|
| Status |
Public on Aug 04, 2014 |
| Title |
Genome-wide maps of NME2 in A549 lung adenocarcinoma cells. |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
It is widely believed that reorganization of nucleosomes result in availability of transcription factor (TF) binding sites for eukaryotic gene regulation. Recent findings also show TFs induced during physiological perturbations can alter nucleosome occupancy to facilitate DNA binding. Although, these suggest a close relationship between TF binding and nucleosomes, the nature of this interaction, or to what extent it influences transcription is not clear. Moreover, since physiological perturbations induced multiple TFs, relatively direct effect of any TF on nucleosome occupancy remains poorly addressed. With these in mind, we used a single TF to induce physiological changes and following characterization of the two states (before and after induction of the TF) we determined: (a) genome wide binding sites of the TF, (b) promoter nucleosome occupancy and (c) transcriptome profiles, independently in both conditions. We find only ~20% of TF binding results from nucleosome repositioning - interestingly, almost all corresponding genes were transcriptionally altered. Whereas, when TF-occupancy was independent of nucleosome repositioning only a small fraction of corresponding genes were expressed/repressed. These observations suggest a model where TF occupancy leads to transcriptional change only when coupled with nucleosome repositioning in close proximity. This, to our knowledge, for the first time also helps explain why genome wide TF occupancy (e.g., from ChIP-sequencing) typically overlaps with only a small fraction of genes that change expression.
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| |
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| Overall design |
The nature of interaction between TF binding and nucleosomes and what extent it influences transcription
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| |
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| Contributor(s) |
Yadav VK, Thakur RK, Singh A, Baral A, Kumar A, Chowdhury S |
| Citation(s) |
25081206 |
| |
| Submission date |
Aug 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Vinod Kumar Yadav |
| E-mail(s) |
[email protected]
|
| Organization name |
IGIB
|
| Department |
Bioinformatics
|
| Street address |
Mall Road
|
| City |
Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110009 |
| Country |
India |
| |
|
| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
|
| Samples (6)
|
| GSM991046 |
NME2 Chip-seq Replicate 1(after NME2 induced A549) |
| GSM991047 |
NME2 Chip-seq Replicate 2(after NME2 induced A549) |
| GSM991048 |
NME2 Chip-seq Replicate 1(before NME2 induced A549) |
| GSM991049 |
NME2 Chip-seq Replicate 2(before NME2 induced A549) |
| GSM991050 |
IgG (after NME2 induced A549) |
| GSM991051 |
IgG (before NME2 induced A549) |
|
| This SubSeries is part of SuperSeries: |
| GSE40433 |
A549 cells before/after NME2 induction |
|
| Relations |
| BioProject |
PRJNA173992 |
| SRA |
SRP015251 |
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