ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing.
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.
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.|Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA, USA.
Sole
S
Gatto
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.|Institute for Applied Mathematics 'Mauro Picone', CNR, Naples 80131, Italy.
Miriam
M
Gagliardi
Institute for Applied Mathematics 'Mauro Picone', CNR, Naples 80131, Italy.
Monica
M
Franzese
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.
Sylwia
S
Leppert
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.
Mariarosaria
M
Papa
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.|Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta 81100, Italy.
Marco
M
Cammisa
CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France.
Giacomo
G
Grillo
CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France.
Guillame
G
Velasco
CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France.
Claire
C
Francastel
Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel.
Shir
S
Toubiana
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.|IRCCS Neuromed, Pozzilli, Italy.
Maurizio
M
D'Esposito
Institute for Applied Mathematics 'Mauro Picone', CNR, Naples 80131, Italy.
Claudia
C
Angelini
Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Naples 80131, Italy.
Maria R
MR
Matarazzo
D017398:Alternative Splicing; D000855:Anorexia / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D001402:B-Lymphocytes / Q000276:immunology / Q000473:pathology; D002100:Cachexia / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D002461:Cell Line, Transformed; D018899:CpG Islands; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics* / Q000276:immunology; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005124:Eye Abnormalities / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D019066:Facies; D005260:Female; D006657:Histones / Q000235:genetics* / Q000276:immunology; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D007156:Immunologic Memory; D017493:Leukocyte Common Antigens / Q000235:genetics / Q000276:immunology; D008297:Male; D009154:Mutation; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics* / Q000276:immunology; D012871:Skin Diseases / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D014158:Transcription, Genetic; D018127:Tumor Necrosis Factor Receptor Superfamily, Member 7 / Q000235:genetics / Q000276:immunology; D000097584:DNA Methyltransferase 3B
D004248:DNA (Cytosine-5-)-Methyltransferases; D006657:Histones; D017493:Leukocyte Common Antigens; D012333:RNA, Messenger; D018127:Tumor Necrosis Factor Receptor Superfamily, Member 7; D000097584:DNA Methyltransferase 3B; C516769:PTPRC protein, human