Fig. 1: Identification of noncoding elements actively transcribed in dopamine neurons of human brain. | Nature Neuroscience

Fig. 1: Identification of noncoding elements actively transcribed in dopamine neurons of human brain.

From: Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease

Fig. 1

a, lcRNAseq was used to systematically identify noncoding elements transcribed in dopamine neurons and pyramidal neurons of human brains. We analyzed dopamine neurons of the substantia nigra from 89 high-quality autopsy brains, pyramidal neurons from temporal cortex of ten brains and from motor cortex of three brains, and fibroblasts from four individuals and peripheral blood mononuclear white cells (non-neuronal cells) from three individuals. b, Cumulatively, 64.4% of the human genome was transcribed in dopamine neurons of human brain. c, More than half (54.7%) of reads mapped to intergenic or intronic genome sequences. d, Schematic of the method for identifying TNEs: a stringent six-step filter was applied to the RNA-seq reads aggregated from dopamine neurons, pyramidal neurons, and non-neuronal cells. Briefly, a putative TNE site was defined as a genomic region with RNA-seq reads density higher than the background transcriptional level (black dashed line) and the peak unique reads per million (RPM; vertical arrow) achieving a local detection P ≤ 0.05. TNEs were required to exceed 100 bp; known genes and splice junctions were excluded. Finally, TNEs were required to achieve Bonferroni-corrected expression P ≤ 0.05 across all samples of one cell type (indicated by multiple copies of the schematic) compared to length-matched, randomly selected background regions using a binomial distribution. See Methods and Supplementary Fig. 14 for details. e, Venn diagram with TNEs detected in dopamine neurons, pyramidal neurons, and non-neuronal cells.

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