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. 2023 Aug 28;3(9):100399. doi: 10.1016/j.xgen.2023.100399

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© 2023 The Author(s)

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

PMC Copyright notice

Long-range chromatin interactions and changes in local chromatin accessibility contribute to the cis effect of rs2027349 on multiple genes

(A) ATAC-seq and Capture Hi-C data from human brain tissue⁴⁶ and Micro-C data from NGN2-Glut neurons. Orange arcs show the multiple long-range interactions between the rs2027349 locus and several high-accessibility sites (ATAC-seq peaks) in proximity. Bold arcs (red in hippocampal DG neurons and blue in NGN2-Glut neurons) indicate the site-specific interaction between rs2027349 and the promoter region of C1orf54.

(B) CRISPR-Cas9 editing of rs2027349 altered both local and remote chromatin accessibility. Note the higher regional OCR peaks (normalized pile-up intensity) on the rs2027349 locus and regions proximal to the C1orf54 gene in AA neurons. ATAC-seq data were from two clones per genotype of line CD0000011.