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Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?
Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889656/ https://www.ncbi.nlm.nih.gov/pubmed/27172194 http://dx.doi.org/10.1534/g3.116.028274 |
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author | Khedkar, Supriya Seshasayee, Aswin Sai Narain |
author_facet | Khedkar, Supriya Seshasayee, Aswin Sai Narain |
author_sort | Khedkar, Supriya |
collection | PubMed |
description | Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences. |
format | Online Article Text |
id | pubmed-4889656 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-48896562016-06-02 Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? Khedkar, Supriya Seshasayee, Aswin Sai Narain G3 (Bethesda) Investigations Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences. Genetics Society of America 2016-03-30 /pmc/articles/PMC4889656/ /pubmed/27172194 http://dx.doi.org/10.1534/g3.116.028274 Text en Copyright © 2016 Khedkar and Seshasayee http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Khedkar, Supriya Seshasayee, Aswin Sai Narain Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? |
title | Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? |
title_full | Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? |
title_fullStr | Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? |
title_full_unstemmed | Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? |
title_short | Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? |
title_sort | comparative genomics of interreplichore translocations in bacteria: a measure of chromosome topology? |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889656/ https://www.ncbi.nlm.nih.gov/pubmed/27172194 http://dx.doi.org/10.1534/g3.116.028274 |
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