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The identification and functional annotation of RNA structures conserved in vertebrates

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Harvard

Seemann, SE, Mirza, AH, Hansen, C, Bang-Berthelsen, CH, Garde, C, Christensen-Dalsgaard, M, Torarinsson, E, Yao, Z, Workman, CT, Pociot, F, Nielsen, H, Tommerup, N, Ruzzo, WL & Gorodkin, J 2017, 'The identification and functional annotation of RNA structures conserved in vertebrates' Genome Research, bind 27, nr. 8, s. 1371-1383. https://doi.org/10.1101/gr.208652.116

APA

Seemann, S. E., 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(8), 1371-1383. https://doi.org/10.1101/gr.208652.116

CBE

Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J. 2017. The identification and functional annotation of RNA structures conserved in vertebrates. Genome Research. 27(8):1371-1383. https://doi.org/10.1101/gr.208652.116

MLA

Vancouver

Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M o.a. The identification and functional annotation of RNA structures conserved in vertebrates. Genome Research. 2017 aug;27(8):1371-1383. https://doi.org/10.1101/gr.208652.116

Author

Seemann, Stefan E ; Mirza, Aashiq H ; Hansen, Claus ; Bang-Berthelsen, Claus H ; Garde, Christian ; Christensen-Dalsgaard, Mikkel ; Torarinsson, Elfar ; Yao, Zizhen ; Workman, Christopher T ; Pociot, Flemming ; Nielsen, Henrik ; Tommerup, Niels ; Ruzzo, Walter L ; Gorodkin, Jan. / The identification and functional annotation of RNA structures conserved in vertebrates. I: Genome Research. 2017 ; Bind 27, Nr. 8. s. 1371-1383.

Bibtex

@article{3ed8d2ae366c4e10897b79b1f87b698e,
title = "The identification and functional annotation of RNA structures conserved in vertebrates",
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 ∼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.",
keywords = "Journal Article",
author = "Seemann, {Stefan E} and Mirza, {Aashiq H} and Claus Hansen and Bang-Berthelsen, {Claus H} and Christian Garde and Mikkel Christensen-Dalsgaard and Elfar Torarinsson and Zizhen Yao and Workman, {Christopher T} and Flemming Pociot and Henrik Nielsen and Niels Tommerup and Ruzzo, {Walter L} and Jan Gorodkin",
note = "{\circledC} 2017 Seemann et al.; Published by Cold Spring Harbor Laboratory Press.",
year = "2017",
month = "8",
doi = "10.1101/gr.208652.116",
language = "English",
volume = "27",
pages = "1371--1383",
journal = "Human Genome Variation",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press Publications Department",
number = "8",

}

RIS

TY - JOUR

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

AU - Seemann, Stefan E

AU - Mirza, Aashiq H

AU - Hansen, Claus

AU - Bang-Berthelsen, Claus H

AU - Garde, Christian

AU - Christensen-Dalsgaard, Mikkel

AU - Torarinsson, Elfar

AU - Yao, Zizhen

AU - Workman, Christopher T

AU - Pociot, Flemming

AU - Nielsen, Henrik

AU - Tommerup, Niels

AU - Ruzzo, Walter L

AU - Gorodkin, Jan

N1 - © 2017 Seemann et al.; Published by Cold Spring Harbor Laboratory Press.

PY - 2017/8

Y1 - 2017/8

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 ∼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.

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 ∼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.

KW - Journal Article

U2 - 10.1101/gr.208652.116

DO - 10.1101/gr.208652.116

M3 - Journal article

VL - 27

SP - 1371

EP - 1383

JO - Human Genome Variation

JF - Human Genome Variation

SN - 1088-9051

IS - 8

ER -

ID: 52370953