PXD015699

PXD015699 is an original dataset announced via ProteomeXchange.

Title	SPEN is a molecular integrator that bridges Xist with transcriptional and epigenetic control of X-chromosome inactivation
Description	Xist represents a paradigm for long non-coding RNA function in epigenetic regulation, although how it mediates X-chromosome inactivation (XCI) remains largely unexplained. Multiple Xist-RNA binding proteins have recently been identified, including SPEN/SHARP, whose knockdown has been associated with deficient XCI at multiple loci. Here we demonstrate that SPEN is a key orchestrator of XCI in vivo and unravel its mechanism of action. We show that SPEN is essential for initiating gene silencing on the X chromosome in preimplantation mouse embryos and embryonic stem cells. On the other hand, SPEN is dispensable for maintenance of XCI in neural progenitor cells, although it significantly dampens expression of genes that escape from XCI. During initiation of XCI, we show by live-cell imaging and CUT&RUN approaches that SPEN is immediately recruited to the X chromosome upon Xist up-regulation, where it is targeted to enhancers and promoters of actively transcribed genes. SPEN rapidly disengages from chromatin once silencing is accomplished, implying a need for active transcription to tether it to chromatin. We define SPEN’s SPOC (SPEN paralog and ortholog C-terminal) domain as a major effector of SPEN’s gene silencing function, and show that artificial tethering of SPOC to Xist RNA is sufficient to mediate X-linked gene silencing. We identify SPOC’s protein partners which include NCOR/SMRT, the m6A RNA methylation machinery, the NuRD complex, RNA polymerase II and factors involved in regulation of transcription initiation and elongation. We propose that SPEN acts as a molecular integrator for initiation of XCI, bridging Xist RNA with the transcription machinery as well as nucleosome remodelers and histone deacetylases, at active enhancers and promoters.
HostingRepository	PRIDE
AnnounceDate	2021-04-19
AnnouncementXML	Submission_2021-04-19_04:39:14.719.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Valentin SABATET
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-04 02:03:22	ID requested
1	2021-04-19 02:46:42	announced
⏵ 2	2021-04-19 04:39:15	announced	2021-04-19: Updated project metadata.

Dossin F, Pinheiro I, Ż, ylicz JJ, Roensch J, Collombet S, Le Saux A, Chelmicki T, Attia M, Kapoor V, Zhan Y, Dingli F, Loew D, Mercher T, Dekker J, Heard E, SPEN integrates transcriptional and epigenetic control of X-inactivation. Nature, 578(7795):455-460(2020) [pubmed]

10.1038/S41586-020-1974-9;

submitter keyword: XCI, X-chromosome inactivation,Epigenetic, Xist, SPEN

Damarys Loew
contact affiliation	Head of the Curie Institute Mass Spectrometry Platform
contact email	damarys.loew@curie.fr
lab head
Valentin SABATET
contact affiliation	Curie Institute
contact email	valentin.sabatet@curie.fr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/04/PXD015699

PRIDE project URI

• PRIDE
  1. PXD015699
     1. Label: PRIDE project
     2. Name: SPEN is a molecular integrator that bridges Xist with transcriptional and epigenetic control of X-chromosome inactivation