|
| Status |
Public on Jan 25, 2019 |
| Title |
Mitotic chromosome binding predicts transcription factor properties in interphase [ATAC-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/ non-specific DNA binding affinity. How these properties affect the ability of TFs to occupy their specific binding sites in the genome and modify the epigenetic landscape is unclear. Here we combined live cell quantitative measurements of mitotic chromosome binding (MCB) of 502 TFs, measurements of TF mobility by fluorescence recovery after photobleaching, single molecule imaging of DNA binding in live cells, and genome-wide mapping of TF binding and chromatin accessibility. MCB scaled with interphase properties such as association with DNA-rich compartments, mobility, as well as large differences in genome-wide specific site occupancy that correlated with TF impact on chromatin accessibility. As MCB is largely mediated by electrostatic, non-specific TF-DNA interactions, our data suggests that non-specific DNA binding of TFs enhances their search for specific sites and thereby their impact on the accessible chromatin landscape.
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| |
|
| Overall design |
NIH-3T3 cells overexpressing different transcription factors (or no overexpression control) were subjected to ATAC-seq by Tn5 transposition
|
| |
|
| Contributor(s) |
Suter DM, Friman ET |
| Citation(s) |
30700703 |
| |
| Submission date |
Sep 11, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
David Michael Suter |
| Organization name |
École polytechnique fédérale de Lausanne
|
| Department |
Institute of Bioengineering
|
| Lab |
UPSUTER
|
| Street address |
EPFL SV-IN Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (31)
|
|
| This SubSeries is part of SuperSeries: |
| GSE119784 |
Mitotic chromosome binding predicts transcription factor properties in interphase |
|
| Relations |
| BioProject |
PRJNA490288 |
| SRA |
SRP161469 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119781_ATAC_BHLHB8.bw |
139.0 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_BHLHB8_log2_vs_control.bw |
234.1 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_BRACHYURY.bw |
143.2 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_BRACHYURY_log2_vs_control.bw |
234.4 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_CDX2.bw |
157.8 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_CDX2_log2_vs_control.bw |
242.0 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_DLX6.bw |
131.3 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_DLX6_log2_vs_control.bw |
229.4 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_DUXBL.bw |
158.3 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_DUXBL_log2_vs_control.bw |
241.2 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_FOXA1.bw |
131.3 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_FOXA1_log2_vs_control.bw |
229.7 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_HLF.bw |
133.0 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_HLF_log2_vs_control.bw |
230.1 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_NANOG.bw |
121.4 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_NANOG_log2_vs_control.bw |
225.1 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_POU5F1.bw |
135.0 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_POU5F1_log2_vs_control.bw |
231.0 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_RHOX11.bw |
136.0 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_RHOX11_log2_vs_control.bw |
231.4 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_SIX6.bw |
139.9 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_SIX6_log2_vs_control.bw |
234.4 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_SOX15.bw |
123.1 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_SOX15_log2_vs_control.bw |
225.8 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_SOX2.bw |
139.7 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_SOX2_log2_vs_control.bw |
232.6 Mb |
(ftp)(http) |
BW |
| GSE119781_ATAC_rtTA3G.bw |
176.4 Mb |
(ftp)(http) |
BW |
| GSE119781_RAW.tar |
183.0 Mb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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