title: Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.
abstract: Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Viren
authors.initials: V
authors.lastname: Amin
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: R Alan
authors.initials: RA
authors.lastname: Harris
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Vitor
authors.initials: V
authors.lastname: Onuchic
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jackson
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Tim
authors.initials: T
authors.lastname: Charnecki
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Sameer
authors.initials: S
authors.lastname: Paithankar
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Sai
authors.identifier: 0000000313840722
authors.initials: S
authors.lastname: Lakshmi Subramanian
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Riehle
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Cristian
authors.initials: C
authors.lastname: Coarfa
authors.affiliation: Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Milosavljevic
mesh_terms: D002454:Cell Differentiation; D053595:Embryonic Stem Cells / Q000502:physiology; D044127:Epigenesis, Genetic; D057890:Epigenomics; D006801:Humans; D009928:Organ Specificity; D010641:Phenotype; D063146:Polycomb-Group Proteins / Q000502:physiology; D062085:RNA, Long Noncoding / Q000378:metabolism*; D050436:Regulatory Elements, Transcriptional
chemical_list: D063146:Polycomb-Group Proteins; D062085:RNA, Long Noncoding