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Series GSE169619 Query DataSets for GSE169619
Status Public on May 13, 2024
Title Genome wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression
Organism Homo sapiens
Experiment type Other
Summary DNA replication progression can be affected by the presence of physical barriers on the DNA, like RNA Polymerases, leading to replication stress and DNA damage. To characterize what happens at sites where DNA replication forks stall and pause, we establish a genome-wide approach to identify them. This approach uses multiple timepoints during S-phase, to identify replication fork/stalling hotspots throughout the genome. These sites are typically associated with increased DNA damage, overlap with fragile sites and with breakpoints of rearrangements identified in cancers, but do not overlap with replication origins. Overlaying these sites with a genome-wide analysis of RNA Polymerase II transcription, we found that replication fork stalling/pausing sites inside genes are directly related to transcription progression and activity. This would support data that indicate that transcription and replication can coexist over the same regions. We found instances where transcription activity by reducing histone density favors replication progression through genes, but also found that slowing down transcription elongation slows down directly replication progression through genes. Importantly, rearrangements found in cancers at transcription-replication collision sites can be detected in non-transformed cells and increased following treatment with ATM and ATR inhibitors. Altogether, our findings highlight how transcription and replication overlap during S-phase, with both positive and negative consequences for replication fork progression and genome stability.

Overall design Genome-wide DNA replication profile of BJ-hTERT during S phase with or without indicated treatments generated by NGS
Contributor(s) Rojas P, Wang J, Saponaro M
Citation(s) 38773641
Submission date Mar 25, 2021
Last update date Jun 06, 2024
Contact name Marco Saponaro
Organization name University of Birmingham
Department Institute of Cancer and Genomic Sciences
Street address Vincent Drive
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (10)
GSM5211121 ATMi 1_16h
GSM5211122 ATMi 2_16h
GSM5211123 ATRi 1_16h
This SubSeries is part of SuperSeries:
GSE169620 Genome wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression
BioProject PRJNA717229
SRA SRP312120

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Supplementary file Size Download File type/resource
GSE169619_Brdu-Seq_quant.txt.gz 264.3 Kb (ftp)(http) TXT
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