DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

Abstract

Dysregulation of DNA methylation and mRNA alternative cleavage and polyadenylation (APA) are both prevalent in cancer and have been studied as independent processes. We discovered a DNA methylation-regulated APA mechanism when we compared genome-wide DNA methylation and polyadenylation site usage between DNA methylation-competent and DNA methylation-deficient cells. Here, we show that removal of DNA methylation enables CTCF binding and recruitment of the cohesin complex, which, in turn, form chromatin loops that promote proximal polyadenylation site usage. In this DNA demethylated context, either deletion of the CTCF binding site or depletion of RAD21 cohesin complex protein can recover distal polyadenylation site usage. Using data from The Cancer Genome Atlas, we authenticated the relationship between DNA methylation and mRNA polyadenylation isoform expression in vivo. This DNA methylation-regulated APA mechanism demonstrates how aberrant DNA methylation impacts transcriptome diversity and highlights the potential sequelae of global DNA methylation inhibition as a cancer treatment.

Comprehensive analysis of epigenetic signatures of human transcription control†

“…A weak negative correlation between DNA methylation and gene expression level at TTS was observed for a subset of genes when comparing the same gene across cell and tissue types ( figure 2D). This is in agreement with recent findings 32 . The negative correlation between DNA methylation and gene expression was evident only in 'long' genes, and in protein coding genes.…”

CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers

“…Так как достаточно большая часть сайтов CTCF находится в интронах генов, можно ожидать, что СTCF, неспецифично связываясь с РНК, участвует в регуляции процессов сплайсинга и терминации синтеза пре-мРНК, которые протекают сопряженно с этапами транскрипции. Например, СTCF способен замедлять движение РНК-полимеразы II, тем самым приводя к выбору альтернативного экзона при сплайсинге [53,54] или альтернативного сигнала полиаденилирования при терминации транскрипции [55]. В С-концевом домене белка CTCF картирован домен, способный взаимодействовать с РНК-полимеразой II, что может объяснить эффект ее торможения при движении через сайты связывания CTCF [56].…”

Crosstalk Between mRNA 3'-End Processing and Epigenetics

“…The same mechanism also underlies DNA methylation-mediated APA regulation. CTCF binds to unmethylated CpG islands within introns to recruit the cohesin complex and enhance RNAPII pausing, which in turn promotes the usage of nearby intronic PAS ( Figure 2A ; Nanavaty et al, 2020 ). This mechanism is likely to be responsible for generating the differential APA patterns of imprinted genes.…”