Evolution and genetic architecture of chromatin accessibility and function in yeast.
Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolutio...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-07-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC4081003?pdf=render |
| _version_ | 1811232849723916288 |
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| author | Caitlin F Connelly Jon Wakefield Joshua M Akey |
| author_facet | Caitlin F Connelly Jon Wakefield Joshua M Akey |
| author_sort | Caitlin F Connelly |
| collection | DOAJ |
| description | Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. |
| first_indexed | 2024-04-12T11:11:13Z |
| format | Article |
| id | doaj.art-52122d90a349445ea27e8e109e14da11 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-12T11:11:13Z |
| publishDate | 2014-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-52122d90a349445ea27e8e109e14da112022-12-22T03:35:37ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042014-07-01107e100442710.1371/journal.pgen.1004427Evolution and genetic architecture of chromatin accessibility and function in yeast.Caitlin F ConnellyJon WakefieldJoshua M AkeyChromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign.http://europepmc.org/articles/PMC4081003?pdf=render |
| spellingShingle | Caitlin F Connelly Jon Wakefield Joshua M Akey Evolution and genetic architecture of chromatin accessibility and function in yeast. PLoS Genetics |
| title | Evolution and genetic architecture of chromatin accessibility and function in yeast. |
| title_full | Evolution and genetic architecture of chromatin accessibility and function in yeast. |
| title_fullStr | Evolution and genetic architecture of chromatin accessibility and function in yeast. |
| title_full_unstemmed | Evolution and genetic architecture of chromatin accessibility and function in yeast. |
| title_short | Evolution and genetic architecture of chromatin accessibility and function in yeast. |
| title_sort | evolution and genetic architecture of chromatin accessibility and function in yeast |
| url | http://europepmc.org/articles/PMC4081003?pdf=render |
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