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| Status |
Public on Nov 28, 2012 |
| Title |
Decoupling epigenetic and genetic effects through systematic analysis of gene position |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Classic ‘position effect’ experiments repositioned genes to the telomere to demonstrate that the epigenetic landscape can dramatically alter gene expression. Here we show that systematic gene knockout collections provide an exceptional resource for interrogating position effects, not only at the telomere but at every single genetic locus. Because deleted genes are replaced by the same reporter gene, interrogation of this reporter provides a sensitive probe into many different chromatin environments while controlling for genetic context. Using this approach we find that, whereas replacement of yeast genes with the kanMX marker does not perturb the chromatin landscape, differences due to gene position account for more than 35% of marker gene activity. We observe chromatin influences different from those reported previously, including an antagonistic interaction between histone H3 lysine 36 trimethylation (H3K36me3) and the Rap1 transcriptional activation site in kanMX that is mediated through a Set2-Rpd3-dependent pathway. This interaction explains why some yeast genes have been resistant to deletion and allows successful generation of these deletion strains using a modified transformation procedure. These findings demonstrate that chromatin regulation is not governed by a uniform ‘histone code’, but by specific interactions between chromatin and genetic factors.
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| Overall design |
Data included are RNA-Seq data for 4 heterzygous diploid yeast strains and diploid wild-type. Therea re three replicates for each heterzygous strain, and six replicates for wild-type.
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| Contributor(s) |
Menzies C, Fan Z |
| Citation(s) |
23291096 |
| Submission date |
Nov 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Menzies Chen |
| E-mail(s) |
mec001@ucsd.edu
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| Organization name |
UCSD
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| Department |
Bioengineering
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| Lab |
Ideker Lab
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| Street address |
9500 Gilman Drive MC 0688
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (18)
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| GSM1045039 |
Wild-type, Replicate 4 |
| GSM1045040 |
Wild-type, Replicate 5 |
| GSM1045041 |
Wild-type, Replicate 6 |
| GSM1045042 |
yal067c heterozygous diploid, Replicate 1 |
| GSM1045043 |
yal067c heterozygous diploid, Replicate 2 |
| GSM1045044 |
yal067c heterozygous diploid, Replicate 3 |
| GSM1045045 |
yal031c heterozygous diploid, Replicate 1 |
| GSM1045046 |
yal031c heterozygous diploid, Replicate 2 |
| GSM1045047 |
yal031c heterozygous diploid, Replicate 3 |
| GSM1045048 |
yal022c heterozygous diploid, Replicate 1 |
| GSM1045049 |
yal022c heterozygous diploid, Replicate 2 |
| GSM1045050 |
yal022c heterozygous diploid, Replicate 3 |
| GSM1045051 |
yal008w heterozygous diploid, Replicate 1 |
| GSM1045052 |
yal008w heterozygous diploid, Replicate 2 |
| GSM1045053 |
yal008w heterozygous diploid, Replicate 3 |
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| Relations |
| BioProject |
PRJNA182259 |
| SRA |
SRP017325 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42554_RNASeqCounts_last200_ORFs.tab.txt.gz |
173.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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