一种基于邻近连接的方法用于定量测量酿酒酵母中D环延伸
A Proximity Ligation-Based Method for Quantitative Measurement of D-Loop Extension in S. cerevisiae.
作者信息
Piazza Aurèle, Koszul Romain, Heyer Wolf-Dietrich
机构信息
University of California, Davis, Davis, CA, United States; Institut Pasteur, Paris, France.
Institut Pasteur, Paris, France.
出版信息
Methods Enzymol. 2018;601:27-44. doi: 10.1016/bs.mie.2017.11.024. Epub 2018 Feb 24.
Abstract
Homologous recombination faithfully restores the sequence information interrupted by a DNA double-strand break by referencing an intact DNA molecule as a template for repair DNA synthesis. DNA synthesis is primed from 3'-OH end of the invading DNA strand in the displacement loop (D-loop). Here, we describe a simple and quantitative proximity ligation-based assay to study the initiation of homologous recombination-associated DNA synthesis initiated at the D-loop and final product formation. The D-loop extension assay overcomes the semiquantitative nature and some limitations of the current PCR-based technique and facilitates the study of the recombination-associated DNA synthesis.
摘要
同源重组通过将完整的DNA分子作为修复DNA合成的模板，如实地恢复被DNA双链断裂中断的序列信息。DNA合成由置换环（D环）中入侵DNA链的3'-OH末端引发。在这里，我们描述了一种基于邻近连接的简单定量分析方法，用于研究在D环处启动的同源重组相关DNA合成及最终产物的形成。D环延伸分析克服了当前基于PCR技术的半定量性质和一些局限性，并有助于对重组相关DNA合成的研究。
相似文献
1
A Proximity Ligation-Based Method for Quantitative Measurement of D-Loop Extension in S. cerevisiae.
Methods Enzymol. 2018;601:27-44. doi: 10.1016/bs.mie.2017.11.024. Epub 2018 Feb 24.
2
Biochemical Analysis of D-Loop Extension and DNA Strand Displacement Synthesis.
Methods Mol Biol. 2021;2153:87-99. doi: 10.1007/978-1-0716-0644-5_7.
3
An Approach to Detect and Study DNA Double-Strand Break Repair by Transcript RNA Using a Spliced-Antisense RNA Template.
Methods Enzymol. 2018;601:59-70. doi: 10.1016/bs.mie.2017.11.026. Epub 2018 Feb 3.
4
Pathways and assays for DNA double-strand break repair by homologous recombination.
Acta Biochim Biophys Sin (Shanghai). 2019 Sep 6;51(9):879-889. doi: 10.1093/abbs/gmz076.
5
Identification of Saccharomyces cerevisiae DNA ligase IV: involvement in DNA double-strand break repair.
EMBO J. 1997 Aug 1;16(15):4788-95. doi: 10.1093/emboj/16.15.4788.
6
S1-seq Assay for Mapping Processed DNA Ends.
Methods Enzymol. 2018;601:309-330. doi: 10.1016/bs.mie.2017.11.031. Epub 2018 Feb 24.
7
Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae.
J Vis Exp. 2022 Sep 11(187). doi: 10.3791/64240.
8
The SWI/SNF ATP-dependent nucleosome remodeler promotes resection initiation at a DNA double-strand break in yeast.
Nucleic Acids Res. 2017 Jun 2;45(10):5887-5900. doi: 10.1093/nar/gkx221.
9
Investigation of Break-Induced Replication in Yeast.
Methods Enzymol. 2018;601:161-203. doi: 10.1016/bs.mie.2017.12.010. Epub 2018 Feb 3.
10
Regulation of hetDNA Length during Mitotic Double-Strand Break Repair in Yeast.
Mol Cell. 2017 Aug 17;67(4):539-549.e4. doi: 10.1016/j.molcel.2017.07.009. Epub 2017 Aug 3.
引用本文的文献
1
Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair.
