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Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms

Complementary sequences in cellular transcripts base-pair to form double-stranded RNA (dsRNA) structures. Because transposon-derived repeats often give rise to self-complementary sequences, dsRNA structures are prevalent in eukaryotic genomes, typically occurring in gene introns and untranslated reg...

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Autores principales: Reich, Daniel P., Bass, Brenda L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6239182/
https://www.ncbi.nlm.nih.gov/pubmed/30190375
http://dx.doi.org/10.1261/rna.067405.118
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author Reich, Daniel P.
Bass, Brenda L.
author_facet Reich, Daniel P.
Bass, Brenda L.
author_sort Reich, Daniel P.
collection PubMed
description Complementary sequences in cellular transcripts base-pair to form double-stranded RNA (dsRNA) structures. Because transposon-derived repeats often give rise to self-complementary sequences, dsRNA structures are prevalent in eukaryotic genomes, typically occurring in gene introns and untranslated regions (UTRs). However, the regulatory impact of double-stranded structures within genes is not fully understood. We used three independent methods to define loci in Caenorhabditis elegans predicted to form dsRNA and correlated these structures with patterns of gene expression, gene essentiality, and genome organization. As previously observed, dsRNA loci are enriched on distal arms of C. elegans autosomes, where genes typically show less conservation and lower overall expression. In contrast, we find that dsRNAs are associated with essential genes on autosome arms, and dsRNA-associated genes exhibit higher-than-expected expression and histone modification patterns associated with transcriptional elongation. Genes with significant repetitive sequence content are also highly expressed, and, thus, observed gene expression trends may relate either to dsRNA structures or to repeat content. Our results raise the possibility that as-yet-undescribed mechanisms promote expression of loci that produce dsRNAs, despite their well-characterized roles in gene silencing.
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spelling pubmed-62391822019-12-01 Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms Reich, Daniel P. Bass, Brenda L. RNA Bioinformatics Complementary sequences in cellular transcripts base-pair to form double-stranded RNA (dsRNA) structures. Because transposon-derived repeats often give rise to self-complementary sequences, dsRNA structures are prevalent in eukaryotic genomes, typically occurring in gene introns and untranslated regions (UTRs). However, the regulatory impact of double-stranded structures within genes is not fully understood. We used three independent methods to define loci in Caenorhabditis elegans predicted to form dsRNA and correlated these structures with patterns of gene expression, gene essentiality, and genome organization. As previously observed, dsRNA loci are enriched on distal arms of C. elegans autosomes, where genes typically show less conservation and lower overall expression. In contrast, we find that dsRNAs are associated with essential genes on autosome arms, and dsRNA-associated genes exhibit higher-than-expected expression and histone modification patterns associated with transcriptional elongation. Genes with significant repetitive sequence content are also highly expressed, and, thus, observed gene expression trends may relate either to dsRNA structures or to repeat content. Our results raise the possibility that as-yet-undescribed mechanisms promote expression of loci that produce dsRNAs, despite their well-characterized roles in gene silencing. Cold Spring Harbor Laboratory Press 2018-12 /pmc/articles/PMC6239182/ /pubmed/30190375 http://dx.doi.org/10.1261/rna.067405.118 Text en © 2018 Reich and Bass; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Bioinformatics
Reich, Daniel P.
Bass, Brenda L.
Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms
title Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms
title_full Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms
title_fullStr Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms
title_full_unstemmed Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms
title_short Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms
title_sort inverted repeat structures are associated with essential and highly expressed genes on c. elegans autosome distal arms
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6239182/
https://www.ncbi.nlm.nih.gov/pubmed/30190375
http://dx.doi.org/10.1261/rna.067405.118
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