Epigenetic signatures of autism: trimethylated H3K4 landscapes in prefrontal neurons

UMMS Affiliation

Department of Psychiatry; Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology; Brudnick Neuropsychiatric Research Institute

Publication Date


Document Type



Adolescent; Adult; Aged; Autistic Disorder; Case-Control Studies; Child; Child, Preschool; Chromatin; DNA Fingerprinting; DNA Methylation; Epigenesis, Genetic; Female; Flow Cytometry; Histones; Humans; Male; Middle Aged; Models, Genetic; Neurons; Prefrontal Cortex; Risk Factors; Young Adult


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


CONTEXT: Neuronal dysfunction in cerebral cortex and other brain regions could contribute to the cognitive and behavioral defects in autism.

OBJECTIVE: To characterize epigenetic signatures of autism in prefrontal cortex neurons.

DESIGN: We performed fluorescence-activated sorting and separation of neuronal and nonneuronal nuclei from postmortem prefrontal cortex, digested the chromatin with micrococcal nuclease, and deeply sequenced the DNA from the mononucleosomes with trimethylated H3K4 (H3K4me3), a histone mark associated with transcriptional regulation. Approximately 15 billion base pairs of H3K4me3-enriched sequences were collected from 32 brains.

SETTING: Academic medical center.

PARTICIPANTS: A total of 16 subjects diagnosed as having autism and 16 control subjects ranging in age from 0.5 to 70 years.

MAIN OUTCOME MEASURES: Identification of genomic loci showing autism-associated H3K4me3 changes in prefrontal cortex neurons.

RESULTS: Subjects with autism showed no evidence for generalized disruption of the developmentally regulated remodeling of the H3K4me3 landscape that defines normal prefrontal cortex neurons in early infancy. However, excess spreading of H3K4me3 from the transcription start sites into downstream gene bodies and upstream promoters was observed specifically in neuronal chromatin from 4 of 16 autism cases but not in controls. Variable subsets of autism cases exhibit altered H3K4me3 peaks at numerous genes regulating neuronal connectivity, social behaviors, and cognition, often in conjunction with altered expression of the corresponding transcripts. Autism-associated H3K4me3 peaks were significantly enriched in genes and loci implicated in neurodevelopmental diseases.

CONCLUSIONS: Prefrontal cortex neurons from subjects with autism show changes in chromatin structures at hundreds of loci genome-wide, revealing considerable overlap between genetic and epigenetic risk maps of developmental brain disorders.

DOI of Published Version



Arch Gen Psychiatry. 2012 Mar;69(3):314-24. doi: 10.1001/archgenpsychiatry.2011.151. Link to article on publisher's site

Journal/Book/Conference Title

Archives of general psychiatry

Related Resources

Link to Article in PubMed

PubMed ID