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Cited by 126DNA Repair MechanismsGenomics and Chromatin DynamicsGenomic variations and chromosomal abnormalities

Isolation and analysis of rereplicated DNA by Rerep-Seq

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Menzel, Johannes, Tatman, Philip, Black, Joshua C·2020·Nucleic Acids Research
DOI 10.1093/nar/gkaa197PMC PMC7261181
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Abstract

Changes in gene copy number contribute to genomic instability, the onset and progression of cancer, developmental abnormalities and adaptive potential. The origins of gene amplifications have remained elusive; however, DNA rereplication has been implicated as a source of gene amplifications. The inability to determine which sequences are rereplicated and under what conditions have made it difficult to determine the validity of the proposed models. Here we present Rerep-Seq, a technique that selectively enriches for rereplicated DNA in preparation for analysis by DNA sequencing that can be applied to any species. We validated Rerep-Seq by simulating DNA rereplication in yeast and human cells. Using Rerep-Seq, we demonstrate that rereplication induced in Saccharomyces cerevisiae by deregulated origin licensing is non-random and defined by broad domains that span multiple replication origins and topological boundaries.

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  • We filtered intragenic CAGE TCs with GG-initiation and those overlapping with coding exons and annotated enhancers.

    “We filtered intragenic CAGE TCs with GG-initiation and those overlapping with coding exons and annotated enhancers24,70”

    From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [70]

    The Materials and Methods sections describe filtering Rerep-Seq data and analyzing replication-timing regions, not intragenic CAGE transcription clusters. Searches for GG-initiation, CAGE clusters, coding exons, and enhancer filtering found no passage addressing the cited claim; page numbers are unavailable in our copy. (LLM, conf=0.76)

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Research works printed but not linked: 38

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Authors
Menzel, J., Tatman, P., & Black, J. C.
Affiliations
University of Colorado Anschutz (US)
Corresponding author
Black, Joshua C
ORCID
Black, Joshua C
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2020-04-02
Volume
48
Issue
10
Pages
e58-e58
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkaa197
PMC
PMC7261181
OpenAlex
W3014366315
Cited by
126
References
0
Citations by year
2026: 17 · 2025: 27 · 2024: 22 · 2023: 23 · 2022: 23 · 2021: 12 · 2020: 2
FWCI
4.87
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Institute of General Medical Sciences (1R35GM128720-01)
  • Boettcher Foundation (25A6182)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords
DNA re-replication, gene amplification, genomic instability, origin of replication, origin licensing, Saccharomyces cerevisiae, topological domains, copy number variation
MeSH terms
Cell Line, DNA Replication, Humans, Saccharomyces cerevisiae, Sequence Analysis, DNA

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