|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on May 24, 2023 |
Title |
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct [ChIP-seq] |
Organism |
Homo sapiens |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
Summary |
Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma (NC). Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
|
|
|
Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HEK293 T-Rex Flp-In - based stable cell lines, expressing BRD4-NUT, BRD4-NUT(MIN) or BRD4-p300, in a doxycycline-inducible manner. ChIP-seq performed using anti-NUT antibody for BRD4-NUT and BRD4-NUT(MIN) - expressing cell lines. ChIP-seq performed using anti-histone H3K27 acetyl antibody for BRD4-NUT(MIN) and BRD4-p300 - expressing cell lines.
|
|
|
Contributor(s) |
Kosno M, Currie SL, Kumar A, Xing C, Rosen MK |
Citation(s) |
37488172 |
|
Submission date |
May 24, 2023 |
Last update date |
Aug 23, 2023 |
Contact name |
Michael K Rosen |
E-mail(s) |
michael.rosen@utsouthwestern.edu
|
Organization name |
UT Southwestern Medical Center
|
Department |
Biophysics
|
Lab |
Michael Rosen Laboratory
|
Street address |
6001 Forest Park Rd., ND8.124
|
City |
Dallas |
State/province |
TX |
ZIP/Postal code |
75235 |
Country |
USA |
|
|
Platforms (1) |
GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
Samples (14)
|
GSM7421832 |
HEK293 T-Rex Flp-In cells, BRD4-NUT, input |
GSM7421833 |
HEK293 T-Rex Flp-In cells, BRD4-NUT, NUT antibody, biol rep 1 |
GSM7421834 |
HEK293 T-Rex Flp-In cells, BRD4-NUT, NUT antibody, biol rep 2 |
GSM7421835 |
HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), input 1 |
GSM7421836 |
HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), input 2 |
GSM7421837 |
HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), NUT antibody, biol rep 1 |
GSM7421838 |
HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), NUT antibody, biol rep 2 |
GSM7421839 |
HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), H3K27Ac antibody, biol rep 1 |
GSM7421840 |
HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), H3K27Ac antibody, biol rep 2 |
GSM7421841 |
HEK293 T-Rex Flp-In cells, BRD4-p300, input |
GSM7421842 |
HEK293 T-Rex Flp-In cells, BRD4-p300, H3K27Ac antibody, biol rep 1 |
GSM7421843 |
HEK293 T-Rex Flp-In cells, BRD4-p300, H3K27Ac antibody, biol rep 2 |
GSM7421844 |
HEK293 T-Rex Flp-In cells, input |
GSM7421845 |
HEK293 T-Rex Flp-In cells, H3K27Ac antibody |
|
This SubSeries is part of SuperSeries: |
GSE233303 |
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct |
|
Relations |
BioProject |
PRJNA975834 |
Supplementary file |
Size |
Download |
File type/resource |
GSE233301_RAW.tar |
50.6 Mb |
(http)(custom) |
TAR (of BROADPEAK, GAPPEDPEAK, NARROWPEAK) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|