The identification and functional annotation of RNA structures conserved in vertebrates

Ernst Stefan Seemann, Aashiq Hussain Mirza, Claus Hansen, Claus Heiner Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Elfar Torarinsson, Christopher Workman, Flemming Pociot, Henrik Nielsen, Niels Tommerup, Walter L. Ruzzo, Jan Gorodkin

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Abstract

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 ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins (RBPs) or (ii) 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 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.
Original languageEnglish
JournalGenome Research
Volume27
Pages (from-to)1371-1383
Number of pages14
ISSN1088-9051
DOIs
Publication statusPublished - 2017

Cite this

Seemann, E. S., Mirza, A. H., Hansen, C., Bang-Berthelsen, C. H., Garde, C., Christensen-Dalsgaard, M., ... Gorodkin, J. (2017). The identification and functional annotation of RNA structures conserved in vertebrates. Genome Research, 27, 1371-1383. https://doi.org/10.1101/gr.208652.116
Seemann, Ernst Stefan ; Mirza, Aashiq Hussain ; Hansen, Claus ; Bang-Berthelsen, Claus Heiner ; Garde, Christian ; Christensen-Dalsgaard, Mikkel ; Torarinsson, Elfar ; Workman, Christopher ; Pociot, Flemming ; Nielsen, Henrik ; Tommerup, Niels ; Ruzzo, Walter L. ; Gorodkin, Jan. / The identification and functional annotation of RNA structures conserved in vertebrates. In: Genome Research. 2017 ; Vol. 27. pp. 1371-1383.
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abstract = "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 ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins (RBPs) or (ii) 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 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.",
author = "Seemann, {Ernst Stefan} and Mirza, {Aashiq Hussain} and Claus Hansen and Bang-Berthelsen, {Claus Heiner} and Christian Garde and Mikkel Christensen-Dalsgaard and Elfar Torarinsson and Christopher Workman and Flemming Pociot and Henrik Nielsen and Niels Tommerup and Ruzzo, {Walter L.} and Jan Gorodkin",
year = "2017",
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Seemann, ES, Mirza, AH, Hansen, C, Bang-Berthelsen, CH, Garde, C, Christensen-Dalsgaard, M, Torarinsson, E, Workman, C, Pociot, F, Nielsen, H, Tommerup, N, Ruzzo, WL & Gorodkin, J 2017, 'The identification and functional annotation of RNA structures conserved in vertebrates', Genome Research, vol. 27, pp. 1371-1383. https://doi.org/10.1101/gr.208652.116

The identification and functional annotation of RNA structures conserved in vertebrates. / Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus; Bang-Berthelsen, Claus Heiner; Garde, Christian; Christensen-Dalsgaard, Mikkel ; Torarinsson, Elfar; Workman, Christopher; Pociot, Flemming; Nielsen, Henrik; Tommerup, Niels; Ruzzo, Walter L.; Gorodkin, Jan.

In: Genome Research, Vol. 27, 2017, p. 1371-1383.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - The identification and functional annotation of RNA structures conserved in vertebrates

AU - Seemann, Ernst Stefan

AU - Mirza, Aashiq Hussain

AU - Hansen, Claus

AU - Bang-Berthelsen, Claus Heiner

AU - Garde, Christian

AU - Christensen-Dalsgaard, Mikkel

AU - Torarinsson, Elfar

AU - Workman, Christopher

AU - Pociot, Flemming

AU - Nielsen, Henrik

AU - Tommerup, Niels

AU - Ruzzo, Walter L.

AU - Gorodkin, Jan

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N2 - 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 ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins (RBPs) or (ii) 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 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.

AB - 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 ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins (RBPs) or (ii) 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 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.

U2 - 10.1101/gr.208652.116

DO - 10.1101/gr.208652.116

M3 - Journal article

C2 - 28487280

VL - 27

SP - 1371

EP - 1383

JO - Genome Research

JF - Genome Research

SN - 1088-9051

ER -