Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex.
Little is known about the regulation of neuronal and other cell-type specific epigenomes from the brain. Here, we map the genome-wide distribution of trimethylated histone H3K4 (H3K4me3), a mark associated with transcriptional regulation, in neuronal and nonneuronal nuclei collected from prefrontal cortex (PFC) of 11 individuals ranging in age from 0.5 to 69 years. Massively parallel sequencing identified 12,732-19,704 H3K4me3 enriched regions (peaks), the majority located proximal to (within 2 kb of) the transcription start site (TSS) of annotated genes. These included peaks shared by neurons in comparison with three control (lymphocyte) cell types, as well as peaks specific to individual subjects. We identified 6,213 genes that show highly enriched H3K4me3 in neurons versus control. At least 1,370 loci, including annotated genes and novel transcripts, were selectively tagged with H3K4me3 in neuronal but not in nonneuronal PFC chromatin. Our results reveal age-correlated neuronal epigenome reorganization, including decreased H3K4me3 at approximately 600 genes (many function in developmental processes) during the first year after birth. In comparison, the epigenome of aging (>60 years) PFC neurons showed less extensive changes, including increased H3K4me3 at 100 genes. These findings demonstrate that H3K4me3 in human PFC is highly regulated in a cell type- and subject-specific manner and highlight the importance of early childhood for developmentally regulated chromatin remodeling in prefrontal neurons.
Cheung
Iris
I
Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA.
Shulha
Hennady P
HP
Jiang
Yan
Y
Matevossian
Anouch
A
Wang
Jie
J
Weng
Zhiping
Z
Akbarian
Schahram
S
D000293:Adolescent; D000328:Adult; D000368:Aged; D034961:Antigens, Nuclear / Q000378:metabolism; D002452:Cell Count; D002648:Child; D002675:Child, Preschool; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016678:Genome / Q000235:genetics*; D006657:Histones / Q000378:metabolism*; D006801:Humans; D007223:Infant; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D008875:Middle Aged; D009419:Nerve Tissue Proteins / Q000378:metabolism; D009474:Neurons / Q000378:metabolism*; D017397:Prefrontal Cortex / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D055815:Young Adult
D034961:Antigens, Nuclear; D006657:Histones; D009419:Nerve Tissue Proteins; D012333:RNA, Messenger; C506808:neuronal nuclear antigen NeuN, human; D008239:Lysine