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Patterns and rates of intron divergence between humans and chimpanzees

BACKGROUND: Introns, which constitute the largest fraction of eukaryotic genes and which had been considered to be neutral sequences, are increasingly acknowledged as having important functions. Several studies have investigated levels of evolutionary constraint along introns and across classes of i...

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Autores principales: Gazave, Elodie, Marqués-Bonet, Tomàs, Fernando, Olga, Charlesworth, Brian, Navarro, Arcadi
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852421/
https://www.ncbi.nlm.nih.gov/pubmed/17309804
http://dx.doi.org/10.1186/gb-2007-8-2-r21
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author Gazave, Elodie
Marqués-Bonet, Tomàs
Fernando, Olga
Charlesworth, Brian
Navarro, Arcadi
author_facet Gazave, Elodie
Marqués-Bonet, Tomàs
Fernando, Olga
Charlesworth, Brian
Navarro, Arcadi
author_sort Gazave, Elodie
collection PubMed
description BACKGROUND: Introns, which constitute the largest fraction of eukaryotic genes and which had been considered to be neutral sequences, are increasingly acknowledged as having important functions. Several studies have investigated levels of evolutionary constraint along introns and across classes of introns of different length and location within genes. However, thus far these studies have yielded contradictory results. RESULTS: We present the first analysis of human-chimpanzee intron divergence, in which differences in the number of substitutions per intronic site (K(i)) can be interpreted as the footprint of different intensities and directions of the pressures of natural selection. Our main findings are as follows: there was a strong positive correlation between intron length and divergence; there was a strong negative correlation between intron length and GC content; and divergence rates vary along introns and depending on their ordinal position within genes (for instance, first introns are more GC rich, longer and more divergent, and divergence is lower at the 3' and 5' ends of all types of introns). CONCLUSION: We show that the higher divergence of first introns is related to their larger size. Also, the lower divergence of short introns suggests that they may harbor a relatively greater proportion of regulatory elements than long introns. Moreover, our results are consistent with the presence of functionally relevant sequences near the 5' and 3' ends of introns. Finally, our findings suggest that other parts of introns may also be under selective constraints.
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spelling pubmed-18524212007-04-18 Patterns and rates of intron divergence between humans and chimpanzees Gazave, Elodie Marqués-Bonet, Tomàs Fernando, Olga Charlesworth, Brian Navarro, Arcadi Genome Biol Research BACKGROUND: Introns, which constitute the largest fraction of eukaryotic genes and which had been considered to be neutral sequences, are increasingly acknowledged as having important functions. Several studies have investigated levels of evolutionary constraint along introns and across classes of introns of different length and location within genes. However, thus far these studies have yielded contradictory results. RESULTS: We present the first analysis of human-chimpanzee intron divergence, in which differences in the number of substitutions per intronic site (K(i)) can be interpreted as the footprint of different intensities and directions of the pressures of natural selection. Our main findings are as follows: there was a strong positive correlation between intron length and divergence; there was a strong negative correlation between intron length and GC content; and divergence rates vary along introns and depending on their ordinal position within genes (for instance, first introns are more GC rich, longer and more divergent, and divergence is lower at the 3' and 5' ends of all types of introns). CONCLUSION: We show that the higher divergence of first introns is related to their larger size. Also, the lower divergence of short introns suggests that they may harbor a relatively greater proportion of regulatory elements than long introns. Moreover, our results are consistent with the presence of functionally relevant sequences near the 5' and 3' ends of introns. Finally, our findings suggest that other parts of introns may also be under selective constraints. BioMed Central 2007 2007-02-19 /pmc/articles/PMC1852421/ /pubmed/17309804 http://dx.doi.org/10.1186/gb-2007-8-2-r21 Text en Copyright © 2007 Gazave 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
Gazave, Elodie
Marqués-Bonet, Tomàs
Fernando, Olga
Charlesworth, Brian
Navarro, Arcadi
Patterns and rates of intron divergence between humans and chimpanzees
title Patterns and rates of intron divergence between humans and chimpanzees
title_full Patterns and rates of intron divergence between humans and chimpanzees
title_fullStr Patterns and rates of intron divergence between humans and chimpanzees
title_full_unstemmed Patterns and rates of intron divergence between humans and chimpanzees
title_short Patterns and rates of intron divergence between humans and chimpanzees
title_sort patterns and rates of intron divergence between humans and chimpanzees
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852421/
https://www.ncbi.nlm.nih.gov/pubmed/17309804
http://dx.doi.org/10.1186/gb-2007-8-2-r21
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