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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
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Identification of expressed and conserved human noncoding RNAs.

Morten Muhlig Nielsen, Disa Tehler, Søren Vang

    RNA (New York, N.Y.)
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    Summary

    Mammalian genomes produce thousands of noncoding (nc) transcripts, but their functions remain largely unknown. This study identifies potentially functional nc transcripts by analyzing expression, conservation, and epigenetic data.

    Keywords:
    EvoFold predictionscomparative genomicslncRNAnoncoding RNAultraconserved elements

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Mammalian genomes are pervasively transcribed, yielding numerous noncoding (nc) transcripts.
    • The functional significance of most nc transcripts is experimentally unverified.
    • Understanding nc RNA roles is crucial for deciphering genome complexity.

    Purpose of the Study:

    • To characterize expression and evolutionary conservation of 12,115 known and novel nc transcripts.
    • To identify novel nc transcripts with functional potential using integrated data.
    • To provide a foundation for future functional studies of nc RNAs.

    Main Methods:

    • Expression profiling across 12 human tissues using custom microarrays and RNAseq.
    • Assessment of base-level and syntenic evolutionary conservation.
    • Integration of expression, conservation, and epigenetic mark data.

    Main Results:

    • Few novel nc transcripts exhibited both high expression and conservation.
    • A positive correlation was observed between expression and conservation/epigenetic annotations.
    • Subsets of novel nc transcripts showed characteristics of functional ncRNAs.

    Conclusions:

    • A subset of expressed nc transcripts is likely functional and under purifying selection.
    • Integrated analysis aids in identifying potentially functional nc transcripts.
    • This work facilitates further experimental validation of novel nc RNA functions.