ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing

Abstract

Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown. We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate the genome-scale effects of DNMT3B dysfunction. We highlighted that altered intragenic CpG-methylation impairs multiple aspects of transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing. These defects preferentially associate with changes of intragenic H3K4me3 and at lesser extent of H3K27me3 and H3K36me3. In addition, we highlighted a novel DNMT3B activity in modulating the self-regulatory circuit of sense-antisense pairs and the exon skipping during alternative splicing, through interacting with RNA molecules. Strikingly, altered transcription affects disease relevant genes, as for instance the memory-B cell marker CD27 and PTPRC genes, providing us with biological insights into the ICF1-syndrome pathogenesis. Our genome-scale approach sheds light on the mechanisms still poorly understood of the intragenic function of DNMT3B and DNA methylation in gene expression regulation.

Collagen Prolyl Hydroxylation–Dependent Metabolic Perturbation Governs Epigenetic Remodeling and Mesenchymal Transition in Pluripotent and Cancer Cells

“…DNA methylation comparison between L-Pro treated-and Tet TKO mESCs was performed as described (17). Briefly, the Tet TKO hyper-DMRs (18) in which at least 3 CpGs were covered by L-Pro RRBS experiments (6) were selected for the analysis.…”

Compound Heterozygous Mutations of IL2-Inducible T cell Kinase in a Swedish Patient: the Importance of Early Genetic Diagnosis

“…It is well known that both during immune cell differentiation and B or T cell activation, DNA methylation combined with the transcription factors play a vital role in the regulation of gene expression (78), which through DNA methylation of cytosines in the context of cytosineguanine dinucleotides (CpG), often located in clusters (CpG islands) within regulatory regions such as promoters and enhancers. Epigenetics is also thought to be essential for V(D)J rearrangement, and immunological memory (79,80) and recent studies have identified DNA methylation alterations in common variable immunodeficiency (CVID) (78), the Immunodeficiency, Centromere instability and Facial anomalies (ICF) (81,82) and ATM deficiency (83).…”

DNMT3B Functions: Novel Insights From Human Disease

“…Indeed, the aberrant hypomethylation at alternative or cryptic TSSs caused by DNMT3B dysfunction leads to their illegitimate activation interfering with the transcription and elongation of the appropriate mRNA. Switching to an alternative intragenic TSS may be caused by the hypermethylation of the canonical TSS following an altered recruitment of DNMT3A/3B proteins (Figure 1A ; Gatto et al, 2017 ).…”