PXD011156

PXD011156 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of DNA synthesis on a structured DNA template in human cellular extracts: Interplay between NHEJ and replication-associated proteins
Description	It has been established that short inverted repeats (SIRs) trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with this structured DNA is unknown. We have previously reported that in human cell-free extracts, DNA primer extension using a structured single-stranded DNA template is transiently blocked at DNA hairpins [1](Schmutz et al., 2007). Here, we report the proteomic analysis of proteins bound to the DNA template providing evidence that proteins of the NHEJ pathway, particularly the DNA-PK complex (composed of DNA-PKcs and the Ku70/Ku80 dimer) recognize structured single-stranded DNA. DNA-PKcs inhibition results in the mobilization on the template DNA of the DNA-PK complex, along with other proteins acting downstream in the NHEJ pathway, especially the XRCC4-DNA Ligase 4 complex and the recently identified cofactor PAXX. The retention of NHEJ factors to the template DNA in the absence of DNA-PKcs activity correlates with additional halts of primer extension, suggesting that NHEJ proteins may hinder the progression of the DNA synthesis at these sites. Conversely, hijacking of the DNA-PK complex by double-stranded oligos (dsO) results in a large removal of the pausing sites and an elevated DNA extension efficiency. Overall these results raise the possibility that, upon binding to DNA hairpins formed onto ssDNA during fork progression, the DNA-PK complex may play some role in replication fork dynamics in vivo, role that is however not related to repair of double-strand breaks.
HostingRepository	PRIDE
AnnounceDate	2020-02-04
AnnouncementXML	Submission_2020-02-04_04:27:55.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011156
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Lauriane Kuhn
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-20 08:31:04	ID requested
⏵ 1	2020-02-04 04:27:56	announced

Janel-Bintz R, Kuhn L, Frit P, Chicher J, Wagner J, Haracska L, Hammann P, Cordonnier AM, Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication-Associated Proteins. Proteomics, 20(3-4):e1900184(2020) [pubmed]

curator keyword: Technical

submitter keyword: DNA replication, short inverted repeats, NHEJ

Régine Janel
contact affiliation	Biotechnologie et Signalisation Cellulaire, Université de Strasbourg, UMR 7242, Illkirch 67412, France.
contact email	regine.janel@unistra.fr
lab head
Lauriane Kuhn
contact affiliation	CNRS, IBMC, FRC1589
contact email	l.kuhn@ibmc-cnrs.unistra.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011156
     1. Label: PRIDE project
     2. Name: Proteomic analysis of DNA synthesis on a structured DNA template in human cellular extracts: Interplay between NHEJ and replication-associated proteins