Open Access
Open access
Nature Communications, volume 12, issue 1, publication number 2300

Conserved long-range base pairings are associated with pre-mRNA processing of human genes

Kalmykova Svetlana 1
Denisov Stepan 1
Mironov Alexey 1
Pervouchine Dmitri 1
Publication typeJournal Article
Publication date2021-04-16
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor16.6
ISSN20411723
General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy
Abstract

The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3’-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.

Citations by journals

1
2
Nucleic Acids Research
Nucleic Acids Research, 2, 8%
Nucleic Acids Research
2 publications, 8%
Wiley interdisciplinary reviews. RNA
Wiley interdisciplinary reviews. RNA, 2, 8%
Wiley interdisciplinary reviews. RNA
2 publications, 8%
Genes
Genes, 1, 4%
Genes
1 publication, 4%
Computational and Structural Biotechnology Journal
Computational and Structural Biotechnology Journal, 1, 4%
Computational and Structural Biotechnology Journal
1 publication, 4%
Nature Reviews Genetics
Nature Reviews Genetics, 1, 4%
Nature Reviews Genetics
1 publication, 4%
Molecular genetics & genomic medicine
Molecular genetics & genomic medicine, 1, 4%
Molecular genetics & genomic medicine
1 publication, 4%
Bioscience Reports
Bioscience Reports, 1, 4%
Bioscience Reports
1 publication, 4%
Physical Chemistry Chemical Physics
Physical Chemistry Chemical Physics, 1, 4%
Physical Chemistry Chemical Physics
1 publication, 4%
Science advances
Science advances, 1, 4%
Science advances
1 publication, 4%
Scientific Reports
Scientific Reports, 1, 4%
Scientific Reports
1 publication, 4%
RNA
RNA, 1, 4%
RNA
1 publication, 4%
Journal of Bioinformatics and Computational Biology
Journal of Bioinformatics and Computational Biology, 1, 4%
Journal of Bioinformatics and Computational Biology
1 publication, 4%
PeerJ
PeerJ, 1, 4%
PeerJ
1 publication, 4%
Cell Chemical Biology
Cell Chemical Biology, 1, 4%
Cell Chemical Biology
1 publication, 4%
Acta Naturae, 1, 4%
Acta Naturae
1 publication, 4%
NAR Genomics and Bioinformatics
NAR Genomics and Bioinformatics, 1, 4%
NAR Genomics and Bioinformatics
1 publication, 4%
1
2

Citations by publishers

1
2
3
Springer Nature
Springer Nature, 3, 12%
Springer Nature
3 publications, 12%
Oxford University Press
Oxford University Press, 3, 12%
Oxford University Press
3 publications, 12%
Wiley
Wiley, 3, 12%
Wiley
3 publications, 12%
Elsevier
Elsevier, 2, 8%
Elsevier
2 publications, 8%
Multidisciplinary Digital Publishing Institute (MDPI)
Multidisciplinary Digital Publishing Institute (MDPI), 1, 4%
Multidisciplinary Digital Publishing Institute (MDPI)
1 publication, 4%
Royal Society of Chemistry (RSC)
Royal Society of Chemistry (RSC), 1, 4%
Royal Society of Chemistry (RSC)
1 publication, 4%
American Association for the Advancement of Science (AAAS)
American Association for the Advancement of Science (AAAS), 1, 4%
American Association for the Advancement of Science (AAAS)
1 publication, 4%
Cold Spring Harbor Laboratory
Cold Spring Harbor Laboratory, 1, 4%
Cold Spring Harbor Laboratory
1 publication, 4%
World Scientific
World Scientific, 1, 4%
World Scientific
1 publication, 4%
PeerJ
PeerJ, 1, 4%
PeerJ
1 publication, 4%
Acta Naturae Ltd, 1, 4%
Acta Naturae Ltd
1 publication, 4%
1
2
3
  • We do not take into account publications that without a DOI.
  • Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
  • Statistics recalculated weekly.
Metrics
Share
Cite this
GOST |
Cite this
GOST Copy
Kalmykova S. et al. Conserved long-range base pairings are associated with pre-mRNA processing of human genes // Nature Communications. 2021. Vol. 12. No. 1. 2300
GOST all authors (up to 50) Copy
Kalmykova S., Kalinina M. A., Denisov S., Mironov A., Skvortsov D., Guigo R., Pervouchine D. Conserved long-range base pairings are associated with pre-mRNA processing of human genes // Nature Communications. 2021. Vol. 12. No. 1. 2300
RIS |
Cite this
RIS Copy
TY - JOUR
DO - 10.1038/s41467-021-22549-7
UR - https://doi.org/10.1038%2Fs41467-021-22549-7
TI - Conserved long-range base pairings are associated with pre-mRNA processing of human genes
T2 - Nature Communications
AU - Kalmykova, Svetlana
AU - Kalinina, Marina A
AU - Denisov, Stepan
AU - Mironov, Alexey
AU - Skvortsov, Dmitry
AU - Guigo, Roderic
AU - Pervouchine, Dmitri
PY - 2021
DA - 2021/04/16 00:00:00
PB - Springer Nature
IS - 1
VL - 12
PMID - 33863890
SN - 2041-1723
ER -
BibTex
Cite this
BibTex Copy
@article{2021_Kalmykova
author = {Svetlana Kalmykova and Marina A Kalinina and Stepan Denisov and Alexey Mironov and Dmitry Skvortsov and Roderic Guigo and Dmitri Pervouchine},
title = {Conserved long-range base pairings are associated with pre-mRNA processing of human genes},
journal = {Nature Communications},
year = {2021},
volume = {12},
publisher = {Springer Nature},
month = {apr},
url = {https://doi.org/10.1038%2Fs41467-021-22549-7},
number = {1},
doi = {10.1038/s41467-021-22549-7}
}
Found error?