|
| Status |
Public on Jul 04, 2020 |
| Title |
Time series data of chromatin occupancy and transcription under cadmium stress |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists in a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins---including histones, transcription factors (TFs), and polymerases---interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. While gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state is modified and how those modifications connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA binding factors.
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| Overall design |
Time course of cadmium treated yeast for T=0 min (prior to cadmium addition), 7.5 min, 15 min, 30 min, 60 min, and 120 min. 12 samples of MNase chromatin (2 technical replicates) and 6 samples of RNA
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| Contributor(s) |
Tran TQ, Tripuraneni V, MacAlpine HK, Mitra S, MacAlpine DM, Hartemink AJ |
| Citation(s) |
33893157, 34255854 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 GM127062 |
Chromatin-mediated mechanisms of genome integrity |
DUKE UNIVERSITY |
David M MacAlpine |
| R01 GM118551 |
Exploring the Role of Dynamic Chromatin Occupancy in Transcriptional Regulation |
DUKE UNIVERSITY |
Alexander J Hartemink |
|
| Submission date |
Jul 01, 2020 |
| Last update date |
Aug 24, 2021 |
| Contact name |
David M MacAlpine |
| Organization name |
Duke University Medical Center
|
| Department |
Department of Pharmacology and Cancer Biology
|
| Lab |
MacAlpine Laboratory
|
| Street address |
Duke University
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA643422 |
| SRA |
SRP269500 |
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