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Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

Author

Listed:
  • Viren Amin

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • R. Alan Harris

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Vitor Onuchic

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Andrew R. Jackson

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Tim Charnecki

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Sameer Paithankar

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Sai Lakshmi Subramanian

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Kevin Riehle

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Cristian Coarfa

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

  • Aleksandar Milosavljevic

    (Epigenome Center, Bioinformatics Research Laboratory, Genetics, Baylor College of Medicine)

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.

Suggested Citation

  • Viren Amin & R. Alan Harris & Vitor Onuchic & Andrew R. Jackson & Tim Charnecki & Sameer Paithankar & Sai Lakshmi Subramanian & Kevin Riehle & Cristian Coarfa & Aleksandar Milosavljevic, 2015. "Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs," Nature Communications, Nature, vol. 6(1), pages 1-10, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7370
    DOI: 10.1038/ncomms7370
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