CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals

Abstract

The CCCTC-binding factor (CTCF) is known to establish long-range DNA contacts that alter the three-dimensional architecture of chromatin, but how the presence of CTCF influences nearby gene expression is still poorly understood. Here, we analyze CTCF chromatin immunoprecipitation sequencing, RNA sequencing, and Hi-C data, together with genotypes from a healthy human cohort, and measure statistical associations between inter-individual variability in CTCF binding and alternative exon usage. We demonstrate that CTCF-mediated chromatin loops between promoters and intragenic regions are prevalent and that when exons are in physical proximity with their promoters, CTCF binding correlates with exon inclusion in spliced mRNA. Genome-wide, CTCF-bound exons are enriched for genes involved in signaling and cellular stress-response pathways. Structural analysis of three specific examples, checkpoint kinase 2 (CHK2), CDC-like kinase 3 (CLK3), and euchromatic histone-lysine N-methyltransferase (EHMT1), suggests that CTCF-mediated exon inclusion is likely to downregulate enzyme activity by disrupting annotated protein domains. In total, our study suggests that alternative exon usage is regulated by CTCF-dependent chromatin structure.

The CTCF Anatomy of Topologically Associating Domains

“…1, S1D). Such regulatory consequences are likely to be locus-specific and idiosyncratic (Ruiz-Velasco et al, 2017). Indeed, it is fascinating that 5,886 gene promoters are equipped with a functional CTCF site, such as CTCF11 at PPARD and CTCF16 at RPL10A.…”

“…We speculate that, beyond helping to compact the genome, the intragenic CTCF sites may also facilitate mechanistic aspects of gene expression control such as bringing together gene promoters and enhancers (eg; Fig. S1D), or marking alternative exon usage (Ruiz-Velasco et al, 2017). Thus, 'intragenic' CTCF sites are likely to contribute to the formation of CTCF-determined chromosome topology together with 'intergenic' CTCF sites.…”

“…On the other hand it was shown that convergent CTCF sites are located at the synapses between long range interacting DNA regions, explaining multiple features of HiC data sets Sanborn et al, 2015). Hence the current view is that large loops are constrained at their basis by Cohesin rings (Alipour and Marko, 2012;Dorsett, 2019;Fudenberg et al, 2016;Nasmyth, 2001;Parelho et al, 2008;Wendt et al, 2008) that accumulate at pairs of convergent CTCF sites to organize chromosome 3D architectures (de Wit et al, 2015;Dixon et al, 2016;Guo et al, 2015;Haarhuis et al, 2017;Nichols and Corces, 2015;Ong and Corces, 2014;Pugacheva et al, 2015;Rao et al, 2014;Remeseiro et al, 2016;Ruiz-Velasco et al, 2017;Sanborn et al, 2015;Vietri Rudan et al, 2015;Zuin et al, 2014).…”

CtcfHaploinsufficiency Mediates Intron Retention in A Tissue-specific Manner

“…CTCF ChIP-seq studies have found that approximately 30% and 50% of CTCF binding sites are located in intronic and intergenic regions, respectively [2,5,9]. It has been shown that the intragenic localization of CTCF binding sites influences pre-mRNA splicing decisions leading to alternative exon splicing [20,21,25]. To determine whether Ctcf binding sites are enriched in the proximity of retained introns in liver, we analyzed a publicly available ChIP-seq data set from C57BL/6 normal mouse liver (E-MTAB-5769) [42].…”

“…Compelling evidence has linked CTCF to alternative splicing (AS) regulation due to its direct or indirect role in modulating splicing decisions via complex mechanisms including RNA Polymerase II (Pol II) elongation, transcriptional regulation of splicing factors, DNA methylation and chromatin organization [20][21][22][23][24][25]. Despite its potential importance, the impact of altered CTCF dosage on AS has not been investigated at a global scale.…”