Created by Jessica Johnson
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BOCA: Brain Open Chromatin Atlas

We have characterized the open chromatin by ATAC-seq assay in 14 brain regions and 2 cell types from 5 postmortem human brains.

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Abstract

Within each cell, specific patterns of open chromatin expose the cis regulatory elements required for proper spatiotemporal regulation of gene expression. To further understand the complex mechanisms that modulate gene expression in the human brain, we generated maps of neuronal and non-neuronal chromatin accessibility across 14 distinct brain regions of 5 adult individuals. Chromatin structure varies markedly by cell type and, across the brain, the most extensive differences are seen between neurons of the cortical regions, hippocampus, thalamus, and striatum. Differentially accessible chromatin overlaps with neuropsychiatric trait variants and identifies differences in molecular pathways and biological functions. Transcription factor footprinting and regulatory divergence analyses identify protein coding and long noncoding RNA with cell type and brain region specificity. Overall, these findings emphasize the importance of conducting cell-type and region-specific epigenetic studies to elucidate regulatory and disease-associated mechanisms in the human brain.

Data: UCSC hub

You can view the open chromatin tracks in the UCSC genome browser as a track hub by clicking this link:

Data: Downloads and individual tracks

You can view or download the individual files as individual tracks by following the links below. Be aware that the downloadable files are large (approximately 30GB in total). You can also access the GEO page for access to the individual sample data here or download BED files with region- & cell-type specific peaks (hg19, hg38), consensus peaks (hg19 hg38), raw count matrix (here), and normalized count matrix (here).

Brain region Bigwig hg19 Bigwig hg38 Sample
Broad area name abbreviation neuronal non-Neuronal neuronal non-Neuronal 351 372 437 440 446
Neocortex (NCX) Dorsolateral prefrontal cortex DLPFC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Orbitofrontal cortex OFC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Ventrolatelar prefrontal cortex VLPFC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Anterior cingulate cortex ACC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Superior temporal cortex STC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Inferior temporal cortex ITC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Primary motor cortex PMC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ★ ✓ ✓ ✓
Insula INS Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ✓ ✓
Primary visual cortex Primary visual cortex PVC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✝ ✓ ✓ ✓
Amygdala (AMY) Amygdala AMY Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✕ ★ ✕ ✕ ✓
Hippocampus (HIP) Hippocampus HIP Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✕ ✓ ✓ ✕ ✓
Mediodorsal thalamus (MDT) Mediodorsal thalamus MDT Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✧ ★ ✓
Striatum (STR) Nucleus accumbens NAC Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✕ ✓ ✕ ✕ ✕
Putamen PUT Download bigWig file Download bigWig file Download bigWig file Download bigWig file ✓ ✓ ✓ ★ ✓
    ✓ indicates the brain region and sample where dissection was available. From these samples, ATAC-seq in both neuronal and non-neuronal nuclei was available.
    ★ indicates the brain region and sample where dissection was available. From these samples only non-neuronal ATAC-seq was available, as the neuronal ATAC-seq did not pass QC.
    ✝ indicates the brain region and sample where dissection was available. From these samples only neuronal ATAC-seq was available, as the non-neuronal ATAC-seq did not pass QC.
    ✧ indicates the brain region and sample where dissection and ATAC-seq in both neuronal and non-neuronal nuclei were available. From these samples, ATAC-seq were excluded due to potential contamination with tissue from other brain region during the dissection.
    ✕ indicates the brain region and sample where dissection was not available.

Interactive data visualisation

Multidimensional scaling of brain regions and cell types (n=28) using the pi1 estimates of statistical dissimilarity as distance (same abbreviations as in the above table are used). The MDT (mediodorsal thalamus) non-neuronal group is immediately adjacent to, and partly obscured by, the leftmost non-neuronal STR group (putamen). Move cursor over the data points to see full description.
© 2018 Roussos Lab at Icahn School of Medicine at Mount Sinai