PXD035892

PXD035892 is an original dataset announced via ProteomeXchange.

Title	The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site usage in Arabidopsis
Description	Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of the plant BAF-like complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of expressed genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5´-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcriptional start site (TSS) usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and upstream TSS usage suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and alternative TSS usage.
HostingRepository	PRIDE
AnnounceDate	2022-09-20
AnnouncementXML	Submission_2022-09-19_19:06:04.793.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yasaman Jami-Alahmadi
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-08 10:18:05	ID requested
⏵ 1	2022-09-19 19:06:05	announced

Dataset with its publication pending

submitter keyword: Arabidopsis, SWI/SNF complex, proteomics

Javier Gallego Bartolom
contact affiliation	Ramón y Cajal Fellow IBMCP (UPV/CSIC) Valencia, Spain
contact email	jagalbar@gmail.com
lab head
Yasaman Jami-Alahmadi
contact affiliation	UCLA
contact email	yjami@ucla.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD035892
     1. Label: PRIDE project
     2. Name: The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site usage in Arabidopsis