title: Histone modifications are associated with transcript isoform diversity in normal and cancer cells.
abstract: Mechanisms that generate transcript diversity are of fundamental importance in eukaryotes. Although a large fraction of human protein-coding genes and lincRNAs produce more than one mRNA isoform each, the regulation of this phenomenon is still incompletely understood. Much progress has been made in deciphering the role of sequence-specific features as well as DNA-and RNA-binding proteins in alternative splicing. Recently, however, several experimental studies of individual genes have revealed a direct involvement of epigenetic factors in alternative splicing and transcription initiation. While histone modifications are generally correlated with overall gene expression levels, it remains unclear how histone modification enrichment affects relative isoform abundance. Therefore, we sought to investigate the associations between histone modifications and transcript diversity levels measured by the rates of transcription start-site switching and alternative splicing on a genome-wide scale across protein-coding genes and lincRNAs. We found that the relationship between enrichment levels of epigenetic marks and transcription start-site switching is similar for protein-coding genes and lincRNAs. Furthermore, we found associations between splicing rates and enrichment levels of H2az, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3K79me2, and H4K20me, marks traditionally associated with enhancers, transcription initiation, transcriptional repression, and others. These patterns were observed in both normal and cancer cell lines. Additionally, we developed a novel computational method that identified 840 epigenetically regulated candidate genes and predicted transcription start-site switching and alternative exon splicing with up to 92% accuracy based on epigenetic patterning alone. Our results suggest that the epigenetic regulation of transcript isoform diversity may be a relatively common genome-wide phenomenon representing an avenue of deregulation in tumor development.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Ondrej
authors.initials: O
authors.lastname: Podlaha
authors.affiliation: Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, Colorado, United States of America.
authors.forename: Subhajyoti
authors.initials: S
authors.lastname: De
authors.affiliation: Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.
authors.forename: Mithat
authors.initials: M
authors.lastname: Gonen
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Franziska
authors.initials: F
authors.lastname: Michor
mesh_terms: D017398:Alternative Splicing; D002460:Cell Line; D045744:Cell Line, Tumor; D019295:Computational Biology; D044127:Epigenesis, Genetic; D005091:Exons; D014644:Genetic Variation; D006657:Histones / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D008957:Models, Genetic; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism*; D059368:RNA Isoforms / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012334:RNA, Neoplasm / Q000235:genetics* / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; D009363:Neoplasm Proteins; D059368:RNA Isoforms; D012333:RNA, Messenger; D012334:RNA, Neoplasm