Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing

Abstract

<jats:title>Abstract</jats:title> <jats:p>Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.</jats:p>

Intragenic CpG Islands and Their Impact on Gene Regulation

“…Similar polyadenylation site usage was also found when DNA methylation was perturbed at the iCGI within the NFATc1 locus, resulting in alternative NFATc1 isoforms. These locus specific effects have been detected genome-wide by a recent bioinformatic screen, emphasising that iCGI activity leads to premature transcription termination upstream of the iCGI, most likely through APA (Amante et al, 2020) (Figures 2B,D).…”

“…iCGIs are more likely to be DNA methylated (Figure 1C) and those lacking DNA methylation can exhibit bivalent chromatin signatures and when transcriptionally active, show transcription factor binding and the promoter mark, H3K4me3 (Lee et al, 2017;Amante et al, 2020;Choi et al, 2020). iCGIs can therefore exist in the same 'states' as promoter CGIs, albeit in different proportions.…”

“…iCGIs are more prone to DNA methylation during embryonic development and adult development compared to their TSS CGI counterparts (Illingworth et al, 2010;Auclair et al, 2014), implying that regulation of iCGIs is crucial for tissue specific programming. For example, iCGIs are specifically expressed in brain tissues and their host genes function in brain-specific biological processes (Amante et al, 2020). In this case, iCGIs may function as TSSs for novel transcripts or result in APA of the host gene and therefore, expand the transcriptome during developmental processes such as neurogenesis.…”

“…Biochemical methods discovered that a quarter of all CGIs are within genes, existing as iCGIs. Recent studies have now tied iCGIs to multiple functions (Maunakea et al, 2010;Jeziorska et al, 2017;Amante et al, 2020). Comprehensive reviews discuss CGIs more broadly and in the context of development and disease (Deaton and Bird, 2011;Greenberg and Bourc'his, 2019).…”

DNMT3B overexpression downregulates genes with CpG islands, common motifs, and transcription factor binding sites that interact with DNMT3B

“…Our approach was downregulated genes with CGIs but is important to announce that DNMT3B overexpression also was related to the up-regulation of several genes. The methylation in intragenic CGIs 51 is related to cell differentiation 52 , 95 , active transcription, and enrichment of histone modifications such as H3K36me3 50 . We studied genes possibly related to the catalytic DNMT3B function, and a limitation of our study is that we can’t discriminate whether the change observed in all the deregulated genes is a catalytic or accessory function of DNMT3B 96 , we specifically tested the catalytic function in the 4 selected genes.…”