Name: detection of homologous recombination intermediates via proximity ligation and quantitative pcr in saccharomyces cerevisiae
Uploaded: 2022-09-11T13:00:00
Description: Watch this Scientific Journal Video about Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae at JoVE.com

The work in the Heyer laboratory is supported by grants GM58015 and GM137751 to W.-D.H. Research in the Piazza laboratory is supported by the European Research Council (ERC-StG 3D-loop, grand agreement 851006). D.R. is supported by T32CA108459 and the A.P. Giannini Foundation. We thank Shih-Hsun Hung (Heyer Lab) for sharing his DLC/DLE assay results and for additionally validating the changes to the assays that are detailed in this protocol.

1. Pre-growth, DSB induction, and sample collection
NOTE: Supplementation of all media with 0.01% adenine is recommended for Ade- strains.
<ol>
	<li>Streak out the appropriate haploid strains (see Table 1) on yeast peptone dextrose adenine (YPDA) (1% yeast extract, 2% peptone, 2% glucose, 2% agar, 0.001% adenine) and grow for 2 days at 30 &#176;C.</li>
	<li>Use a single colony to inoculate 5 mL of YPDA in a 15 mL glass culture tube. Grow cultures to saturati...

<ol>
	<li>Symington, L. S., Gautier, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Double-strand+break+end+resection+and+repair+pathway+choice.">Double-strand break end resection and repair pathway choice.</a> Annual Review of Genetics. 45 (1), 247-271 (2011).</li><li>Heyer, W. -. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+recombination+and+genomic+maintenance.">Regulation of recombination and genomic maintenance.</a> Cold Spring Harbor Perspectives in Biology. 7 (8), 016501 (2015).</li><li>Mimitou, E. P., Symington, L. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sae2,+Exo1+and+Sgs1+collaborate+in+DNA+double-strand+break+processing.">Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing.</a> Nature. 455 (7214), 770-774 (2008).</li><li>Bzymek, M., Thayer, N. H., Oh, S. D., Kleckner, N., Hunter, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Double+Holliday+junctions+are+intermediates+of+DNA+break+repair.">Double Holliday junctions are intermediates of DNA break repair.</a> Nature. 464 (7290), 937-941 (2010).</li><li>Chen, H., Lisby, M., Symington, L. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RPA+coordinates+DNA+end+resection+and+prevents+formation+of+DNA+hairpins.">RPA coordinates DNA end resection and prevents formation of DNA hairpins.</a> Molecular Cell. 50 (4), 589-600 (2013).</li><li>Maz&#243;n, G., Symington, L. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mph1+and+Mus81-Mms4+prevent+aberrant+processing+of+mitotic+recombination+intermediates.">Mph1 and Mus81-Mms4 prevent aberrant processing of mitotic recombination intermediates.</a> Molecular Cell. 52 (1), 63-74 (2013).</li><li>Saini, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Migrating+bubble+during+break-induced+replication+drives+conservative+DNA+synthesis.">Migrating bubble during break-induced replication drives conservative DNA synthesis.</a> Nature. 502 (7471), 389-392 (2013).</li><li>Piazza, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+processing+of+displacement+loops+during+recombinational+DNA+repair.">Dynamic processing of displacement loops during recombinational DNA repair.</a> Molecular Cell. 73 (6), 1255-1266 (2019).</li><li>Piazza, A., Koszul, R., Heyer, W. -. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+proximity+ligation-based+method+for+quantitative+measurement+of+D-loop+extension+in+S.+cerevisiae.">A proximity ligation-based method for quantitative measurement of D-loop extension in S. cerevisiae.</a> Methods in Enzymology. 601, 27-44 (2018).</li><li>Sugawara, N., Wang, X., Haber, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+roles+of+Rad52,+Rad54,+and+Rad55+proteins+in+Rad51-mediated+recombination.">In vivo roles of Rad52, Rad54, and Rad55 proteins in Rad51-mediated recombination.</a> Molecular Cell. 12 (1), 209-219 (2003).</li><li>Renkawitz, J., Lademann, C. A., Kalocsay, M., Jentsch, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monitoring+homology+search+during+DNA+double-strand+break+repair+in+vivo.">Monitoring homology search during DNA double-strand break repair in vivo.</a> Molecular Cell. 50 (2), 261-272 (2013).</li><li>Petukhova, G., Stratton, S., Sung, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Catalysis+of+homologous+DNA+pairing+by+yeast+Rad51+and+Rad54+proteins.">Catalysis of homologous DNA pairing by yeast Rad51 and Rad54 proteins.