PXD012045

PXD012045 is an original dataset announced via ProteomeXchange.

Title	Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation
Description	DNA double strand break (DSB) repair through homologous recombination (HR) is crucial to maintain genome stability. DSB resection generates a single strand DNA intermediate, which is crucial for the HR process. We used a synthetic DNA structure, mimicking a resection intermediate, as a bait to identify proteins involved in this process. Among these, LC/MS analysis identified the RNA binding protein, HNRNPD. We found that HNRNPD was able to bind chromatin, although this binding occurred independently of DNA damage. However, upon damage, HNRNPD re-localized to γH2Ax foci and its silencing impaired CHK1 S345 phosphorylation and the DNA end resection process. Indeed, HNRNPD silencing reduced the ssDNA fraction upon camptothecin treatment and AsiSI-induced DSB resection and reduced RPA32 S4/8 phosphorylation. CRISPR/Cas9-mediated HNRNPD knockout impaired in vitro DNA resection and sensitized cells to camptothecin and olaparib treatment. We found that HNRNPD interacts with the heterogeneous nuclear ribonucleoprotein SAF-A previously associated with DNA damage repair. HNRNPD depletion resulted in an increased amount of RNA:DNA hybrids upon DNA damage . Both the expression of RNase H1 and RNA pol II inhibition recovered the ability to phosphorylate RPA32 S4/8 in HNRNPD knockout cells upon DNA damage, suggesting that RNA:DNA hybrid resolution likely rescues the defective DNA damage response of HNRNPD-depleted cells.
HostingRepository	PRIDE
AnnounceDate	2019-02-26
AnnouncementXML	Submission_2019-03-05_07:27:46.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD012045
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Claudia Landi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Carbamidomethyl
Instrument	LCQ Classic

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-13 01:45:10	ID requested
1	2019-02-26 05:18:23	announced
⏵ 2	2019-03-05 07:27:48	announced	Updated publication reference for PubMed record(s): 30799487.

Alfano L, Caporaso A, Altieri A, Dell'Aquila M, Landi C, Bini L, Pentimalli F, Giordano A, Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation. Nucleic Acids Res, 47(8):4068-4085(2019) [pubmed]

submitter keyword: RNA binding proteins

HNRNPD

DNA damage

DNA end resection

RNA binding proteins

R-loop

Luca Bini
contact affiliation	Functional Proteomics Lab, Life Sciences Dept. University of Siena, Siena, Italy
contact email	luca.bini@unisi.it
lab head
Claudia Landi
contact affiliation	University of Siena
contact email	landi35@unisi.it
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD012045
     1. Label: PRIDE project
     2. Name: Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation