 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 08, 2022 |
| Title |
Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [Cut&Run] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Transcription factors (TFs) are classically attributed a modular construction, containing well-structured sequence specific DNA-binding domains (DBDs) paired with disordered activation domains (ADs) responsible for protein-protein interactions targeting cofactors or the core transcription initiation machinery. However, this simple division of labor model struggles to explain why TFs with identical DNA binding sequence specificity determined in vitro exhibit distinct binding profiles in vivo. The family of Hypoxia-Inducible Factors (HIFs) offer a stark example: aberrantly expressed in several cancer types, HIF-1α and HIF-2α subunit isoforms recognize the same DNA motif in vitro – the hypoxia response element (HRE) – but only share a subset of their target genes in vivo, while eliciting contrasting effects on cancer development and progression under certain circumstances. To probe the mechanisms mediating isoform-specific gene regulation, we used live cell single particle tracking (SPT) to investigate HIF nuclear dynamics and how they change upon genetic perturbation or drug treatment. We found that HIF-α subunits and their dimerization partner HIF-1β exhibit distinct diffusion and binding characteristics that are exquisitely sensitive to concentration and subunit stoichiometry. Using domain-swap variants, mutations, and a HIF-2α specific inhibitor, we found that although the DBD and dimerization domains are important, a major determinant of chromatin binding and diffusion behavior is dictated by the AD-containing intrinsically disordered regions (IDR). Using orthogonal genomic approaches such as Cut-and-Run and RNA-seq, we also confirmed IDR-dependent binding and activation for a specific subset of HIF-target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search process that may play a role in selective functional target site binding on chromatin.
|
| |
|
| Overall design |
Cut&Run: WT 786-O cells (anti-V5 antibody, IgG control), 786-O cells with either HIF-2a (anti-V5 antibody, IgG control) endogenously tagged with a V5-Halo moiety, and 786-O cells exogenously expressing HIF-1a (anti-V5 antibody, IgG control), HIF-2a (anti-V5 antibody, IgG control) or chimeric HIF-2a/1a (anti-V5 antibody, IgG control) or HIF-1a/2a (anti-V5 antibody, IgG control) transcription factors. 3 biological replicates for each condition.
|
| |
|
| Contributor(s) |
Cattoglio C, Chen Y, Dailey G, Zhu Q, Tjian R, Darzacq X |
| Citation(s) |
36322456 |
| |
| Submission date |
Jul 06, 2022 |
| Last update date |
Nov 18, 2022 |
| Contact name |
Robert Tjian |
| E-mail(s) |
jmlim@berkeley.edu
|
| Phone |
(510) 642-0884
|
| Organization name |
UC Berkeley
|
| Department |
MCB
|
| Lab |
Tjian Lab
|
| Street address |
University of California, Berkeley 450 Li Ka Shing #3370
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (36)
|
| GSM6297405 |
WT, IgG, rep1 [CUT&Run] |
| GSM6297406 |
WT, IgG, rep2 [CUT&Run] |
| GSM6297407 |
WT, IgG, rep3 [CUT&Run] |
| GSM6297408 |
HIF-2a KIN, anti-V5, rep1 [CUT&Run] |
| GSM6297409 |
HIF-2a KIN, anti-V5, rep2 [CUT&Run] |
| GSM6297410 |
HIF-2a KIN, anti-V5, rep3 [CUT&Run] |
| GSM6297411 |
HIF-2a KIN, IgG, rep1 [CUT&Run] |
| GSM6297412 |
HIF-2a KIN, IgG, rep2 [CUT&Run] |
| GSM6297413 |
HIF-2a KIN, IgG, rep3 [CUT&Run] |
| GSM6297414 |
HIF-2a, anti-V5, rep1 [CUT&Run] |
