified CpG beacon clusters define points of intersection where a substantial two-way interaction between genetic sequence and epigenetic state has occurred. Taken together, our data support a model for CpG beacons to contribute to CGI evolution from genesis to tissue-specific to constitutively active CGIs."],["dc.identifier.doi","10.4161/epi.22127"],["dc.identifier.pmid","22968434"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/10647"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/58091"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/018883"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/257082/EU//EPIGENESYS"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/282510/EU//BLUEPRINT"],["dc.relation.euproject","HEROIC"],["dc.relation.euproject","EPIGENESYS"],["dc.relation.euproject","BLUEPRINT"],["dc.relation.issn","1559-2308"],["dc.rights","CC BY-NC 3.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/3.0"],["dc.subject.mesh","Animals"],["dc.subject.mesh","CpG Islands"],["dc.subject.mesh","DNA Methylation"],["dc.subject.mesh","Epigenesis, Genetic"],["dc.subject.mesh","Evolution, Molecular"],["dc.subject.mesh","Gene Expression Regulation"],["dc.subject.mesh","Genetic Variation"],["dc.subject.mesh","Humans"],["dc.subject.mesh","Primates"],["dc.subject.mesh","Promoter Regions, Genetic"],["dc.subject.mesh","Species Specificity"],["dc.title","Human-specific CpG \"beacons\" identify loci associated with human-specific traits and disease."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e4859"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","PloS one"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Zinner, Dietmar"],["dc.contributor.author","Arnold, Michael L."],["dc.contributor.author","Roos, Christian"],["dc.date.accessioned","2019-07-09T11:52:42Z"],["dc.date.available","2019-07-09T11:52:42Z"],["dc.date.issued","2009"],["dc.description.abstract","BACKGROUND: In 2005, a new primate species from Tanzania, the kipunji, was described and recognized as a member of the mangabey genus Lophocebus. However, molecular investigations based upon a number of papionins, including a limited sample of baboons of mainly unknown geographic origin, identified the kipunji as a sister taxon to Papio and not as a member of Lophocebus. Accordingly, the kipunji was separated into its own monotypic genus, Rungwecebus. METHODOLOGY/PRINCIPAL FINDINGS: We compare available mitochondrial and nuclear sequence data from the voucher specimen of Rungwecebus to other papionin lineages, including a set of geographically proximal (parapatric) baboon samples. Based on mitochondrial sequence data the kipunji clusters with baboon lineages that lie nearest to it geographically, i.e. populations of yellow and chacma baboons from south-eastern Africa, and thus does not represent a sister taxon to Papio. Nuclear data support a Papio+Rungwecebus clade, but it remains questionable whether Rungwecebus represents a sister taxon to Papio, or whether it is nested within the genus as depicted by the mitochondrial phylogeny. CONCLUSIONS/SIGNIFICANCE: Our study clearly supports a close relationship between Rungwecebus and Papio and might indicate that the kipunji is congeneric with baboon species. However, due to its morphological and ecological uniqueness Rungwecebus more likely represents a sister lineage to Papio and experienced later introgressive hybridization. Presumably, male (proto-)kipunjis reproduced with sympatric female baboons. Subsequent backcrossing of the hybrids with kipunjis would have resulted in a population with a nuclear kipunji genome, but which retained the yellow/chacma baboon mitochondrial genome. Since only one kipunji specimen was studied, it remains unclear whether all members of the new genus have been impacted by intergeneric introgression or rather only some populations. Further studies with additional Rungwecebus samples are necessary to elucidate the complete evolutionary history of this newly-described