Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae.
Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is t...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3248464?pdf=render |
| _version_ | 1819151519859081216 |
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| author | Loren Hansen Nak-Kyeong Kim Leonardo Mariño-Ramírez David Landsman |
| author_facet | Loren Hansen Nak-Kyeong Kim Leonardo Mariño-Ramírez David Landsman |
| author_sort | Loren Hansen |
| collection | DOAJ |
| description | Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; and GC content. Previous studies have associated H3K4me3, H3K36me3, and GC content with areas of mitotic recombination. H3K14ac and H3K79me3 are novel predictions and thus represent good candidates for further experimental study. We also show nucleosome occupancy maps produced using next generation sequencing exhibit a bias at DSB hot spots and this bias is strong enough to obscure biologically relevant information. A computational approach using feature selection can productively be used to identify promising biological associations. H3K14ac and H3K79me3 are novel predictions of chromatin marks associated with meiotic DSBs. Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented. |
| first_indexed | 2024-12-22T14:34:42Z |
| format | Article |
| id | doaj.art-fa5ff33fa52d46a18ca97902a0b2e640 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T14:34:42Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-fa5ff33fa52d46a18ca97902a0b2e6402022-12-21T18:22:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-01612e2971110.1371/journal.pone.0029711Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae.Loren HansenNak-Kyeong KimLeonardo Mariño-RamírezDavid LandsmanMeiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; and GC content. Previous studies have associated H3K4me3, H3K36me3, and GC content with areas of mitotic recombination. H3K14ac and H3K79me3 are novel predictions and thus represent good candidates for further experimental study. We also show nucleosome occupancy maps produced using next generation sequencing exhibit a bias at DSB hot spots and this bias is strong enough to obscure biologically relevant information. A computational approach using feature selection can productively be used to identify promising biological associations. H3K14ac and H3K79me3 are novel predictions of chromatin marks associated with meiotic DSBs. Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented.http://europepmc.org/articles/PMC3248464?pdf=render |
| spellingShingle | Loren Hansen Nak-Kyeong Kim Leonardo Mariño-Ramírez David Landsman Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. PLoS ONE |
| title | Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. |
| title_full | Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. |
| title_fullStr | Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. |
| title_full_unstemmed | Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. |
| title_short | Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. |
| title_sort | analysis of biological features associated with meiotic recombination hot and cold spots in saccharomyces cerevisiae |
| url | http://europepmc.org/articles/PMC3248464?pdf=render |
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