PXD039547

PXD039547 is an original dataset announced via ProteomeXchange.

Title	Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1
Description	DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol d. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIa (LigIIIa)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol e, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIa/XRCC1 and Pol d at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is present in the chromatin of LigI-deficient mouse and human cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome.
HostingRepository	PRIDE
AnnounceDate	2023-04-04
AnnouncementXML	Submission_2023-04-04_12:55:04.150.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	SeemaKhattri Bhandari
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-18 16:25:03	ID requested
⏵ 1	2023-04-04 12:55:04	announced

Dataset with its publication pending

submitter keyword: DNA Ligase I, aniPOND-MS, DNA replication

Alan ETomkinson
contact affiliation	department of internal medicine, university of new mexico
contact email	atomkinson@salud.unm.edu
lab head
SeemaKhattri Bhandari
contact affiliation	University of New Mexico
contact email	skhattribhandari@salud.unm.edu
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/PXD039547

PRIDE project URI

• PRIDE
  1. PXD039547
     1. Label: PRIDE project
     2. Name: Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1