ArticleNucleic acids research2013
Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.Genome biology · 2023Article
- The prognostic value of RASGEF1A RNA expression and DNA methylation in cytogenetically normal acute myeloid leukemia.Cancer biomarkers : section A of Disease markers · 2023Article
- Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets.Endocrinology · 2022Article
- Decoding regulatory associations of G-quadruplex with epigenetic and transcriptomic functional components.Frontiers in genetics · 2022Article
- CTCF as a regulator of alternative splicing: new tricks for an old player.Nucleic acids research · 2021Review
- Splicing alterations in healthy aging and disease.Wiley interdisciplinary reviews. RNA · 2021Review
- Article
- Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy.Journal of clinical medicine · 2020Article
- Dysregulation of Neuronal Genes by Fetal-Neonatal Iron Deficiency Anemia Is Associated with Altered DNA Methylation in the Rat Hippocampus.Nutrients · 2019Article
- Does co-transcriptional regulation of alternative splicing mediate plant stress responses?Nucleic acids research · 2019Review
- DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield.BMC genomics · 2018Article
- Landscape of alternative splicing in Capra_hircus.Scientific reports · 2018Article
- The effect of maternal care on gene expression and DNA methylation in a subsocial bee.Nature communications · 2018Article
- Epigenetic control of gene regulation during development and disease: A view from the retina.Progress in retinal and eye research · 2018Review
- Estimating the prevalence of functional exonic splice regulatory information.Human genetics · 2017Review
- Whole genome DNA methylation: beyond genes silencing.Oncotarget · 2017Review
- DNA methylation in oligodendroglial cells during developmental myelination and in disease.Neurogenesis (Austin, Tex.) · 2017Article
- Transcription factors as readers and effectors of DNA methylation.Nature reviews. Genetics · 2016Review
- Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes.Nature communications · 2016Article
- In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene.Cell stress & chaperones · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The exact role of intragenic DNA methylation in regulating tissue-specific gene regulation is unclear. Recently, the DNA-binding protein CTCF has been shown to participate in the regulation of alternative splicing in a DNA methylation-dependent manner. To globally evaluate the relationship between DNA methylation and tissue-specific alternative splicing, we performed genome-wide DNA methylation profiling of mouse retina and brain. In protein-coding genes, tissue-specific differentially methylated regions (T-DMRs) were preferentially located in exons and introns. Gene ontology and evolutionary conservation analysis suggest that these T-DMRs are likely to be biologically relevant. More than 14% of alternatively spliced genes were associated with a T-DMR. T-DMR-associated genes were enriched for developmental genes, suggesting that a specific set of alternatively spliced genes may be regulated through DNA methylation. Novel DNA sequences motifs overrepresented in T-DMRs were identified as being associated with positive and/or negative regulation of alternative splicing in a position-dependent context. The majority of these evolutionarily conserved motifs contain a CpG dinucleotide. Some transcription factors, which recognize these motifs, are known to be involved in splicing. Our results suggest that DNA methylation-dependent alternative splicing is widespread and lay the foundation for further mechanistic studies of the role of DNA methylation in tissue-specific splicing regulation.
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