Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content
<p>Abstract</p> <p>Background</p> <p>Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10–11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. Ho...
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| Format: | Article |
| Language: | English |
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BMC
2012-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/188 |
| _version_ | 1818752857692700672 |
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| author | Abel Jacob Mrázek Jan |
| author_facet | Abel Jacob Mrázek Jan |
| author_sort | Abel Jacob |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10–11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in many prokaryotic genomes is not clear.</p> <p>Results</p> <p>We developed measures of intensity and persistency of DNA curvature-related sequence periodicity and applied them to prokaryotic chromosomes and phages. The results indicate that strong periodic signals present in chromosomes are generally absent in phage genomes. Moreover, chromosomes containing prophages are less likely to possess a persistent periodic signal than chromosomes with no prophages.</p> <p>Conclusions</p> <p>Absence of DNA curvature-related sequence periodicity in phages could arise from constraints associated with DNA packaging in the viral capsid. Lack of prophages in chromosomes with persistent periodic signal suggests that the sequence periodicity and concomitant DNA curvature could play a role in protecting the chromosomes from integration of phage DNA.</p> |
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| format | Article |
| id | doaj.art-bb1ec73cca994f77b9b6810490b1b170 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T04:58:08Z |
| publishDate | 2012-05-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-bb1ec73cca994f77b9b6810490b1b1702022-12-21T21:20:13ZengBMCBMC Genomics1471-21642012-05-0113118810.1186/1471-2164-13-188Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage contentAbel JacobMrázek Jan<p>Abstract</p> <p>Background</p> <p>Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10–11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in many prokaryotic genomes is not clear.</p> <p>Results</p> <p>We developed measures of intensity and persistency of DNA curvature-related sequence periodicity and applied them to prokaryotic chromosomes and phages. The results indicate that strong periodic signals present in chromosomes are generally absent in phage genomes. Moreover, chromosomes containing prophages are less likely to possess a persistent periodic signal than chromosomes with no prophages.</p> <p>Conclusions</p> <p>Absence of DNA curvature-related sequence periodicity in phages could arise from constraints associated with DNA packaging in the viral capsid. Lack of prophages in chromosomes with persistent periodic signal suggests that the sequence periodicity and concomitant DNA curvature could play a role in protecting the chromosomes from integration of phage DNA.</p>http://www.biomedcentral.com/1471-2164/13/188Prokaryotic genomeDNA bendingNucleoid structureProphage integrationVirusDNA packaging |
| spellingShingle | Abel Jacob Mrázek Jan Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content BMC Genomics Prokaryotic genome DNA bending Nucleoid structure Prophage integration Virus DNA packaging |
| title | Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content |
| title_full | Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content |
| title_fullStr | Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content |
| title_full_unstemmed | Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content |
| title_short | Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content |
| title_sort | differences in dna curvature related sequence periodicity between prokaryotic chromosomes and phages and relationship to chromosomal prophage content |
| topic | Prokaryotic genome DNA bending Nucleoid structure Prophage integration Virus DNA packaging |
| url | http://www.biomedcentral.com/1471-2164/13/188 |
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