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Series GSE46918 Query DataSets for GSE46918
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)
GSM1141165 pSM33-0hr-Xist-R1
GSM1141166 pSM33-1hr-Xist-R1
GSM1141167 pSM33-2hr-Xist-R1
BioProject PRJNA203042
SRA SRP022711

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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
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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