Knotting of replication intermediates is narrowly restricted

2020 ◽  
pp. 85-100
Author(s):  
Dorothy Buck ◽  
Danielle O’Donnol
Keyword(s):  
Replication Intermediates

Altered formation of DNA replication intermediates in cells growing in different culture conditions

1989 ◽  
Vol 138 (1) ◽  
pp. 45-49
Author(s):  
Ulf lönn ◽  
Sigrid Lönn ◽  
Urban Nylen ◽  
Gerard Winblad
Keyword(s):  
Dna Replication ◽  
Culture Conditions ◽  
Replication Intermediates ◽  
In Cells

scholarly journals Changes in the topology of DNA replication intermediates: Important discrepancies between in vitro and in vivo

BioEssays ◽  
2021 ◽  
Vol 43 (5) ◽  
pp. 2000309
Author(s):  
Jorge B. Schvartzman ◽  
Víctor Martínez ◽  
Pablo Hernández ◽  
Dora B. Krimer ◽  
María‐José Fernández‐Nestosa
Keyword(s):  
Dna Replication ◽  
Replication Intermediates

scholarly journals UV-induced Hyperphosphorylation of Replication Protein A Depends on DNA Replication and Expression of ATM Protein

2001 ◽  
Vol 12 (5) ◽  
pp. 1199-1213 ◽  
Author(s):  
Gregory G. Oakley ◽  
Lisa I. Loberg ◽  
Jiaqin Yao ◽  
Mary A. Risinger ◽  
Remy L. Yunker ◽  
...  
Keyword(s):  
Dna Replication ◽  
Uv Radiation ◽  
Excision Repair ◽  
Genetic Disorder ◽  
Protein A ◽  
Dna Recombination ◽  
Delayed Response ◽  
Replication Intermediates

Exposure to DNA-damaging agents triggers signal transduction pathways that are thought to play a role in maintenance of genomic stability. A key protein in the cellular processes of nucleotide excision repair, DNA recombination, and DNA double-strand break repair is the single-stranded DNA binding protein, RPA. We showed previously that the p34 subunit of RPA becomes hyperphosphorylated as a delayed response (4–8 h) to UV radiation (10–30 J/m2). Here we show that UV-induced RPA-p34 hyperphosphorylation depends on expression of ATM, the product of the gene mutated in the human genetic disorder ataxia telangiectasia (A-T). UV-induced RPA-p34 hyperphosphorylation was not observed in A-T cells, but this response was restored by ATM expression. Furthermore, purified ATM kinase phosphorylates the p34 subunit of RPA complex in vitro at many of the same sites that are phosphorylated in vivo after UV radiation. Induction of this DNA damage response was also dependent on DNA replication; inhibition of DNA replication by aphidicolin prevented induction of RPA-p34 hyperphosphorylation by UV radiation. We postulate that this pathway is triggered by the accumulation of aberrant DNA replication intermediates, resulting from DNA replication fork blockage by UV photoproducts. Further, we suggest that RPA-p34 is hyperphosphorylated as a participant in the recombinational postreplication repair of these replication products. Successful resolution of these replication intermediates reduces the accumulation of chromosomal aberrations that would otherwise occur as a consequence of UV radiation.

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method

1994 ◽  
Vol 14 (2) ◽  
pp. 1520-1529
Author(s):  
C Liang ◽  
S A Gerbi
Keyword(s):  
Three Dimensional ◽  
Dna Amplification ◽  
Gel Method ◽  
Dna Molecule ◽  
Cutting Out ◽  
Origin Region ◽  
2D Gel ◽  
Third Dimension ◽  
Single Dna Molecule ◽  
Replication Intermediates

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

scholarly journals Arabidopsis LTR retrotransposons and their regulation by epigenetically activated small RNA

2020 ◽  
Author(s):  
Seung Cho Lee ◽  
Evan Ernst ◽  
Benjamin Berube ◽  
Filipe Borges ◽  
Jean-Sebastien Parent ◽  
...  
Keyword(s):  
Small Rna ◽  
Histone H3 ◽  
Ltr Retrotransposons ◽  
Genomic Rna ◽  
Rna Dependent Rna Polymerase ◽  
Subgenomic Rna ◽  
Circular Dna ◽  
Genomic Copy Number ◽  
Long Read ◽  
Replication Intermediates

AbstractIn Arabidopsis, LTR-retrotransposons are activated by mutations in the chromatin remodeler DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21-22nt epigenetically activated siRNAs (easiRNAs) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like-particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. Next generation short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR-retrotransposons without the need for mapping transposition, and independent of genomic copy number. Linear replication intermediates of a functionally intact copia element EVADE revealed multiple central polypurine tracts (cPPT), a feature shared with HIV where cPPT promote nuclear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon “suicide” by auto-integration within the VLP. easiRNA targeted EVADE genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethylation. VLP DNA-seq provides a comprehensive landscape of LTR-retrotransposons, and their control at transcriptional, post-transcriptional and reverse transcriptional levels.

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