GSE135394
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [I]
CTCF is a key insulator-binding protein and mammalian genomes contain numerous CTCF-binding sites (CBSs), many of which are organized in tandem arrays. Here we provide direct evidence that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation and experimental capture revealed balanced promoter usage in vivo in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation. Overall design: Single-cell mRNA profiles of P0 cortex from wild type (WT) and b-e deletion mice were separately generated by deep sequencing using Illumina HiSeq X-ten. b-e deletion range: chr18:38011471-38040871(mm9). 43 single-cell mRNA profiles of HEC-1-B wild type (WT) cells were separately generated by deep sequencing using Illumina HiSeq X-ten.