PXD030928

PXD030928 is an original dataset announced via ProteomeXchange.

Title	BRAHMA-containing chromatin remodelling complex prevailing in Arabidopsis vegetative organs is a homolog of mammalian non-canonical SWI/SNF complexes and requires BRD subunits for assembly and stability
Description	The SWI/SNF family of chromatin remodeling complexes is evolutionarily conserved and present in yeast, animals and plants. While the biological functions of plant SWI/SNF complexes have been studied in detail, their composition is still elusive. To clarify this picture we used protein extracts from Arabidopsis plants in vegetative phase of growth to perform a series of immunoprecipitation followed by mass spectrometry experiments, using GFP-tagged BRM ATPase as a bait. The analysis of MS data showed that the dominant form of SWI/SNF complex present in these extracts has a specific subunit composition including ARP4 and 7, SWI3C, SWP73B and BRIP2, as well as three bromodomain containing subunits, BRD1, 2 and 13. This subunit composition and the lack of the core SWI/SNF subunit BSH (SNF5/INI1) both strongly resemble the characteristics of the specific subclass of mammalian SWI/SNF complexes referred to as non-canonical BAFs, indicating that homologues of these complexes also exist in plants. We next found that depletion of the all three BRDs severely affected the assembly of this form of BRM-associated SWI/SNF complex. However, while BRD1 and BRD2 were found sufficient to allow complex formation, BRD13 was only required under BRD1/2 deficiency. The analyses of IP/MS results using BRM-GFP in different brd mutant backgrounds as well as BRD1-GFP indicate that SWI/SNF assemblies containing only one BRD isoform, BRD1 or BRD2, do exist. Furthermore, our data indicate that BRD1/2 may be necessary for the incorporation of BRIP2 subunit into the complex. Together, our results shed new light on the structural and functional diversification of SWI/SNF complexes in Arabidopsis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:33.967.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD030928
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maciej Kotliński
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-13 01:45:58	ID requested
1	2023-04-03 12:15:48	announced
⏵ 2	2023-11-14 08:44:42	announced	2023-11-14: Updated project metadata.

Stachula P, Kapela K, Malecka E, Jaronczyk K, Patryn J, Siwirykow N, Bucholc M, Marczak M, Kotlinski M, Archacki R, BRM Complex in Arabidopsis Adopts ncBAF-like Composition and Requires BRD Subunits for Assembly and Stability. Int J Mol Sci, 24(4):(2023) [pubmed]

10.6019/PXD030928;

submitter keyword: Arabidopsis, BRM, BRAHMA,BRD, SWI/SNF

Rafał Archacki
contact affiliation	Laboratory of Systems Biology, University of Warsaw
contact email	rafa@ibb.waw.pl
lab head
Maciej Kotliński
contact affiliation	University of Warsaw
contact email	m.kotlinski@uw.edu.pl
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/2023/04/PXD030928

PRIDE project URI

• PRIDE
  1. PXD030928
     1. Label: PRIDE project
     2. Name: BRAHMA-containing chromatin remodelling complex prevailing in Arabidopsis vegetative organs is a homolog of mammalian non-canonical SWI/SNF complexes and requires BRD subunits for assembly and stability