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Evolution of conserved secondary structures and their function in transcriptional regulation networks

BACKGROUND: Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in human populations and their biological functio...

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Autores principales: Xie, Hai-Bing, Irwin, David M, Zhang, Ya-Ping
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2584662/
https://www.ncbi.nlm.nih.gov/pubmed/18976501
http://dx.doi.org/10.1186/1471-2164-9-520
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author Xie, Hai-Bing
Irwin, David M
Zhang, Ya-Ping
author_facet Xie, Hai-Bing
Irwin, David M
Zhang, Ya-Ping
author_sort Xie, Hai-Bing
collection PubMed
description BACKGROUND: Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in human populations and their biological functions have not been fully studied. RESULTS: We searched for polymorphisms within conserved secondary structures and identified a number of SNPs within these elements even though they are highly conserved among species. The density of SNPs in conserved secondary structures is about 65% of that of their flanking, non-conserved, sequences. Classification of sites as stems or as loops/bulges revealed that the density of SNPs in stems is about 62% of that found in loops/bulges. Analysis of derived allele frequency data indicates that sites in stems are under stronger evolutionary constraint than sites in loops/bulges. Intergenic conserved secondary structures tend to associate with transcription factor-encoding genes with genetic distance being the measure of regulator-gene associations. A substantial fraction of intergenic conserved secondary structures overlap characterized binding sites for multiple transcription factors. CONCLUSION: Strong purifying selection implies that secondary structures are probably important carriers of biological functions for conserved sequences. The overlap between intergenic conserved secondary structures and transcription factor binding sites further suggests that intergenic conserved secondary structures have essential roles in directing gene expression in transcriptional regulation networks.
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spelling pubmed-25846622008-11-19 Evolution of conserved secondary structures and their function in transcriptional regulation networks Xie, Hai-Bing Irwin, David M Zhang, Ya-Ping BMC Genomics Research Article BACKGROUND: Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in human populations and their biological functions have not been fully studied. RESULTS: We searched for polymorphisms within conserved secondary structures and identified a number of SNPs within these elements even though they are highly conserved among species. The density of SNPs in conserved secondary structures is about 65% of that of their flanking, non-conserved, sequences. Classification of sites as stems or as loops/bulges revealed that the density of SNPs in stems is about 62% of that found in loops/bulges. Analysis of derived allele frequency data indicates that sites in stems are under stronger evolutionary constraint than sites in loops/bulges. Intergenic conserved secondary structures tend to associate with transcription factor-encoding genes with genetic distance being the measure of regulator-gene associations. A substantial fraction of intergenic conserved secondary structures overlap characterized binding sites for multiple transcription factors. CONCLUSION: Strong purifying selection implies that secondary structures are probably important carriers of biological functions for conserved sequences. The overlap between intergenic conserved secondary structures and transcription factor binding sites further suggests that intergenic conserved secondary structures have essential roles in directing gene expression in transcriptional regulation networks. BioMed Central 2008-11-02 /pmc/articles/PMC2584662/ /pubmed/18976501 http://dx.doi.org/10.1186/1471-2164-9-520 Text en Copyright © 2008 Xie et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Xie, Hai-Bing
Irwin, David M
Zhang, Ya-Ping
Evolution of conserved secondary structures and their function in transcriptional regulation networks
title Evolution of conserved secondary structures and their function in transcriptional regulation networks
title_full Evolution of conserved secondary structures and their function in transcriptional regulation networks
title_fullStr Evolution of conserved secondary structures and their function in transcriptional regulation networks
title_full_unstemmed Evolution of conserved secondary structures and their function in transcriptional regulation networks
title_short Evolution of conserved secondary structures and their function in transcriptional regulation networks
title_sort evolution of conserved secondary structures and their function in transcriptional regulation networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2584662/
https://www.ncbi.nlm.nih.gov/pubmed/18976501
http://dx.doi.org/10.1186/1471-2164-9-520
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