Nucleic Acids Res. 2025 Feb 8;53(4). doi: 10.1093/nar/gkaf081.
2
Multi-step control of homologous recombination via Mec1/ATR suppresses chromosomal rearrangements.
EMBO J. 2024 Jul;43(14):3027-3043. doi: 10.1038/s44318-024-00139-9. Epub 2024 Jun 5.
3
Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability.
Genes Dev. 2023 Jul 1;37(13-14):621-639. doi: 10.1101/gad.350618.123. Epub 2023 Aug 4.
4
Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability.
bioRxiv. 2023 Mar 16:2023.03.15.532751. doi: 10.1101/2023.03.15.532751.
5
Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae.
J Vis Exp. 2022 Sep 11(187). doi: 10.3791/64240.
6
Break-induced replication: unraveling each step.
Trends Genet. 2022 Jul;38(7):752-765. doi: 10.1016/j.tig.2022.03.011. Epub 2022 Apr 19.
7
Tracking break-induced replication shows that it stalls at roadblocks.
Nature. 2021 Feb;590(7847):655-659. doi: 10.1038/s41586-020-03172-w. Epub 2021 Jan 20.
8
Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution.
Elife. 2020 Nov 13;9:e59111. doi: 10.7554/eLife.59111.
9
Physical and Genetic Assays for the Study of DNA Joint Molecules Metabolism and Multi-invasion-Induced Rearrangements in S. cerevisiae.
Methods Mol Biol. 2021;2153:535-554. doi: 10.1007/978-1-0716-0644-5_36.
10
Dynamic Processing of Displacement Loops during Recombinational DNA Repair.
Mol Cell. 2019 Mar 21;73(6):1255-1266.e4. doi: 10.1016/j.molcel.2019.01.005. Epub 2019 Feb 5.
本文引用的文献
1
Multi-invasions Are Recombination Byproducts that Induce Chromosomal Rearrangements.
Cell. 2017 Aug 10;170(4):760-773.e15. doi: 10.1016/j.cell.2017.06.052. Epub 2017 Aug 3.
2
Homology Requirements and Competition between Gene Conversion and Break-Induced Replication during Double-Strand Break Repair.
Mol Cell. 2017 Feb 2;65(3):515-526.e3. doi: 10.1016/j.molcel.2016.12.003. Epub 2017 Jan 5.
3
Sgs1 and Mph1 Helicases Enforce the Recombination Execution Checkpoint During DNA Double-Strand Break Repair in Saccharomyces cerevisiae.
Genetics. 2016 Jun;203(2):667-75. doi: 10.1534/genetics.115.184317. Epub 2016 Apr 13.
4
Regulation of recombination and genomic maintenance.
Cold Spring Harb Perspect Biol. 2015 Aug 3;7(8):a016501. doi: 10.1101/cshperspect.a016501.
5
Frequent Interchromosomal Template Switches during Gene Conversion in S. cerevisiae.
Mol Cell. 2014 Aug 21;55(4):615-25. doi: 10.1016/j.molcel.2014.06.025. Epub 2014 Jul 24.
6
Migrating bubble during break-induced replication drives conservative DNA synthesis.
Nature. 2013 Oct 17;502(7471):389-92. doi: 10.1038/nature12584. Epub 2013 Sep 11.
7
Break-induced replication occurs by conservative DNA synthesis.
Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13475-80. doi: 10.1073/pnas.1309800110. Epub 2013 Jul 29.
8
Effect of nuclear architecture on the efficiency of double-strand break repair.
Nat Cell Biol. 2013 Jun;15(6):694-9. doi: 10.1038/ncb2745. Epub 2013 May 5.
9
Increased chromosome mobility facilitates homology search during recombination.
Nat Cell Biol. 2012 Apr 8;14(5):510-7. doi: 10.1038/ncb2472.
10
Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search.
Nature. 2012 Feb 8;482(7385):423-7. doi: 10.1038/nature10782.
Zotero 插件