</a> Nature. 393 (6680), 91-94 (1998).</li><li>Wright, W. D., Heyer, W. -. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rad54+functions+as+a+heteroduplex+DNA+pump+modulated+by+its+DNA+substrates+and+Rad51+during+D-loop+formation.">Rad54 functions as a heteroduplex DNA pump modulated by its DNA substrates and Rad51 during D-loop formation.</a> Molecular Cell. 53 (3), 420-432 (2014).</li><li>Tavares, E. M., Wright, W. D., Heyer, W. -. D., Cam, E. L., Dupaigne, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+role+of+Rad54+in+Rad51-ssDNA+filament-dependent+homology+search+and+synaptic+complexes+formation.">In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation.</a> Nature Communications. 10 (1), 4058 (2019).</li><li>Crickard, J. B., Moevus, C. J., Kwon, Y., Sung, P., Greene, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rad54+drives+ATP+hydrolysis-dependent+DNA+sequence+alignment+during+homologous+recombination.">Rad54 drives ATP hydrolysis-dependent DNA sequence alignment during homologous recombination.</a> Cell. 181 (6), 1380-1394 (2020).</li><li>Lydeard, J. R., Jain, S., Yamaguchi, M., Haber, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Break-induced+replication+and+telomerase-independent+telomere+maintenance+require+Pol32.">Break-induced replication and telomerase-independent telomere maintenance require Pol32.</a> Nature. 448 (7155), 820-823 (2007).</li><li>Jain, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+recombination+execution+checkpoint+regulates+the+choice+of+homologous+recombination+pathway+during+DNA+double-strand+break+repair.">A recombination execution checkpoint regulates the choice of homologous recombination pathway during DNA double-strand break repair.</a> Genes &amp; Development. 23 (3), 291-303 (2009).</li><li>Donnianni, R. A., Symington, L. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Break-induced+replication+occurs+by+conservative+DNA+synthesis.">Break-induced replication occurs by conservative DNA synthesis.</a> Proceedings of the National Academy of Sciences of the United States of America. 110 (33), 13475-13480 (2013).</li><li>Liu, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tracking+break-induced+replication+shows+that+it+stalls+at+roadblocks.">Tracking break-induced replication shows that it stalls at roadblocks.</a> Nature. 590 (7847), 655-659 (2021).</li><li>Liu, L., Sugawara, N., Malkova, A., Haber, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determining+the+kinetics+of+break-induced+replication+(BIR)+by+the+assay+for+monitoring+BIR+elongation+rate+(AMBER).">Determining the kinetics of break-induced replication (BIR) by the assay for monitoring BIR elongation rate (AMBER).</a> Methods in Enzymology. 661, 139-154 (2021).</li><li>Pham, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+restraining+break-induced+replication+at+two-ended+DNA+double-strand+breaks.">Mechanisms restraining break-induced replication at two-ended DNA double-strand breaks.</a> The EMBO Journal. 40 (10), 104847 (2021).</li><li>Cimino, G. D., Gamper, H. B., Isaacs, S. T., Hearst, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Psoralens+as+photoactive+probes+of+nucleic+acid+structure+and+function:+Organic+chemistry,+photochemistry,+and+biochemistry.">Psoralens as photoactive probes of nucleic acid structure and function: Organic chemistry, photochemistry, and biochemistry.</a> Annual Review of Biochemistry. 54 (1), 1151-1193 (1985).</li><li>Yeung, A. T., Dinehart, W. J., Jones, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alkali+reversal+of+psoralen+cross-link+for+the+targeted+delivery+of+psoralen+monoadduct+lesion.">Alkali reversal of psoralen cross-link for the targeted delivery of psoralen monoadduct lesion.</a> Biochemistry. 27 (17), 6332-6338 (1988).</li><li>Shi, Y. B., Spielmann, H. P., Hearst, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Base-catalyzed+reversal+of+a+psoralen-DNA+cross-link.">Base-catalyzed reversal of a psoralen-DNA cross-link.</a> Biochemistry. 27 (14), 5174-5178 (1988).</li><li>Prakash, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Yeast+Mph1+helicase+dissociates+Rad51-made+D-loops:+Implications+for+crossover+control+in+mitotic+recombination.">Yeast Mph1 helicase dissociates Rad51-made D-loops: Implications for crossover control in mitotic recombination.</a> Genes &amp; Development. 23 (1), 67-79 (2009).