| GSM6297415 |
HIF-2a, anti-V5, rep2 [CUT&Run] |
| GSM6297416 |
HIF-2a, anti-V5, rep3 [CUT&Run] |
| GSM6297417 |
HIF-2a, IgG, rep1 [CUT&Run] |
| GSM6297418 |
HIF-2a, IgG, rep2 [CUT&Run] |
| GSM6297419 |
HIF-2a, IgG, rep3 [CUT&Run] |
| GSM6297420 |
HIF-2a/1a, anti-V5, rep1 [CUT&Run] |
| GSM6297421 |
HIF-2a/1a, anti-V5, rep2 [CUT&Run] |
| GSM6297422 |
HIF-2a/1a, anti-V5, rep3 [CUT&Run] |
| GSM6297423 |
HIF-2a/1a, IgG, rep1 [CUT&Run] |
| GSM6297424 |
HIF-2a/1a, IgG, rep2 [CUT&Run] |
| GSM6297425 |
HIF-2a/1a, IgG, rep3 [CUT&Run] |
| GSM6297426 |
HIF-1a, anti-V5, rep1 [CUT&Run] |
| GSM6297427 |
HIF-1a, anti-V5, rep2 [CUT&Run] |
| GSM6297428 |
HIF-1a, anti-V5, rep3 [CUT&Run] |
| GSM6297429 |
HIF-1a, IgG, rep1 [CUT&Run] |
| GSM6297430 |
HIF-1a, IgG, rep2 [CUT&Run] |
| GSM6297431 |
HIF-1a, IgG, rep3 [CUT&Run] |
| GSM6297432 |
HIF-1a/2a, anti-V5, rep1 [CUT&Run] |
| GSM6297433 |
HIF-1a/2a, anti-V5, rep2 [CUT&Run] |
| GSM6297434 |
HIF-1a/2a, anti-V5, rep3 [CUT&Run] |
| GSM6297435 |
HIF-1a/2a, IgG, rep1 [CUT&Run] |
| GSM6297436 |
HIF-1a/2a, IgG, rep2 [CUT&Run] |
| GSM6297437 |
HIF-1a/2a, IgG, rep3 [CUT&Run] |
|
| This SubSeries is part of SuperSeries: |
| GSE207575 |
Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors |
|
| Relations |
| BioProject |
PRJNA856256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207573_RAW.tar |
3.1 Gb |
(http)(custom) |
TAR (of BW) |
| GSE207573_YC033_on_YC027_peaks_peaks.removedblacklist.narrowPeak.gz |
7.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC034_on_YC028_peaks_peaks.removedblacklist.narrowPeak.gz |
95.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC035_on_YC029_peaks_peaks.removedblacklist.narrowPeak.gz |
159.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC036_on_YC030_peaks_peaks.removedblacklist.narrowPeak.gz |
411.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC037_on_YC031_peaks_peaks.removedblacklist.narrowPeak.gz |
352.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC038_on_YC032_peaks_peaks.removedblacklist.narrowPeak.gz |
310.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC057_on_YC051_peaks_peaks.removedblacklist.narrowPeak.gz |
194.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC058_on_YC052_peaks_peaks.removedblacklist.narrowPeak.gz |
308.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC059_on_YC053_peaks_peaks.removedblacklist.narrowPeak.gz |
518.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC060_on_YC054_peaks_peaks.removedblacklist.narrowPeak.gz |
558.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC061_on_YC055_peaks_peaks.removedblacklist.narrowPeak.gz |
517.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC062_on_YC056_peaks_peaks.removedblacklist.narrowPeak.gz |
466.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC071_on_YC064_peaks_peaks.removedblacklist.narrowPeak.gz |
17.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC072_on_YC065_peaks_peaks.removedblacklist.narrowPeak.gz |
173.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC073_on_YC066_peaks_peaks.removedblacklist.narrowPeak.gz |
134.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC074_on_YC067_peaks_peaks.removedblacklist.narrowPeak.gz |
296.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC075_on_YC068_peaks_peaks.removedblacklist.narrowPeak.gz |
369.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE207573_YC076_on_YC069_peaks_peaks.removedblacklist.narrowPeak.gz |
274.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...