Where does mediator bind in vivo?
The Mediator complex associates with RNA polymerase (Pol) II, and it is recruited to enhancer regions by activator proteins under appropriate environmental conditions. However, the issue of Mediator association in yeast cells is controversial. Under optimal growth conditions (YPD medium), we were un...
Main Authors: | , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2009-01-01
|
Series: | PLoS ONE |
Online Access: | http://europepmc.org/articles/PMC2661142?pdf=render |
id |
doaj-dd84418720b84706ada5b6ef5b85fa21 |
---|---|
record_format |
Article |
spelling |
doaj-dd84418720b84706ada5b6ef5b85fa212020-11-25T01:41:55ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-0144e502910.1371/journal.pone.0005029Where does mediator bind in vivo?Xiaochun FanKevin StruhlThe Mediator complex associates with RNA polymerase (Pol) II, and it is recruited to enhancer regions by activator proteins under appropriate environmental conditions. However, the issue of Mediator association in yeast cells is controversial. Under optimal growth conditions (YPD medium), we were unable to detect Mediator at essentially any S. cerevisiae promoter region, including those supporting very high levels of transcription. In contrast, whole genome microarray experiments in synthetic complete (SC) medium reported that Mediator associates with many genes at both promoter and coding regions.As assayed by chromatin immunoprecipitation, we show that there are a small number of Mediator targets in SC medium that are not observed in YPD medium. However, most Mediator targets identified in the genome-wide analysis are false positives that arose for several interrelated reasons: the use of overly lenient cut-offs; artifactual differences in apparent IP efficiencies among different genomic regions in the untagged strain; low fold-enrichments making it difficult to distinguish true Mediator targets from false positives that occur in the absence of the tagged Mediator protein. Lastly, apparent Mediator association in highly active coding regions is due to a non-specific effect on accessibility due to the lack of nucleosomes, not to a specific association of Mediator.These results indicate that Mediator does not bind to numerous sites in the yeast genome, but rather selectively associates with a limited number of upstream promoter regions in an activator- and stress-specific manner.http://europepmc.org/articles/PMC2661142?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xiaochun Fan Kevin Struhl |
spellingShingle |
Xiaochun Fan Kevin Struhl Where does mediator bind in vivo? PLoS ONE |
author_facet |
Xiaochun Fan Kevin Struhl |
author_sort |
Xiaochun Fan |
title |
Where does mediator bind in vivo? |
title_short |
Where does mediator bind in vivo? |
title_full |
Where does mediator bind in vivo? |
title_fullStr |
Where does mediator bind in vivo? |
title_full_unstemmed |
Where does mediator bind in vivo? |
title_sort |
where does mediator bind in vivo? |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2009-01-01 |
description |
The Mediator complex associates with RNA polymerase (Pol) II, and it is recruited to enhancer regions by activator proteins under appropriate environmental conditions. However, the issue of Mediator association in yeast cells is controversial. Under optimal growth conditions (YPD medium), we were unable to detect Mediator at essentially any S. cerevisiae promoter region, including those supporting very high levels of transcription. In contrast, whole genome microarray experiments in synthetic complete (SC) medium reported that Mediator associates with many genes at both promoter and coding regions.As assayed by chromatin immunoprecipitation, we show that there are a small number of Mediator targets in SC medium that are not observed in YPD medium. However, most Mediator targets identified in the genome-wide analysis are false positives that arose for several interrelated reasons: the use of overly lenient cut-offs; artifactual differences in apparent IP efficiencies among different genomic regions in the untagged strain; low fold-enrichments making it difficult to distinguish true Mediator targets from false positives that occur in the absence of the tagged Mediator protein. Lastly, apparent Mediator association in highly active coding regions is due to a non-specific effect on accessibility due to the lack of nucleosomes, not to a specific association of Mediator.These results indicate that Mediator does not bind to numerous sites in the yeast genome, but rather selectively associates with a limited number of upstream promoter regions in an activator- and stress-specific manner. |
url |
http://europepmc.org/articles/PMC2661142?pdf=render |
work_keys_str_mv |
AT xiaochunfan wheredoesmediatorbindinvivo AT kevinstruhl wheredoesmediatorbindinvivo |
_version_ |
1725038878001201152 |