</li><li>Liu, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Srs2+promotes+synthesis-dependent+strand+annealing+by+disrupting+DNA+polymerase+&#948;-extending+D-loops.">Srs2 promotes synthesis-dependent strand annealing by disrupting DNA polymerase &#948;-extending D-loops.</a> eLife. 6, 22195 (2017).</li><li>Fasching, C. L., Cejka, P., Kowalczykowski, S. C., Heyer, W. -. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Top3-Rmi1+dissolve+Rad51-mediated+D+loops+by+a+topoisomerase-based+mechanism.">Top3-Rmi1 dissolve Rad51-mediated D loops by a topoisomerase-based mechanism.</a> Molecular Cell. 57 (4), 595-606 (2015).</li><li>Shah, S. S., Hartono, S. R., Ch&#233;din, F., Heyer, W. -. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bisulfite+treatment+and+single-molecule+real-time+sequencing+reveal+D-loop+length,+position,+and+distribution.">Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution.</a> eLife. 9, 59111 (2020).</li></ol>

The assays presented allow for the detection of nascent and extended D-loops (DLC assay), D-loop extension (DLE assay), and BIR product formation (DLE assay with no hybridizing oligonucleotides) using proximity ligation and qPCR. ChIP-qPCR of Rad51 to sites distant from the DSB has previously been used as a proxy for Rad51-mediated homology search and D-loop formation. However, this ChIP-qPCR signal is independent of the sequence homology between the break site and a potential donor, as well as the Rad51-associated facto...

Homologous recombination (HR) is a high-fidelity mechanism of repair of DNA double-stranded breaks (DSBs), inter-strand cross-links, and ssDNA gaps, as well as a pathway for DNA damage tolerance. HR differs from error-prone pathways for DNA damage repair/tolerance, such as non-homologous end-joining (NHEJ) and translesion synthesis, in that it utilizes an intact, homologous duplex DNA as a donor to template the repair event. Moreover, many of the key intermediates in the HR pathway are reversible, allowing for exquisite regulation of the individual pathway steps. During the S, G2, and M phases of the cell cycle, HR competes with NHEJ for the repair of the two-ended DSBs1. In addition, HR is essential to DNA replication for the repair of replication-associated DNA damage, including ssDNA gaps and one-sided DSBs, and as a mechanism of DNA lesion bypass2.
A critical intermediate in the HR pathway is the displacement loop, or D-loop (Figure 1). Following end resection, the central recombinase in the reaction, Rad51, loads onto the newly resected ssDNA of the broken molecule, forming a helical filament2. Rad51 then carries out a homology search to identify a suitable homologous donor, typically the sister chromatid in somatic cells. The D-loop is formed when the Rad51-ssDNA filament invades a homologous duplex DNA, which leads to the Watson-Crick base pairing of the broken strand with the complementary strand of the donor, displacing the opposite donor strand. Extension of the 3&#39; end of the broken strand by a DNA polymerase replaces the bases that were lost during the DNA damage event and promotes resolution of the extended D-loop intermediate into a dsDNA product through the synthesis-dependent strand annealing (SDSA), the double-Holliday junction (dHJ), or the break-induced replication (BIR) HR sub-pathways.
Assays that physically monitor the intermediates in the HR pathway permit the analysis of the genetic requirements for each step (i.e., pathway analysis). DSB formation, end resection, dHJs, BIR replication bubbles, and HR products are readily observed by Southern blotting3,4,5,6,7. Yet, Southern blotting fails to report on nascent and extended D-loops, and, thus, an alternative method to reliably measure these joint molecules is required4,8,9. One widely used strategy to analyze nascent D-loop formation is chromatin-immunoprecipitation (ChIP) of Rad51 coupled with quantitative PCR (qPCR)10,11. However, Rad51 association with dsDNA as measured by ChIP-qPCR is independent of sequence homology and the Rad51 accessory factor Rad5410,11. In contrast, an appreciable signal using the method of D-loop analysis presented here, called the D-loop capture (DLC) assay, depends on DSB formation, sequence homology, Rad51, and the Rad51 accessory proteins Rad52 and Rad548. The finding that Saccharomyces cerevisiae Rad51-promoted D-loop formation depends on Rad54 in vivo is&#160;in agreement with numerous in vitro reconstitution experiments indicating that Rad54 is required for homology search and D-loop formation by budding yeast Rad518,12,13,14,15.
