PXD007677

PXD007677 is an original dataset announced via ProteomeXchange.

Title	DNA Affinity chromatografy on Mycoplasma pneumoniae extracts III
Description	Determining the gene regulatory network of an organism is fundamental to achieving a global understanding of cell behavior. In general, studies of transcription regulation are limited to the annotated transcription factors, not considering other non-canonical regulators. Here we describe the first systematic analysis of the DNA-interactome of a bacterium with a minimal proteome (Mycoplasma pneumoniae). We first determined by DNA affinity chromatography and intact chromatin isolation all potential DNA binding proteins. We then mapped the DNA binding of these factors by ChIP-seq, as well as their functionality by gain- and loss-of-function experiments, by transcriptomics and proteomics. This identified new DNA binding proteins and novel regulators with moonlighting properties like proteases and metabolic enzymes and allowed to reconstruct the gene regulatory network.
HostingRepository	PRIDE
AnnounceDate	2019-11-12
AnnouncementXML	Submission_2019-11-12_09:40:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eva Yus
SpeciesList	scientific name: Mycoplasma pneumoniae (strain ATCC 29342 / M129); NCBI TaxID: 272634;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-06 07:26:34	ID requested
⏵ 1	2019-11-12 09:40:21	announced

Yus E, Llor, é, ns-Rico V, Mart, í, nez S, Gallo C, Eilers H, Bl, ö, tz C, St, ü, lke J, Lluch-Senar M, Serrano L, Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors. Cell Syst, 9(2):143-158.e13(2019) [pubmed]

curator keyword: Biological

submitter keyword: system biology, microbiology, minimal cell, proteome, transcription factor, gene expression, regulation, Mycoplasma pneumoniae, Affinity chromatography, DNA binding protein

Luis Serrano
contact affiliation	Centre for Genomic Regulation
contact email	luis.serrano@crg.eu
lab head
Eva Yus
contact affiliation	Centre for Genomic Regulation
contact email	eva.yus@crg.eu
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/2019/11/PXD007677

PRIDE project URI

• PRIDE
  1. PXD007677
     1. Label: PRIDE project
     2. Name: DNA Affinity chromatografy on Mycoplasma pneumoniae extracts III