primate genus."],["dc.identifier.doi","10.1371/journal.pone.0004859"],["dc.identifier.fs","573495"],["dc.identifier.pmid","19295908"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/5850"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60256"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1932-6203"],["dc.rights","CC BY 2.5"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.5"],["dc.subject.ddc","570"],["dc.subject.mesh","Africa"],["dc.subject.mesh","Animals"],["dc.subject.mesh","Biological Evolution"],["dc.subject.mesh","DNA"],["dc.subject.mesh","DNA, Mitochondrial"],["dc.subject.mesh","Female"],["dc.subject.mesh","Male"],["dc.subject.mesh","Papio"],["dc.subject.mesh","Phylogeny"],["dc.subject.mesh","Primates"],["dc.subject.mesh","Sequence Analysis, DNA"],["dc.title","Is the new primate genus rungwecebus a baboon?"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","195"],["dc.bibliographiccitation.issue","7517"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.lastpage","201"],["dc.bibliographiccitation.volume","513"],["dc.contributor.author","Carbone, Lucia"],["dc.contributor.author","Harris, R. Alan"],["dc.contributor.author","Gnerre, Sante"],["dc.contributor.author","Veeramah, Krishna R."],["dc.contributor.author","Lorente-Galdos, Belen"],["dc.contributor.author","Huddleston, John"],["dc.contributor.author","Meyer, Thomas J."],["dc.contributor.author","Herrero, Javier"],["dc.contributor.author","Roos, Christian"],["dc.contributor.author","Aken, Bronwen"],["dc.contributor.author","Anaclerio, Fabio"],["dc.contributor.author","Archidiacono, Nicoletta"],["dc.contributor.author","Baker, Carl"],["dc.contributor.author","Barrell, Daniel"],["dc.contributor.author","Batzer, Mark A."],["dc.contributor.author","Beal, Kathryn"],["dc.contributor.author","Blancher, Antoine"],["dc.contributor.author","Bohrson, Craig L."],["dc.contributor.author","Brameier, Markus"],["dc.contributor.author","Campbell, Michael S."],["dc.contributor.author","Capozzi, Oronzo"],["dc.contributor.author","Casola, Claudio"],["dc.contributor.author","Chiatante, Giorgia"],["dc.contributor.author","Cree, Andrew"],["dc.contributor.author","Damert, Annette"],["dc.contributor.author","de Jong, Pieter J."],["dc.contributor.author","Dumas, Laura"],["dc.contributor.author","Fernandez-Callejo, Marcos"],["dc.contributor.author","Flicek, Paul"],["dc.contributor.author","Fuchs, Nina V."],["dc.contributor.author","Gut, Ivo"],["dc.contributor.author","Gut, Marta"],["dc.contributor.author","Hahn, Matthew W."],["dc.contributor.author","Hernandez-Rodriguez, Jessica"],["dc.contributor.author","Hillier, LaDeana W."],["dc.contributor.author","Hubley, Robert"],["dc.contributor.author","Ianc, Bianca"],["dc.contributor.author","Izsvák, Zsuzsanna"],["dc.contributor.author","Jablonski, Nina G."],["dc.contributor.author","Johnstone, Laurel M."],["dc.contributor.author","Karimpour-Fard, Anis"],["dc.contributor.author","Konkel, Miriam K."],["dc.contributor.author","Kostka, Dennis"],["dc.contributor.author","Lazar, Nathan H."],["dc.contributor.author","Lee, Sandra L."],["dc.contributor.author","Lewis, Lora R."],["dc.contributor.author","Liu, Yue"],["dc.contributor.author","Locke, Devin P."],["dc.contributor.author","Mallick, Swapan"],["dc.contributor.author","Mendez, Fernando L."],["dc.contributor.author","Muffato, Matthieu"],["dc.contributor.author","Nazareth, Lynne V."],["dc.contributor.author","Nevonen, Kimberly A."],["dc.contributor.author","O'Bleness, Majesta"],["dc.contributor.author","Ochis, Cornelia"],["dc.contributor.author","Odom, Duncan T."],["dc.contributor.author","Pollard, Katherine S."],["dc.contributor.author","Quilez, Javier"],["dc.contributor.author","Reich, David"],["dc.contributor.author","Rocchi, Mariano"],["dc.contributor.author","Schumann, Gerald G."],["dc.contributor.author","Searle, Stephen"],["dc.contributor.author","Sikela, James M."],["dc.contributor.author","Skollar, Gabriella"],["dc.contributor.author","Smit, Arian"],["dc.contributor.author","Sonmez, Kemal"],["dc.contributor.author","ten