Current approaches to measuring D-loop extension, primarily through semi-quantitative PCR, are similarly problematic. A typical PCR-based assay to detect D-loop extension amplifies a unique sequence, resulting from recombination between a break site and an ectopic donor and the subsequent recombination-associated DNA synthesis, via a primer upstream of the region of homology on the broken strand and another primer downstream of the region of homology on the donor strand. Using this method, the detection of recombination-associated DNA synthesis requires the non-essential Pol &#948; processivity factor Pol3216. This finding conflicts with the observation that POL32 deletion has only a mild effect on gene conversion in vivo17. Moreover, these PCR-based assays fail to temporally resolve D-loop extension and BIR product formation, suggesting that the signal results from dsDNA products rather than ssDNA intermediates17,18,19. The D-loop extension (DLE) assay was recently developed to address these discrepancies. The DLE assay quantifies recombination-associated DNA synthesis at a site ~400 base pairs (bp) downstream of the initial 3&#39; invading end9. By this method, D-loop extension is independent of Pol32 and is detectable within 4 h post-DSB induction, whereas BIR products are first observed at 6 h. Indeed, a recent publication from the Haber and Malkova laboratories noted that using this method of preparation of genomic DNA singularly results in ssDNA preservation9,20.
Here, the DLC and DLE assays are described in detail. These assays rely on proximity ligation to detect nascent and extended D-loops in S. cerevisiae (Figure 2)8,9. BIR products can be quantified using this same assay system. For both assays, DSB formation at an HO endonuclease cut site located at the URA3 locus on chromosome (Chr.) V is induced by the expression of the HO endonuclease under the control of a galactose-inducible promoter. Rad51-mediated DNA strand invasion leads to nascent D-loop formation at the site of an ectopic donor located at the LYS2 locus on Chr. II. As the right side of the DSB lacks homology to the donor, repair via SDSA and dHJ formation is not feasible. Initial repair of the DSB by BIR is possible, but the formation of viable products is inhibited by the presence of the centromere21. This deliberate design prevents productive DSB repair, thereby avoiding the resumption of growth by cells with repaired DBSs, which could otherwise overtake the culture during the time course analysis.
In the DLC assay, psoralen crosslinking of the two strands of the heteroduplex DNA within the D-loop preserves the recombination intermediate. Following restriction enzyme site restoration on the broken (resected) strand and digestion, the crosslinking allows for ligation of the unique sequences upstream of the homologous broken and donor DNAs. Using qPCR, the level of chimeric DNA molecule present in each sample is quantified. In the DLE assay, crosslinking is not required, and restriction enzyme site restoration and digestion followed by intramolecular ligation instead link the 5&#39; end of the broken molecule to the newly extended 3&#39; end. Again, qPCR is used to quantify the relative amounts of this chimeric product in each sample. In the absence of restriction enzyme site restoration, the DLE assay reports on the relative levels of the BIR (dsDNA) product that is formed following D-loop extension.
