CTCF: from insulators to alternative splicing regulation

Abstract

The zinc-finger DNA-binding protein CTCF has been known for being a constituent of insulators. A recent paper in Nature reports an unforeseen intragenic role for CTCF that links DNA methylation with alternative splicing. By binding to its target DNA site placed within an alternative exon, CTCF creates a roadblock to transcriptional elongation that favors inclusion of the exon into mature mRNA. DNA methylation prevents CTCF binding, which releases pol II transient blockage and promotes exon exclusion.One of the most exciting aspects of scientific research is not discovery per se but the fall of preconceptions. In the history of the knowledge of the flow of gene expression in eukaryotic cells, many preconceptions have fallen. Perhaps the most striking one is that eukaryotic genes are not contiguous with their corresponding mRNAs, as thought in the 60's and early 70's of the last century, but split in exons and introns, which calls for the splicing mechanism that gets rid of the introns from a precursor mRNA and joins the exons to give rise to the mature, translatable mRNA molecule. Soon after the discovery of splicing in 1976, alternative splicing was reported, but only recently we learnt that this mechanism, responsible for the generation of a vast proteomic diversity from a limited number of genes, seems to be present in 90% of the approximately 23 000 human genes, which also represents an unexpected surprise compared to previous estimations of 20%. A third preconception that has been violated more recently is that splicing is a post-transcriptional event, and therefore independent from transcription. On the contrary, not only splicing is mostly co-transcriptional but both splicing and alternative splicing are coupled to transcription and in consequence, splicing is not only affected by the splicing machinery but also by the chromatin structure and factors regulating the transcription process, such as promoters, transcription factors and co-activators, which may affect either the speed of RNA polymerase II (pol II) elongation or the recruitment of splicing factors to the transcription apparatus (for reviews see [1,2]). Differential transcriptional elongation rates inside genes create different windows of time for the splicing machinery to be recruited to and act on relevant sequences as they are present in the nascent pre-mRNA [3].A role for chromatin in the control of intragenic elongation rates and in consequence, in alternative splicing has been demonstrated by several groups who used drugs or signal cascades that promote either more compact or more relaxed chromatin configurations that impede or facilitate elongation, respectively. For example, trichostatin A [4, 5], recruitment to promoters of histone acetyltransferases [6] and neuron depolarization [7] regulate alternative splicing because of chromatin relaxation promoted by histone acetylation. Consistently, the transcription-associated H3K36me3 modification is less prominently enriched in alternatively spliced exons than in constitutive exons [8]. In an ...

Human telomerase reverse transcriptase regulation by DNA methylation, transcription factor binding and alternative splicing (Review)

“…They also demonstrated that the pausing was methylation dependent; when CTCF cannot bind the methylated site, weak exons are not included in the final spliced transcript ( Fig. 2A) (55,56). multiple additional genes have been shown to have promoterproximal CTCF binding (100 bases downstream of the Tss) that results in longer Pol II pausing compared to genes without promoter-proximal binding sites.…”

Anchor: trans-cell type prediction of transcription factor binding sites

“…The TF binding landscapes vary in different cell types and genetic contexts (Kasowski et al 2010). Understanding TF binding behaviors is critical to decoding the regulatory mechanisms underlying transcription processes and diseases (Shilatifard et al 2003; Thomas and Chiang 2006;Hawkins et al 2011;Kornblihtt 2012;Yin et al 2017). Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) is a widely used method for detecting genome-wide in vivo TF binding profiles (Johnson et al 2007;Kulakovskiy et al 2010).…”

SLC45A3-ELK4 Chimera in Prostate Cancer: Spotlight on cis-Splicing

“…Insulator sequences typically lie within intergenic regions and prevent runaway transcription across neighboring genes, through association with CCCTC-binding factor (CTCF) (13). The role of CTCF has been described in the regulation of alternative splicing (14), as well as through association of DNA methylation at CTCF binding sites, in the generation of alternative splice variants (15). Here, the authors show that CTCF binds to the two insulators and this binding is attenuated upon androgen treatment.…”