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Genome Res. 2017 Aug;27(8):1371-1383. doi: 10.1101/gr.208652.116. Epub 2017 May 9.

The identification and functional annotation of RNA structures conserved in vertebrates.

Author information

Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, DK-1870 Frederiksberg, Denmark.
Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark.
Copenhagen Diabetes Research Center (CPH-DIRECT), Herlev University Hospital, DK-2730 Herlev, Denmark.
Department of Cellular and Molecular Medicine (ICMM), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
Department of Obesity Biology and Department of Molecular Genetics, Novo Nordisk A/S, DK-2880 Bagsværd, Denmark.
Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
Allen Institute for Brain Science, Seattle, Washington 98109, USA.
School of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.


Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.

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