PXD035225

PXD035225 is an original dataset announced via ProteomeXchange.

Title	Cohesin is involved in transcriptional repression of invasion-related genes
Description	The most virulent human malaria parasite, Plasmodium falciparum, has a complex life cycle between its human host and mosquito vector. Each stage is driven by a specific transcriptional program, but with a relatively high ratio of genes to specific transcription factors, it is unclear how genes are activated or silenced at specific times. The P. falciparum genome is relatively euchromatic compared to the mammalian genome, except for specific genes that are uniquely heterochromatinized via HP1. There seems to be an association between gene activity and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks lamins and CTCF – key metazoan genome-organizing proteins – it does have all core components of the cohesin complex. In other eukaryotes, cohesin is involved in sister chromatid cohesion, transcription, and genome organization. To investigate the role of cohesin in P. falciparum, we combined genome editing, mass-spectrometry, chromatin immunoprecipitation and sequencing (ChIP-seq), and RNA sequencing to functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown in early stages of the intraerythrocytic developmental cycle (IDC) resulted in significant up-regulation of a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq of SMC3 revealed that over the IDC, enrichment at the promoter regions of these genes inversely correlates with their expression. These data suggest that SMC3 binding helps to repress specific genes until their appropriate time of expression, revealing a new mode of gene repression in P. falciparum.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:05:41.976.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD035225
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	AMEYA SINHA
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-11 08:03:17	ID requested
1	2023-10-04 02:02:38	announced
⏵ 2	2023-11-14 09:05:48	announced	2023-11-14: Updated project metadata.

10.6019/PXD035225;

Rosa C, Singh P, Chen P, Sinha A, Cla, ë, s A, Preiser PR, Dedon PC, Baumgarten S, Scherf A, Bryant JM, Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite. EMBO Rep, 24(10):e57090(2023) [pubmed]

submitter keyword: Plasmodium, SMC3, Cohesin

Peter R. Preiser
contact affiliation	Vice President of Research, Nanyang Technological University
contact email	prpreiser@ntu.edu.sg
lab head
AMEYA SINHA
contact affiliation	NTU
contact email	ameya.sinha@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD035225
     1. Label: PRIDE project
     2. Name: Cohesin is involved in transcriptional repression of invasion-related genes