Gatto Sole, Gagliardi Miriam, Franzese Monica, Leppert Sylwia, Papa Mariarosaria, Cammisa Marco, Grillo Giacomo, Velasco Guillame, Francastel Claire, Toubiana Shir, D'Esposito Maurizio, Angelini Claudia, Matarazzo Maria R
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.
Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA, USA.
Nucleic Acids Res. 2017 Jun 2;45(10):5739-5756. doi: 10.1093/nar/gkx163.
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.
DNA甲基转移酶DNMT3B中的亚效突变导致了大多数罕见疾病免疫缺陷、着丝粒不稳定和面部异常综合征病例（ICF1）。通过未明确的机制，突变型DNMT3B干扰淋巴特异性途径，导致免疫反应缺陷。有趣的是，最近的研究发现报告称，DNMT3B塑造了高转录基因的基因内CpG甲基化。然而，DNMT3B依赖的表观遗传网络如何调节转录以及ICF1特异性突变是否会损害这一过程仍然未知。我们在患者来源的B细胞系中进行了转录组和表观基因组研究，以研究DNMT3B功能障碍的基因组规模效应。我们强调，基因内CpG甲基化的改变会损害转录调控的多个方面，如可变转录起始位点的使用、反义转录和外显子剪接。这些缺陷优先与基因内H3K4me3的变化相关，在较小程度上与H3K27me3和H3K36me3的变化相关。此外，我们强调了DNMT3B在通过与RNA分子相互作用来调节有义-反义对的自我调节回路和可变剪接过程中的外显子跳跃方面的新活性。引人注目的是，转录改变会影响疾病相关基因，例如记忆B细胞标志物CD27和PTPRC基因，这为我们提供了关于ICF1综合征发病机制的生物学见解。我们的基因组规模方法揭示了对DNMT3B的基因内功能和DNA甲基化在基因表达调控中仍知之甚少的机制。