Hallers, Boudewijn"],["dc.contributor.author","Terhune, Elizabeth"],["dc.contributor.author","Thomas, Gregg W. C."],["dc.contributor.author","Ullmer, Brygg"],["dc.contributor.author","Ventura, Mario"],["dc.contributor.author","Walker, Jerilyn A."],["dc.contributor.author","Wall, Jeffrey D."],["dc.contributor.author","Walter, Lutz"],["dc.contributor.author","Ward, Michelle C."],["dc.contributor.author","Wheelan, Sarah J."],["dc.contributor.author","Whelan, Christopher W."],["dc.contributor.author","White, Simon"],["dc.contributor.author","Wilhelm, Larry J."],["dc.contributor.author","Woerner, August E."],["dc.contributor.author","Yandell, Mark"],["dc.contributor.author","Zhu, Baoli"],["dc.contributor.author","Hammer, Michael F."],["dc.contributor.author","Marques-Bonet, Tomas"],["dc.contributor.author","Eichler, Evan E."],["dc.contributor.author","Fulton, Lucinda"],["dc.contributor.author","Fronick, Catrina"],["dc.contributor.author","Muzny, Donna M."],["dc.contributor.author","Warren, Wesley C."],["dc.contributor.author","Worley, Kim C."],["dc.contributor.author","Rogers, Jeffrey"],["dc.contributor.author","Wilson, Richard K."],["dc.contributor.author","Gibbs, Richard A."],["dc.date.accessioned","2019-07-09T11:40:35Z"],["dc.date.available","2019-07-09T11:40:35Z"],["dc.date.issued","2014-09-11"],["dc.description.abstract","Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ∼5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat."],["dc.identifier.doi","10.1038/nature13679"],["dc.identifier.pmid","25209798"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11090"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/58210"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1476-4687"],["dc.rights","CC BY-NC-SA 3.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc-sa/3.0"],["dc.subject.mesh","Animals"],["dc.subject.mesh","Evolution, Molecular"],["dc.subject.mesh","Genome"],["dc.subject.mesh","Hominidae"],["dc.subject.mesh","Humans"],["dc.subject.mesh","Hylobates"],["dc.subject.mesh","Karyotype"],["dc.subject.mesh","Molecular Sequence Data"],["dc.subject.mesh","Phylogeny"],["dc.subject.mesh","Retroelements"],["dc.subject.mesh","Selection, Genetic"],["dc.subject.mesh","Transcription Termination, Genetic"],["dc.title","Gibbon genome and the fast karyotype evolution of small apes."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","150"],["dc.bibliographiccitation.journal","BMC evolutionary biology"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Chan, Yi-Chiao"],["dc.contributor.author","Roos, Christian"],["dc.contributor.author","Inoue-Murayama, Miho"],["dc.contributor.author","Inoue, Eiji"],["dc.contributor.author","Shih, Chih-Chin"],["dc.contributor.author","Vigilant, Linda"],["dc.date.accessioned","2019-07-09T11:54:07Z"],["dc.date.available","2019-07-09T11:54:07Z"],["dc.date.issued","2012"],["dc.description.abstract","BACKGROUND: The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). RESULTS: To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade. CONCLUSIONS: Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance."],["dc.format.extent","13"],["dc.identifier.doi","10.1186/1471-2148-12-150"],["dc.identifier.pmid","22909292"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8487"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60576"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1471-2148"],["dc.rights","CC BY 2.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.0"],["dc.subject.mesh","Animals"],["dc.subject.mesh","DNA Primers"],["dc.subject.mesh","DNA, Mitochondrial"],["dc.subject.mesh","Evolution, Molecular"],["dc.subject.mesh","Female"],["dc.subject.mesh","Genome, Mitochondrial"],["dc.subject.mesh","Hylobates"],["dc.subject.mesh","Male"],["dc.subject.mesh","Phylogeny"],["dc.subject.mesh","Sequence Analysis, DNA"],["dc.subject.mesh","Y Chromosome"],["dc.title","A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]