|
| Status |
Public on Mar 11, 2019 |
| Title |
Condensin II Counters Cohesin and RNA Polymerase II in 3D Chromatin Organization |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
CTCF is present at the anchors of thousands of loops likely formed via cohesin-mediated loop extrusion in mammalian cells. Interaction domains present in D. melanogaster chromosomes form via the segregation of active and inactive chromatin in the absence of CTCF looping, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, results in increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.
|
| |
|
| Overall design |
Hi-C after 3 hours Flv treatment
HiChIP for RNAPII or Rad21
Hi-C after knockdown of Slimb
ChIP-seq under normal conditions
ChIP-seq after knockdown of Rad21 or Cap-H2
ChIP-seq after 3 hours Flv treatment
|
| |
|
| Contributor(s) |
Rowley J, Lyu X, Rana V, Ando-Kuri M, Karns R, Bosco G, Corces VG |
| Citation(s) |
30865881 |
| |
| Submission date |
Aug 20, 2018 |
| Last update date |
May 10, 2019 |
| Contact name |
M Jordan Rowley |
| E-mail(s) |
jordan.rowley@unmc.edu, jordrow@gmail.com
|
| Phone |
7343580454
|
| Organization name |
Univ of Nebraska Medical Center
|
| Department |
GCBA
|
| Lab |
Rowley
|
| Street address |
601 S Saddle Creek Rd
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68106 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
|
| Samples (14)
|
|
| Relations |
| BioProject |
PRJNA486736 |
| SRA |
SRP158369 |
Less...
More...