REPAIRtoire--a database of DNA repair pathways

Milanowska, Kaja; Krwawicz, Joanna; Papaj, Grzegorz; Kosiński, Jan G.; Poleszak, Katarzyna; Lesiak, Justyna; Osińska, Ewelina; Rother, Kristian; Bujnicki, Janusz M.

doi:10.1093/nar/gkq1087

Cited by 65 publications

(60 citation statements)

References 25 publications

(20 reference statements)

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“…23-31 We evaluated for rare PTVs in genes implicated in DNA repair (n=513; Table S2) and in recognized PC susceptibility genes that are not implicated in DNA repair (i.e., CDKN2A, PRSS1, and SPINK1 ). Table S2 lists the 513 recognized and putative DNA repair genes evaluated, which includes genes defined as DNA repair genes in the Gene Ontology project (via AmiGO browser), 32 genes included in the REPAIRtoire database 33 and other genes identified through PUBMED literature search. Primers used to validate variants by Sanger sequencing are listed in Table S3.…”

Section: Methodsmentioning

confidence: 99%

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

et al. 2016

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The genetic basis underlying the majority of hereditary pancreatic adenocarcinoma (PC) is unknown. Since DNA repair genes are widely implicated in gastrointestinal malignancies, including PC, we hypothesized that there are novel DNA repair PC susceptibility genes. As germline DNA repair gene mutations may lead to PC subtypes with selective therapeutic responses, we also hypothesized that there is an overall survival (OS) difference in mutation carriers versus non-carriers. We therefore interrogated the germline exomes of 109 high-risk PC cases for rare protein-truncating variants (PTVs) in 513 putative DNA repair genes. We identified PTVs in 41 novel genes among 36 kindred. Additional genetic evidence for causality was obtained for 17 genes, with FAN1, NEK1 and RHNO1 emerging as the strongest candidates. An OS difference was observed for carriers versus non-carriers of PTVs with early stage (≤ IIB) disease. This adverse survival trend in carriers with early stage disease was also observed in an independent series of 130 PC cases. We identified candidate DNA repair PC susceptibility genes and suggest that carriers of a germline PTV in a DNA repair gene with early stage disease have worse survival.

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Section: Methodsmentioning

confidence: 99%

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

et al. 2016

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“…In this study, we made use of nucleolar proteome data sets (Andersen et al 2005;Moore et al 2011), RBP census (Gerstberger et al 2014), DDR genes (Wood et al 2001;Milanowska et al 2011;Mjelle et al 2015), TP53 target genes (Nikulenkov et al 2012;Menendez et al 2013), spliceosomal subcomplexes (Hegele et al 2012), exon-intron-exon regions (Braunschweig et al 2014), and RNA-seq data sets (Kfir et al 2015;Kesarwani et al 2016;Yoshimoto et al 2017). RNA-seq analysis of TCGA data sets (Sebestyén et al 2016) is described in Supplemental Methods.…”

Section: Additional Data Setsmentioning

confidence: 99%

DDX54 regulates transcriptome dynamics during DNA damage response

et al. 2017

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The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing radiation (IR). Interestingly, more than 260 proteins, including many nucleolar proteins, showed increased binding to poly(A) + RNA in IR-exposed cells. The functional analysis of DDX54, a candidate genotoxic stress responsive RNA helicase, revealed that this protein is an immediate-to-early DDR regulator required for the splicing efficacy of its target IR-induced pre-mRNAs. Upon IR exposure, DDX54 acts by increased interaction with a well-defined class of pre-mRNAs that harbor introns with weak acceptor splice sites, as well as by proteinprotein contacts within components of U2 snRNP and spliceosomal B complex, resulting in lower intron retention and higher processing rates of its target transcripts. Because DDX54 promotes survival after exposure to IR, its expression and/or mutation rate may impact DDR-related pathologies. Our work indicates the relevance of many uncharacterized RBPs potentially involved in the DDR.

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“…We indentified additional molecules interacting with repair proteins listed in the REPAIRtoire database 24 by literature and database (ChEMBL 25 ) search. The additional molecules we test, which have been described to block NHEJ or alternative NHEJ or activate or increase the abundance of proteins involed in HDR or damage-dependent signaling ( Fig.…”

Section: Main Textmentioning

confidence: 99%

Targeting repair pathways with small molecules increases precise genome editing in pluripotent stem cells

Riesenberg

Maričić

2017

Preprint

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A now frequently used method to edit mammalian genomes uses the nucleases CRISPR/Cas9 and CRISPR/Cpf1 or the nickase CRISPR/Cas9n to introduce double-strand breaks (DSBs) which are then repaired by homology-directed repair (HDR) using synthetic or cloned DNA donor molecules carrying desired mutations. However, another pathway, the non-homologous end joining (NHEJ) pathway competes with HDR for repairing DNA breaks in cells. To increase the frequency of precise genome editing in human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) we have tested the capacity of a number of small molecules to enhance HDR or inhibit NHEJ. We identify molecules that increase the frequency of precise genome editing including some that have additive effects when applied together. Using a mixture of such molecules, the 'CRISPY' mix, we achieve 2.8-to 6.7-fold increase in precise genome editing with Cas9n, resulting in the introduction of the intended nucleotide substitutions in almost 50% of chromosomes, to our knowledge the highest editing efficiency in hiPSCs described to date. Furthermore, the CRISPY mix improves precise genome editing with Cpf1 2.9-to 4.0-fold, allowing almost 20% of chromosomes to be edited. Main textThe bacterial nuclease CRISPR/Cas9 is now frequently used to accurately cut chromosomal DNA sequences in eukaryotic cells. The resulting DNA breaks are repaired by two competing pathways: NHEJ and HDR (Fig. 1). In NHEJ, the first proteins to bind the cut DNA ends are Ku70/Ku80, followed by DNA protein kinase catalytic subunit (DNA-PKcs) Since NHEJ of Cas9-induced DSBs is error prone and frequently introduces short insertions and deletions (indels) at the cut site, it is useful for knocking out a targeted gene. In contrast, HDR allows precise repair of a DSB by using a homologous donor DNA. If the donor DNA provided in the experiment carries mutations, these will be introduced into the genome (precise genome editing). Repair with homologous ssDNA or dsDNA has been suggested to engage different pathways 5 . We will refer to Targeted Nucleotide Substitutions using ssDNA donors as 'TNS' and targeted insertion of cassettes . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/136374 doi: bioRxiv preprint first posted online May. 10, 2017; 3 using dsDNA donors as knock-ins, respectively. In order to introduce a DSB Cas9 requires the nucleotide sequence NGG (a "PAM" site) in the target DNA. Targeting of Cas9 is further determined by a guide RNA (gRNA) complementary to 20 nucleotides adjacent to the PAM site. However, the Cas9 may also cut the genome at sites that carry sequence similarity to the gRNA 6 . One strategy to reduce such off-target cuts is to use a mutated Cas9 that introduces single-stranded nicks instead of DSBs (Cas9n) 7 . Using two gRNAs to introduce two nicks on opposite DNA strands in close proximity to each other will result in a staggered D...

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REPAIRtoire--a database of DNA repair pathways

Cited by 65 publications

References 25 publications

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

DDX54 regulates transcriptome dynamics during DNA damage response

Targeting repair pathways with small molecules increases precise genome editing in pluripotent stem cells

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