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| Status |
Public on Sep 03, 2020 |
| Title |
An Xist-dependent protein assembly mediates Xist localization and gene silencing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Nuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation are not well understood. Studying how the lncRNA Xist establishes the inactive-X-chromosome (Xi)-compartment, we found that the Xist RNA-binding-proteins PTBP1, MATR3, TDP43, and CELF1 form a condensate to create an Xi-domain that can be sustained in the absence of Xist. The E-repeat-sequence of Xist serves a multivalent binding-platform for these proteins. Without the E-repeat, Xist initially coats the X-chromosome during XCI onset but subsequently disperses across the nucleus with loss of gene silencing. Recruitment of PTBP1, MATR3, TDP-43 or CELF1 to E-Xist rescues these phenotypes, and requires both self-association of MATR3 and TDP-43 and a heterotypic PTBP1-MATR3-interaction. Together, our data reveal that Xist sequesters itself within the Xi-territory and perpetuates gene silencing by seeding a protein-condensate. Our findings uncover an unanticipated mechanism for epigenetic memory and elucidate the interplay between RNA and RNA-binding-proteins in creating compartments for gene regulation.
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| Overall design |
We examined the localization of RNA binding proteins PTBP1, MATR3 and CELF1 on Xist RNA by CLIP-seq and the localization of PTBP1 on DNA by ChIP-seq in male ESCs in which the Xist promoter is replaced by a doxycycline inducible one. We also examined Xist occupancy over the X-chromosome using RAP (RNA-affinity purification) in cells expressing Xist cDNA transgenes (under dox control) engineered to include (or not) the Xist E-repeat region.
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| Contributor(s) |
Pandya-Jones A, Markaki Y, Serizay J, Chitiashvilli T, Mancia W, Damianov A, Chronis C, Papp B, Chen C, McKee R, Wang X, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K |
| Citation(s) |
32908311 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM115233 |
Mechanism of chromatin remodeling and gene silencing by the lncRNAs Xist and Tsix |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
Kathrin Plath |
| R01 MH109166 |
Elucidating an Xist-dependent program of sexually dimorphic alternative splicing in the mammalian brain |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
Kathrin Plath |
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| Submission date |
Sep 12, 2019 |
| Last update date |
Dec 03, 2020 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
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| Department |
Biological Chemistry
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| Lab |
BSRB 390B
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| Street address |
615 Charles E. Young Drive South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1737 |
| Country |
USA |
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| Platforms (2) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (8)
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| Relations |
| Reanalysis of |
GSM1141184 |
| BioProject |
PRJNA565139 |
| SRA |
SRP221438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE137305_RAW.tar |
69.7 Mb |
(http)(custom) |
TAR (of BW) |
| GSE137305_SRR850637_cutadapt_bwa_PE_mm10_Q30_rm_dup.bw |
19.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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