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Function and evolution of local repeats in the Firre locus

Author

Listed:
  • Ezgi Hacisuleyman

    (Harvard University
    Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard)

  • Chinmay J. Shukla

    (Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard
    Harvard University)

  • Catherine L. Weiner

    (Harvard University
    Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard)

  • John L. Rinn

    (Harvard University
    Broad Institute of Massachusetts Institute of Technology and Harvard
    Beth Israel Deaconess Medical Center)

Abstract

More than half the human and mouse genomes are comprised of repetitive sequences, such as transposable elements (TEs), which have been implicated in many biological processes. In contrast, much less is known about other repeats, such as local repeats that occur in multiple instances within a given locus in the genome but not elsewhere. Here, we systematically characterize local repeats in the genomic locus of the Firre long noncoding RNA (lncRNA). We find a conserved function for the RRD repeat as a ribonucleic nuclear retention signal that is sufficient to retain an otherwise cytoplasmic mRNA in the nucleus. We also identified a repeat, termed R0, that can function as a DNA enhancer element within the intronic sequences of Firre. Collectively, our data suggest that local repeats can have diverse functionalities and molecular modalities in the Firre locus and perhaps more globally in other lncRNAs.

Suggested Citation

  • Ezgi Hacisuleyman & Chinmay J. Shukla & Catherine L. Weiner & John L. Rinn, 2016. "Function and evolution of local repeats in the Firre locus," Nature Communications, Nature, vol. 7(1), pages 1-12, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11021
    DOI: 10.1038/ncomms11021
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    Cited by:

    1. Christian Much & Erika L. Lasda & Isabela T. Pereira & Tenaya K. Vallery & Daniel Ramirez & Jordan P. Lewandowski & Robin D. Dowell & Michael J. Smallegan & John L. Rinn, 2024. "The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

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