 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 30, 2013 |
| Title |
Xist exploits three-dimensional chromosome architecture to spread across the X-chromosome |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. Here we investigate the localization mechanisms of Xist during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maintenance of XCI, Xist binds broadly across the X-chromosome. During initiation of XCI, Xist initially transfers to distal regions across the X-chromosome that are not defined by specific sequences. Instead, Xist identifies these regions by exploiting the three-dimensional conformation of the X-chromosome. Xist initially accumulates on the periphery of actively transcribed regions and requires its silencing domain to spread across active regions. This suggests a model where Xist coats the entire X-chromosome by searching in three dimensions, modifying chromosome structure, and spreading to newly accessible locations.
|
| |
|
| Overall design |
We examined the genomic localization of the Xist lncRNA using RNA Antisense Purification (RAP) in multiple cell contexts: 1) differentiated female cells (MLFs); 2) a time-course of Xist localization in male embryonic stem (ES) cells where the endogenous Xist promoter is replaced by a tet-inducible one (pSM33); 3) a time-course of Xist localization in differentiating female ES cells (F1 2-1); and 4) wild-type (delXF6) and A-repeat deletion (delSXC9) Xist transgenes incorporated into the Hprt locus under the control of a tet-inducible promoter.
|
| |
|
| Contributor(s) |
Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Lander ES, Plath K, Guttman M |
| Citation(s) |
23828888 |
| Submission date |
May 14, 2013 |
| Last update date |
May 07, 2020 |
| Contact name |
Jesse Engreitz |
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (37)
|
|
| Relations |
| BioProject |
PRJNA203042 |
| SRA |
SRP022711 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46918_RAW.tar |
78.2 Mb |
(http)(custom) |
TAR (of BIGWIG) |
| GSE46918_pSM33-0hr-Xist_vs_Input.W10000_O7500.bigWig |
10.3 Mb |
(ftp)(http) |
BIGWIG |
| GSE46918_pSM33-1hr-Xist_vs_Input.W10000_O7500.bigWig |
10.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE46918_pSM33-2hr-Xist_vs_Input.W10000_O7500.bigWig |
10.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE46918_pSM33-3hr-Xist_vs_Input.W10000_O7500.bigWig |
10.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE46918_pSM33-6hr-Xist_vs_Input.W10000_O7500.bigWig |
10.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...