PXD044960

PXD044960 is an original dataset announced via ProteomeXchange.

Title	Investigation of DNA double-strand break repair mechanisms in microsatellite regions using the CRISPR/Cas9 system
Description	Expansion of the CAG/CTG repeats in functionally unrelated genes is a causative factor in many inherited neurodegenerative disorders, including Huntington's disease (HD), spinocerebellar ataxias (SCAs) and myotonic dystrophy type 1 (DM1). Despite many years of research, the mechanism responsible for repeat instability is unknown, and recent findings indicate the key role of DNA repair in this process. The repair of DSBs induced by genome editing tools results in the shortening of long CAG repeats in yeast models. Understanding this mechanism is the first step to developing a therapeutic strategy based on controlled shortening of repeats. The aim of this study was to characterize Cas9-induced DSB repair products in the endogenous HTT locus in human cells and to identify factors affecting the formation of specific types of mutations. The location of the cleavage site and its sequence affect the outcome of DNA repair. DSBs within CAG repeats result in shortening of the repeats in frame in ~90% of products. The mechanism of this contraction involves MRE11-CTIP and RAD51 activity and extensive DNA end resection reaching ~5000 bp. We demonstrated that a DSB located upstream of CAG repeats induces polymerase theta-mediated end joining, resulting in deletion of the entire CAG tract. Furthermore, using unbiased proteomic analysis, we identified novel factors that may be involved in CAG sequence repair.
HostingRepository	PRIDE
AnnounceDate	2024-11-04
AnnouncementXML	Submission_2024-11-04_07:01:31.601.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044960
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Agata Malinowska
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue; monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-30 05:37:01	ID requested
⏵ 1	2024-11-04 07:01:32	announced

10.6019/PXD044960;

submitter keyword: trinucleotide repeats, genome editing, Huntington disease, DNA repair,RISPR-Cas

Marta Olejniczak
contact affiliation	Department of Genome Engineering, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, 61-704, Poland
contact email	marta.olejniczak@ibch.poznan.pl
lab head
Agata Malinowska
contact affiliation	IBB PAS
contact email	esme@ibb.waw.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/2024/11/PXD044960

PRIDE project URI

• PRIDE
  1. PXD044960
     1. Label: PRIDE project
     2. Name: Investigation of DNA double-strand break repair mechanisms in microsatellite regions using the CRISPR/Cas9 system