Description

This track displays maps of histone H3K4me3 in human brain, identified by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). Measurements were made in neuronal and non-neuronal nuclei collected from prefrontal cortex (PFC) of 11 individuals ranging in age from 0.5 to 69 years.

ChIP-Seq begins by using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments.

Methods

Human prefrontal cortex samples used in this study were obtained from the Brain and Tissue Bank for Developmental Disorders, University of Maryland and a brain bank at the University of California, Irvine. Nuclei extraction, chromatin immunoprecipitation and sequencing were carried out as described in Cheung I, et al. (2010). Sequencing was performed on an Illumina Genome Analyzer (GA II).

The length of sequence reads was 36 bp. Mapping was performed using Bowtie (version 0.11.3, Langmead B, Trapnell C, Pop M, Salzberg SL (2009)) allowing up to one mismatch to map all sequence reads to the gender appropriate human genome hg18 (NCBI36), and 67-87% of the reads in the neuronal samples mapped to one unique location in the genome. The mapped reads were analyzed using the MACS software package (version 1.3.5, Zhang Y, et al. (2008)) to identify peaks, with bw = 230 bp, as defined experimentally by PCR, tSize = 36 bp, and other parameters set at default. The scored peaks were then lifted to the hg19 (GRCh37) assembly. Signal tracks were generated directly from a remapping of the reads to hg19.

Verification

Experimental testing was performed on a subset of the peaks that were positioned more than 10 kb from annotated genes for RNA expression in PFC neurons by qRT-PCR and in situ hybridization. These results suggest that H3K4me3 mapping can serve as a guide to uncover potentially hundreds of unannotated novel and cell-specific transcripts in the brain.

Credits

Chromatin immunoprecipitation experiments were carried out by Iris Cheung, Yan Jiang and Schahram Akbarian; analyses were performed by Hennady Shulha, Jie Wang and Zhiping Weng at the University of Massachusetts Medical School.

References

Cheung I, Shulha HP, Jiang Y, Matevossian A, Wang J, Weng Z, Akbarian S. Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8824-9.

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.