Selection upon genome architecture: conservation of functional neighborhoods with changing genes.
An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multi...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC2951340?pdf=render |
| _version_ | 1818034866962300928 |
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| author | Fátima Al-Shahrour Pablo Minguez Tomás Marqués-Bonet Elodie Gazave Arcadi Navarro Joaquín Dopazo |
| author_facet | Fátima Al-Shahrour Pablo Minguez Tomás Marqués-Bonet Elodie Gazave Arcadi Navarro Joaquín Dopazo |
| author_sort | Fátima Al-Shahrour |
| collection | DOAJ |
| description | An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multispecies cartography of genome regions enriched in genes with related functions and study the evolutionary implications of such clustering. Our results indicate that the chromosomes of higher eukaryotic genomes contain up to 12% of genes arranged in functional neighborhoods, with a high level of gene co-expression, which are consistently distributed in phylogenies. Unexpectedly, neighborhoods with homologous functions are formed by different (non-orthologous) genes in different species. Actually, instead of being conserved, functional neighborhoods present a higher degree of synteny breaks than the genome average. This scenario is compatible with the existence of selective pressures optimizing the coordinated transcription of blocks of functionally related genes. If these neighborhoods were broken by chromosomal rearrangements, selection would favor further rearrangements reconstructing other neighborhoods of similar function. The picture arising from this study is a dynamic genomic landscape with a high level of functional organization. |
| first_indexed | 2024-12-10T06:45:58Z |
| format | Article |
| id | doaj.art-10b5e9912acf4e4b8a5319a34c615f7b |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-10T06:45:58Z |
| publishDate | 2010-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-10b5e9912acf4e4b8a5319a34c615f7b2022-12-22T01:58:39ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582010-01-01610e100095310.1371/journal.pcbi.1000953Selection upon genome architecture: conservation of functional neighborhoods with changing genes.Fátima Al-ShahrourPablo MinguezTomás Marqués-BonetElodie GazaveArcadi NavarroJoaquín DopazoAn increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multispecies cartography of genome regions enriched in genes with related functions and study the evolutionary implications of such clustering. Our results indicate that the chromosomes of higher eukaryotic genomes contain up to 12% of genes arranged in functional neighborhoods, with a high level of gene co-expression, which are consistently distributed in phylogenies. Unexpectedly, neighborhoods with homologous functions are formed by different (non-orthologous) genes in different species. Actually, instead of being conserved, functional neighborhoods present a higher degree of synteny breaks than the genome average. This scenario is compatible with the existence of selective pressures optimizing the coordinated transcription of blocks of functionally related genes. If these neighborhoods were broken by chromosomal rearrangements, selection would favor further rearrangements reconstructing other neighborhoods of similar function. The picture arising from this study is a dynamic genomic landscape with a high level of functional organization.http://europepmc.org/articles/PMC2951340?pdf=render |
| spellingShingle | Fátima Al-Shahrour Pablo Minguez Tomás Marqués-Bonet Elodie Gazave Arcadi Navarro Joaquín Dopazo Selection upon genome architecture: conservation of functional neighborhoods with changing genes. PLoS Computational Biology |
| title | Selection upon genome architecture: conservation of functional neighborhoods with changing genes. |
| title_full | Selection upon genome architecture: conservation of functional neighborhoods with changing genes. |
| title_fullStr | Selection upon genome architecture: conservation of functional neighborhoods with changing genes. |
| title_full_unstemmed | Selection upon genome architecture: conservation of functional neighborhoods with changing genes. |
| title_short | Selection upon genome architecture: conservation of functional neighborhoods with changing genes. |
| title_sort | selection upon genome architecture conservation of functional neighborhoods with changing genes |
| url | http://europepmc.org/articles/PMC2951340?pdf=render |
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