Molecular and computational approaches to map regulatory elements in 3D chromatin structure

摘要

Overview of epigenome change in the human genome. a Human cells within an individual are genetically identical across all cell types, but distinct epigenome profiles are detected between cell types. b Epigenome changes when normal cells become diseased cells, and vice versa. DNA methylation, histone marks H3K9me3 (heterochromatin region) and H3K27me3 (repressed region) are usually associated with inactive, closed chromatin, while unmethylated DNA, histone marks H3K4me3 (active promoter) and H3K27ac (active enhancer), and transcription factor (TF) binding are found in active, open chromatin. An insulator marked by CTCF can act as a barrier to prevent enhancer-promoter interaction and decrease the rate of transcription or stop the spreading of heterochromatin to increase rate of transcription. c DNA methylation arrays and bisulfite sequencing are used to measure DNA methylation levels. ChIP-seq, CUT & RUN, and CUT & TAG are used to identify regulatory elements using histone mark and TF enriched regions. 3C, 4C, 5C, Capture-C, Hi-C, DNase Hi-C, ChIA-PET, and HiChIP are used to map chromatin interactions. PolII: RNA Polymerase II, GTF: General transcription factor