Walter, Lutz

[["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.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"]]