RRC ID 59716
Author Hyle J, Zhang Y, Wright S, Xu B, Shao Y, Easton J, Tian L, Feng R, Xu P, Li C.
Title Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping.
Journal Nucleic Acids Res
Abstract Numerous pieces of evidence support the complex, 3D spatial organization of the genome dictates gene expression. CTCF is essential to define topologically associated domain boundaries and to facilitate the formation of insulated chromatin loop structures. To understand CTCF's direct role in global transcriptional regulation, we integrated the miniAID-mClover3 cassette to the endogenous CTCF locus in a human pediatric B-ALL cell line, SEM, and an immortal erythroid precursor cell line, HUDEP-2, to allow for acute depletion of CTCF protein by the auxin-inducible degron system. In SEM cells, CTCF loss notably disrupted intra-TAD loops and TAD integrity in concurrence with a reduction in CTCF-binding affinity, while showing no perturbation to nuclear compartment integrity. Strikingly, the overall effect of CTCF's loss on transcription was minimal. Whole transcriptome analysis showed hundreds of genes differentially expressed in CTCF-depleted cells, among which MYC and a number of MYC target genes were specifically downregulated. Mechanically, acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ∼1.8 Mb downstream. Notably, MYC expression was not profoundly affected upon CTCF loss in HUDEP-2 cells suggesting that CTCF could play a B-ALL cell line specific role in maintaining MYC expression.
Volume 47(13)
Pages 6699-6713
Published 2019-7-26
DOI 10.1093/nar/gkz462
PII 5498628
PMID 31127282
PMC PMC6648894
MeSH CCCTC-Binding Factor / deficiency CCCTC-Binding Factor / physiology* Cell Line, Tumor Cell Nucleus / metabolism Cell Nucleus / ultrastructure Chromatin / genetics Chromatin / ultrastructure* Down-Regulation Enhancer Elements, Genetic / genetics* Erythroid Precursor Cells / metabolism Gene Expression Regulation, Leukemic* Gene Knock-In Techniques Genes, Reporter Genes, myc* Humans Nucleic Acid Conformation Precursor Cell Lymphoblastic Leukemia-Lymphoma / pathology Promoter Regions, Genetic / genetics* Proto-Oncogene Proteins c-myc / biosynthesis* Transcriptome
IF 11.147
Times Cited 7
Human and Animal Cells HUDEP-2(RCB4557)