 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 10, 2024 |
| Title |
Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID) |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors, suggesting that regulation of RNA polymerase pausing can be a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly rewiring of heterochromatin. Our data suggest that fundamental regulatory steps of the transcription process and chromatin remodeling, rather than interaction with NL proteins, have a major role in the regulation of transcription in LADs.
|
| |
|
| Overall design |
pA-DamID experiment were performed on a clonal HAP1 cell line genetically modified to express dCAs9-KRAB domain and transduced with a lentiguide against ADAM22 (negative control in RNAseq as not expressed in HAP1). Lamina association were probed using anti-LaminB2 (LB2) (Abcam, ab8983)
pA-DamID experiment were performed on a HCT116 cells (TOP2A-mAID, from Vassilis Roukos) and HeLa cells. Lamina association were probed using anti-LaminB2 (LB2) (Abcam, ab8983)
|
| |
|
| Contributor(s) |
Manzo SG, Mazouzi A, Leemans C, van Schaik T, Neyazi N, van Ruiten MS, Rowland BD, Brummelkamp T, van Steensel B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Mar 18, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Stefano Giustino Manzo |
| E-mail(s) |
stefano.manzo@unimi.it
|
| Phone |
+393283622562
|
| Organization name |
University of Milan
|
| Department |
Biosciences
|
| Street address |
Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4
|
| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (14)
|
| GSM8153279 |
LB2 pA-DamID, clone SC9, parental, replicate 1, dam only |
| GSM8153280 |
LB2 pA-DamID, clone SC9, parental, replicate 1, dam-LB2 |
| GSM8153281 |
LB2 pA-DamID, clone SC9, parental, replicate 2, dam only |
| GSM8153282 |
LB2 pA-DamID, clone SC9, parental, replicate 2, dam-LB2 |
| GSM8378907 |
LB2 pA-DamID,HCT116, replicate 1, dam-LB2 |
| GSM8378908 |
LB2 pA-DamID,HCT116, replicate 1, dam-only |
| GSM8378909 |
LB2 pA-DamID,HCT116, replicate 2, dam-LB2 |
| GSM8378910 |
LB2 pA-DamID,HCT116, replicate 2, dam-only |
| GSM8378911 |
LB2 pA-DamID,HCT116, replicate 3, dam-LB2 |
| GSM8378912 |
LB2 pA-DamID,HCT116, replicate 3, dam-only |
| GSM8378913 |
LB2 pA-DamID,HeLa, replicate 1, dam only |
| GSM8378914 |
LB2 pA-DamID,HeLa, replicate 1, dam-LB2 |
| GSM8378915 |
LB2 pA-DamID,HeLa, replicate 2, dam only |
| GSM8378916 |
LB2 pA-DamID,HeLa, replicate 2, dam-LB2 |
|
| This SubSeries is part of SuperSeries: |
| GSE261955 |
Identification of Chromatin proteins involved in gene repression in lamina-associated domains |
|
| Relations |
| BioProject |
PRJNA1089230 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE261868_pA-DamID_187_144h_r1_Lmnb2-20kb.bw |
1.3 Mb |
(ftp)(http) |
BW |
| GSE261868_pA-DamID_187_144h_r2_Lmnb2-20kb.bw |
1.4 Mb |
(ftp)(http) |
BW |
| GSE261868_pADamID-HCT116_TOP2AAID_WT_r1_Lmnb2-20kb.bw |
1.4 Mb |
(ftp)(http) |
BW |
| GSE261868_pADamID-HCT116_TOP2AAID_WT_r2_Lmnb2-20kb.bw |
1.4 Mb |
(ftp)(http) |
BW |
| GSE261868_pADamID-HCT116_TOP2AAID_WT_r3_Lmnb2-20kb.bw |
1.4 Mb |
(ftp)(http) |
BW |
| GSE261868_pADamID-Hela_WT_r1_Lmnb2-20kb.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE261868_pADamID-Hela_WT_r2_Lmnb2-20kb.bw |
1.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...