TrAEL-seq for WRN inhibitors
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1064407 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cancers with microsatellite instability (MSI) depend on the WRN helicase enzyme to manage issues during DNA replication caused by long stretches of (TA) repeats in the DNA. Targeting WRN is a promising strategy for treating MSI cancers, and drugs that inhibit WRN are being developed. Through a process called fragment-based screening, we developed powerful and specific drugs that block WRN's action. These drugs effectively slowed down the growth of MSI cancer models in lab and animal studies by acting like WRN is absent, leading to DNA breaks at the long TA repeats and causing DNA damage. The development of these potent and specific drugs targeting WRN in MSI cancers proves that this approach can work and also helps us understand more about WRN's role in biology.
2025-01-10 | GSE253197 | GEO
Project description:We have applied the TrAEL-seq method to profile DNA replication in wild type and Snf2h knockoutmouse embryonic stem cells.
2024-03-15 | GSE259364 | GEO
Project description:We have designed a methodology for capture of DNA 3’ ends that allows mapping of resected DNA breaks, stalled replication forks and also normal replication fork progression. This Transferase-activated end ligation or TrAEL-seq method involves ligation of a functionalised linker to DNA 3’ ends followed by fragmentation, purification of adaptor ligated fragments, second adaptor ligation and library amplification. The major advantages of TrAEL-seq compared to other available methods are: i) an ability to map double strand breaks after resection, ii) excellent sensitivity and signal-to-noise in detecting replication fork stalling and iii) ability to map replication fork progression in unsynchronised, unlabelled populations of both yeast and mammalian cells. The samples provided here were selected to demonstrate different aspects of TrAEL-seq activity: the SfiI and dmc1 datasets shows capture of 3’ extended single strand DNA. The other yeast datasets show replication and replication fork stalling information. The RAF and RAF-GAL grown yeast samples show the effect transcriptional induction on replication fork progression. The hESC samples show the capacity to derive replication profiles from mammalian cells.
2020-07-27 | GSE154811 | GEO
Project description:TrAEL-seq was performed on hydroxyurea-blocked and then released yeast cells to track replication fork stalling and replication fork restart, in wild-type and replisome mutant strains.
2023-07-23 | GSE235881 | GEO
Project description:TrAEL-seq was used to assess the impact of Triapine (3AP), a RRM2 inhibitor, on replication fork accumulation and changes to the replication profile of IMR32 cells.
2022-08-02 | GSE186122 | GEO
Project description:1) The Pgal-3HA cup1 yeast strain, in which all CUP1 ORFs are replaced with 3HA and all CUP1 promoters are replaced by GAL1-10 promoters (PMID: 28654659, which carries ~17 tandem repeats of the modified Pgal-3HA cup1 repeat) undergoes extensive CNV when shifted to galactose. Here we use TrAEL-seq to look for replication fork stalling in this strain with and without induction. 2) We also profile the impact on replication of integrating an ARSH4 origin upstream of the RSC30 gene (so outside the CUP1 locus), using the 3xCUP1 strain which carries 3 repeats of CUP1 (PMID: 28654659). The origin was integrated with a URA3 marker, the control strain has the URA3 marker but no origin.
2021-01-21 | GSE165163 | GEO
Project description:Werner Syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The mutated gene responsible for WS encodes a DNA helicase/exonuclease protein believed to affect different aspects of transcription, replication, and DNA repair. In this study, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to identify regions of the genome bound by the WRN protein in Human Embryonic Kidney (HEK) 293 cells. We found 409 such genomic sites, one third of which corresponded to tRNA genes and another third of which were within RNA polymerase II transcribed genes that tended to contain guanine-rich sequences. We confirmed the specificity of several sites using WRN-depleted HEK293 cells by ChIP followed by quantitative PCR. Expression profiling of the HEK293 cells and RT-PCR analyses indicated that the transcription of the genes (including tRNAs) bound by WRN were not changed. Instead, we found a greater accumulation of WRN protein at these sites during S phase. These results suggest that the WRN protein accumulates at specific genomic sites during S phase of the cell cycle in HEK293 cells.
2016-05-01 | GSE68714 | GEO
Project description:Metabolic dysfunction is one of the main symptoms of Werner syndrome (WS); however, the underlying mechanisms remain unclear. Here, we report that loss of WRN accelerates adipogenesis at an early stage both in vitro (stem cells) and in vivo (zebrafish). Moreover, WRN depletion causes a transient upregulation of late-stage of adipocyte-specific genes at an early stage.
2024-01-26 | GSE248012 | GEO
Project description:Werner Syndrome (WS) is an autosomal recessive disorder characterized by premature aging due to mutations of the WRN gene. A classical sign in WS patients is short stature, but the underlying mechanisms are not well understood. Here we report that WRN is indispensable for chondrogenesis, which is the engine driving the elongation of bones and determines height.
2022-07-28 | GSE206210 | GEO