Does rapid sequence divergence preclude RNA structure conservation in vertebrates?

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Standard

Does rapid sequence divergence preclude RNA structure conservation in vertebrates? / Seemann, Stefan E.; Mirza, Aashiq H.; Bang-Berthelsen, Claus H.; Garde, Christian; Christensen-Dalsgaard, Mikkel; Workman, Christopher T.; Pociot, Flemming; Tommerup, Niels; Gorodkin, Jan; Ruzzo, Walter L.

In: Nucleic Acids Research, Vol. 50, No. 5, 2022, p. 2452-2463.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Seemann, SE, Mirza, AH, Bang-Berthelsen, CH, Garde, C, Christensen-Dalsgaard, M, Workman, CT, Pociot, F, Tommerup, N, Gorodkin, J & Ruzzo, WL 2022, 'Does rapid sequence divergence preclude RNA structure conservation in vertebrates?', Nucleic Acids Research, vol. 50, no. 5, pp. 2452-2463. https://doi.org/10.1093/nar/gkac067

APA

Seemann, S. E., Mirza, A. H., Bang-Berthelsen, C. H., Garde, C., Christensen-Dalsgaard, M., Workman, C. T., Pociot, F., Tommerup, N., Gorodkin, J., & Ruzzo, W. L. (2022). Does rapid sequence divergence preclude RNA structure conservation in vertebrates? Nucleic Acids Research, 50(5), 2452-2463. https://doi.org/10.1093/nar/gkac067

Vancouver

Seemann SE, Mirza AH, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Workman CT et al. Does rapid sequence divergence preclude RNA structure conservation in vertebrates? Nucleic Acids Research. 2022;50(5):2452-2463. https://doi.org/10.1093/nar/gkac067

Author

Seemann, Stefan E. ; Mirza, Aashiq H. ; Bang-Berthelsen, Claus H. ; Garde, Christian ; Christensen-Dalsgaard, Mikkel ; Workman, Christopher T. ; Pociot, Flemming ; Tommerup, Niels ; Gorodkin, Jan ; Ruzzo, Walter L. / Does rapid sequence divergence preclude RNA structure conservation in vertebrates?. In: Nucleic Acids Research. 2022 ; Vol. 50, No. 5. pp. 2452-2463.

Bibtex

@article{47f4491d732f487091d46bfe4b4ae0ac,
title = "Does rapid sequence divergence preclude RNA structure conservation in vertebrates?",
abstract = "Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA's structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can change through evolution while conserving its structure. Specifically, we consider predicted and known structures in vertebrate genomes. After careful control of false discovery rates, we obtain 13 de novo structures (and three known Rfam structures) that we predict to have rapidly evolving sequences-defined as structures where the primary sequences of human and mouse have diverged at least twice as fast (1.5 times for Rfam) as nearby neutrally evolving sequences. Two of the three known structures function in translation inhibition related to infection and immune response. We conclude that rapid sequence divergence does not preclude RNA structure conservation in vertebrates, although these events are relatively rare. ",
author = "Seemann, {Stefan E.} and Mirza, {Aashiq H.} and Bang-Berthelsen, {Claus H.} and Christian Garde and Mikkel Christensen-Dalsgaard and Workman, {Christopher T.} and Flemming Pociot and Niels Tommerup and Jan Gorodkin and Ruzzo, {Walter L.}",
note = "Publisher Copyright: {\textcopyright} 2022 The Author(s) 2022.",
year = "2022",
doi = "10.1093/nar/gkac067",
language = "English",
volume = "50",
pages = "2452--2463",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "5",

}

RIS

TY - JOUR

T1 - Does rapid sequence divergence preclude RNA structure conservation in vertebrates?

AU - Seemann, Stefan E.

AU - Mirza, Aashiq H.

AU - Bang-Berthelsen, Claus H.

AU - Garde, Christian

AU - Christensen-Dalsgaard, Mikkel

AU - Workman, Christopher T.

AU - Pociot, Flemming

AU - Tommerup, Niels

AU - Gorodkin, Jan

AU - Ruzzo, Walter L.

N1 - Publisher Copyright: © 2022 The Author(s) 2022.

PY - 2022

Y1 - 2022

N2 - Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA's structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can change through evolution while conserving its structure. Specifically, we consider predicted and known structures in vertebrate genomes. After careful control of false discovery rates, we obtain 13 de novo structures (and three known Rfam structures) that we predict to have rapidly evolving sequences-defined as structures where the primary sequences of human and mouse have diverged at least twice as fast (1.5 times for Rfam) as nearby neutrally evolving sequences. Two of the three known structures function in translation inhibition related to infection and immune response. We conclude that rapid sequence divergence does not preclude RNA structure conservation in vertebrates, although these events are relatively rare.

AB - Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA's structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can change through evolution while conserving its structure. Specifically, we consider predicted and known structures in vertebrate genomes. After careful control of false discovery rates, we obtain 13 de novo structures (and three known Rfam structures) that we predict to have rapidly evolving sequences-defined as structures where the primary sequences of human and mouse have diverged at least twice as fast (1.5 times for Rfam) as nearby neutrally evolving sequences. Two of the three known structures function in translation inhibition related to infection and immune response. We conclude that rapid sequence divergence does not preclude RNA structure conservation in vertebrates, although these events are relatively rare.

U2 - 10.1093/nar/gkac067

DO - 10.1093/nar/gkac067

M3 - Journal article

C2 - 35188540

AN - SCOPUS:85127614481

VL - 50

SP - 2452

EP - 2463

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 5

ER -

ID: 305713903