Identifying Fetal Brain Enhancers

Roadmap Epigenomic Project (18 (link)) chromHMM segmentations across 127 tissues and cell types were used to define brain-specific enhancers. We selected all genic (intronic) and intergenic enhancers (6_EnhG and 7_Enh) from a male (E081) and a female fetal brain (E082). This was accomplished using genome-wide chromHMM chromatin state classification in rolling 200-bp windows. All consecutive 200-bp windows assigned as an enhancer in the fetal brain were merged to obtain enhancer boundaries. A score was assigned to each enhancer based on the total number of 200-bp windows covered by each enhancer. Next, for each fetal brain enhancer, we counted the number of 200-bp segments assigned as an enhancer in the remaining 125 tissues and cell types. This provided enhancer scores across 127 tissues and cell types for all fetal brain enhancers. To identify FBSEs, Z scores were calculated for each fetal brain enhancer using the enhancer scores. Z scores were calculated independently for male and female fetal brain enhancers. Independent Z scores cutoffs were used for both male and female fetal brain enhancers such that ∼35% of enhancers were selected. To define open accessible chromatin regions within brain-specific enhancers, we intersected enhancers with DNAse-seq data from the Roadmap Epigenomic Project (18 (link)) from a male (E081) and a female fetal brain (E082), respectively. Next, the male and female FBSEs were merged to get a final set of 27,420 FBSEs. We used a similar approach to identify enhancers that were specifically active in adult brain subsections, which include angular gyrus (E067), anterior caudate (E068), cingulate gyrus (E069), germinal matrix (E070), hippocampus middle (E071), inferior temporal lobe (E072), dorsolateral prefrontal cortex (E073), and substantia nigra (E074).