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Title

Human-specific histone methylation signatures at transcription start sites in prefrontal neurons

PubMed ID

23185133

Authors

Hennady P. Shulha, University of Massachusetts Medical SchoolFollow
Jessica L. Crisci, University of Massachusetts Medical SchoolFollow
Denis Reshetov, Vavilov Institute of General Genetics
Jogender S. Tushir, University of Massachusetts Medical SchoolFollow
Iris Cheung, University of Massachusetts Medical SchoolFollow
Rahul Bharadwaj, University of Massachusetts Medical SchoolFollow
Hsin-Jung Chou, University of Massachusetts Medical SchoolFollow
Isaac B. Houston, University of Massachusetts Medical SchoolFollow
Cyril J. Peter, University of Massachusetts Medical SchoolFollow
Amanda C. Mitchell, University of Massachusetts Medical SchoolFollow
Wei-Dong Yao, New England Primate Center
Richard H. Myers, Boston University Medical School
Jiang-Fan Chen, Boston University School of Medicine
Todd M. Preuss, Emory University
Evgeny I. Rogaev, University of Massachusetts Medical SchoolFollow
Jeffrey D. Jensen, University of Massachusetts Medical SchoolFollow
Zhiping Weng, University of Massachusetts Medical SchoolFollow
Schahram Akbarian, University of Massachusetts Medical SchoolFollow

UMMS Affiliation

Program in Bioinformatics and Integrative Biology; Brudnick Neuropsychiatric Research Institute, Department of Psychiatry

Date

11-20-2012

Document Type

Article

Subjects

Transcription Initiation Site; Prefrontal Cortex; Neurons; DNA Methylation

Disciplines

Cell and Developmental Biology | Genetics and Genomics | Neuroscience and Neurobiology

Abstract

Cognitive 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.

Comments

Citation: PLoS Biol. 2012 Nov;10(11):e1001427. doi: 10.1371/journal.pbio.1001427. Link to article on publisher's site

Copyright: © 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.

Related Resources

Link to Article in PubMed