Human-specific histone methylation signatures at transcription start sites in prefrontal neurons
AuthorsShulha, Hennady P.
Crisci, Jessica L.
Tushir, Jogender S.
Houston, Isaac B.
Peter, Cyril J.
Mitchell, Amanda C.
Myers, Richard H.
Preuss, Todd M.
Rogaev, Evgeny I.
Jensen, Jeffrey D.
UMass Chan AffiliationsBrudnick Neuropsychiatric Research Institute, Department of Psychiatry
Program in Bioinformatics and Integrative Biology
Document TypeJournal Article
KeywordsTranscription Initiation Site
Cell and Developmental Biology
Genetics and Genomics
Neuroscience and Neurobiology
MetadataShow full item record
AbstractCognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5-1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans.
SourcePLoS Biol. 2012 Nov;10(11):e1001427. doi: 10.1371/journal.pbio.1001427. Link to article on publisher's site
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/39580
Co-author Jessica Crisci is a student in the Bioinformatics and Computational Biology Program in the Graduate School of Biomedical Sciences (GSBS) at UMass Medical School.
Related ResourcesLink to Article in PubMed
RightsCopyright: © 2012 Shulha et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.