|
| Status |
Public on Aug 10, 2020 |
| Title |
The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Compared to the initiation and elongation stages of transcription, the role of chromatin in transcription termination is poorly understood. Through a yeast genetic screen, we identified histone H3 and H4 substitutions that cause transcription to read through the terminator of a small noncoding gene. The substitutions map to the nucleosome DNA entry-exit site, a region that controls nucleosome stability and certain histone modifications. Genome-wide studies on the strongest mutants revealed evidence of transcription read-through of noncoding and coding genes and reduced nucleosome occupancy. Replacement of the native sequence downstream of a gene with a “superbinder” sequence that increases nucleosome occupancy in vivo increased termination efficiency and suppressed the effect of a DNA entry-exit site substitution at this locus. Our results highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome and suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase.
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| |
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| Overall design |
RNA-seq, 4tU-seq, ChIP-seq, and MNase seq on S. cerevisiae Histone H3 Mutants in biological duplicate
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| Contributor(s) |
Hildreth AE, Ellison MA, Francette AM, Seraly JM, Lotka LM, Arndt KM |
| Citation(s) |
32845241 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM052593 |
Transcription factor mutants of yeast |
UNIVERSITY OF PITTSBURGH AT PITTSBURGH |
KAREN M ARNDT |
| F31 GM129917 |
Understanding the recruitment of a key epigenetic regulator |
UNIVERSITY OF PITTSBURGH AT PITTSBURGH |
Mitchell Ellison |
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| |
| Submission date |
Mar 23, 2020 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Mitchell Alden Ellison |
| E-mail(s) |
mae92@pitt.edu
|
| Phone |
412-624-4268
|
| Organization name |
University of Pittsburgh
|
| Department |
Biological Sciences
|
| Lab |
Arndt
|
| Street address |
Langley Hall
|
| City |
Oakland |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA614509 |
| SRA |
SRP253757 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE147389_R52A_4tU-seq_CombinedReps.bw |
57.3 Mb |
(ftp)(http) |
BW |
| GSE147389_R52A_FLAG-Rpb3-ChIP-seq_CombinedReps.bw |
85.0 Mb |
(ftp)(http) |
BW |
| GSE147389_R52A_MNase-seq_CombinedReps.bw |
21.6 Mb |
(ftp)(http) |
BW |
| GSE147389_R52A_RNA-seq_CombinedReps.bw |
6.2 Mb |
(ftp)(http) |
BW |
| GSE147389_R52AvsGSE147389_WT_l2fc_FLAG-Rpb3-ChIP-seq_CombinedReps.bw |
89.5 Mb |
(ftp)(http) |
BW |
| GSE147389_R52AvsGSE147389_WT_l2fc_MNase-seq_CombinedReps.bw |
79.2 Mb |
(ftp)(http) |
BW |
| GSE147389_R52AvsGSE147389_WT_l2fc_RNA-seq_CombinedReps.bw |
8.1 Mb |
(ftp)(http) |
BW |
| GSE147389_R52vsGSE147389_WT_l2fc_4tU-seq_CombinedReps.bw |
74.2 Mb |
(ftp)(http) |
BW |
| GSE147389_T45A_4tU-seq_CombinedReps.bw |
59.2 Mb |
(ftp)(http) |
BW |
| GSE147389_T45A_RNA-seq_CombinedReps.bw |
5.8 Mb |
(ftp)(http) |
BW |
| GSE147389_T45AvsGSE147389_WT_l2fc_RNA-seq_CombinedReps.bw |
8.0 Mb |
(ftp)(http) |
BW |
| GSE147389_T45vsGSE147389_WT_l2fc_4tU-seq_CombinedReps.bw |
74.2 Mb |
(ftp)(http) |
BW |
| GSE147389_WT_4tU-seq_CombinedReps.bw |
56.4 Mb |
(ftp)(http) |
BW |
| GSE147389_WT_FLAG-Rpb3-ChIP-seq_CombinedReps.bw |
84.6 Mb |
(ftp)(http) |
BW |
| GSE147389_WT_MNase-seq_CombinedReps.bw |
22.2 Mb |
(ftp)(http) |
BW |
| GSE147389_WT_RNA-seq_CombinedReps.bw |
5.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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