Representative results for each assay using a wild type strain are shown, and readers are referred to Piazza et al.8 and Piazza et al.9 for the use of these assays for the analysis of recombination mutants8,9. The intent of this contribution is to enable other laboratories to adopt the DLC and DLE assays, and support for them is available upon request.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1. Pre-growth, DSB induction, and sample collection</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>15 and 50 mL conical tubes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL glass culture tubes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>250 mL, 500 mL, or 1 L flasks</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>60 mm x 15 mm optically clear petri dishes with flat bottom</td>
			<td></td>
			<td></td>
			<td>Suggested: Corning, Catalog Number 430166; or Genesee Scientific, Catalog Number 32-150G</td>
		</tr>
		<tr>
			<td>Benchtop centrifuge with 15 and 50 mL conical tube adapters</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Benchtop orbital shaker or tube rotator/revolver</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Rotator</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>UV crosslinker or light box with 365 nm UV bulbs set atop an orbital shaker</td>
			<td></td>
			<td></td>
			<td>Suggested: Spectrolinker XL-1500 UV Crosslinker (Spectronics Corporation) or Vilbert Lourmat BLX-365 BIO-LINK, Catalog Number 611110831</td>
		</tr>
		<tr>
			<td>Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>60% w/w sodium DL-lactate syrup</td>
			<td>Sigma-Aldrich</td>
			<td>L1375</td>
			<td>For media preparation</td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Fisher</td>
			<td>BP1423500</td>
			<td>For media preparation</td>
		</tr>
		<tr>
			<td>Bacto peptone</td>
			<td>BD Difco</td>
			<td>211840</td>
			<td>For media preparation</td>
		</tr>
		<tr>
			<td>Bacto yeast extract</td>
			<td>BD Difco</td>
			<td>212750</td>
			<td>For media preparation</td>
		</tr>
		<tr>
			<td>D-(+)-glucose</td>
			<td>BD Difco</td>
			<td>0155-17-4</td>
			<td>For media preparation</td>
		</tr>
		<tr>
			<td>Trioxsalen</td>
			<td>Sigma-Aldrich</td>
			<td>T6137</td>
			<td>For psoralen cross-linking</td>
		</tr>
		<tr>
			<td>2. Spheroplasting, lysis, and restriction enzyme site restoration</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Supplies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 mL microcentrifuge tubes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Dry bath</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Liquid nitrogen or dry ice/ethanol</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Refrigerated microcentrifuge or microcentrifuge</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>10X restriction enzyme (CutSmart) buffer (500 mM potassium acetate, 200 mM Tris-acetate, 100 mM magnesium acetate, 1 mg/mL BSA, pH 7.8-8.0)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Zymolyase 100T</td>
			<td>US Biological</td>
			<td>Z1004</td>
			<td>For spheroplasting</td>
		</tr>
		<tr>
			<td>3. Restriction enzyme digest and intramolecular ligation</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Supplies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Water bath</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>EcoRI-HF</td>
			<td>New England Biolabs</td>
			<td>R3101</td>
			<td>Restriction enzyme digest for DLC assay</td>
		</tr>
		<tr>
			<td>HindIII-HF</td>
			<td>New England Biolabs</td>
			<td>R3104</td>
			<td>Restriction enzyme digest for DLE assay</td>
		</tr>
		<tr>
			<td>T4 DNA ligase</td>
			<td>New England Biolabs</td>
			<td>M0202</td>
			<td>Intramolecular ligation</td>
		</tr>
		<tr>
			<td>4. DNA purification</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Supplies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 and 2 mL microcentrifuge tubes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Phenol/chloroform/isoamyl alcohol (P/C/IA) at 25:24:1</td>
			<td>Sigma-Aldrich</td>
			<td>P2069</td>
			<td>DNA purification</td>
		</tr>
		<tr>
			<td>5. Psoralen cross-link reversal</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Supplies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Thermocycler/PCR machine</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>6. qPCR</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Supplies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Lightcycler 480</td>
			<td>Roche</td>
			<td>5015278001</td>
			<td>qPCR machine used by the authors</td>
		</tr>
		<tr>
			<td>Lightcycler 96</td>
			<td>Roche</td>
			<td>5815916001</td>
			<td>qPCR machine used by the authors</td>
		</tr>
		<tr>
			<td>Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>LightCycler 480 96-Well Plate, white</td>
			<td>Roche</td>
			<td>4729692001</td>
			<td>96-well plates for qPCR</td>
		</tr>
		<tr>
			<td>SsoAdvanced Universal SYBR Green Super Mix</td>
			<td>BioRad</td>
			<td>1725271</td>
			<td>qPCR kit used by the authors</td>
		</tr>
		<tr>
			<td>SYBR Green I Master Mix</td>
			<td>Roche</td>
			<td>4707516001</td>
			<td>qPCR kit used by the authors</td>
		</tr>
	</tbody>
</table>

detection of homologous recombination intermediates via proximity ligation and quantitative pcr in saccharomyces cerevisiae

DNA damage, including DNA double-stranded breaks and inter-strand cross-links, incurred during the S and G2 phases of the cell cycle can be repaired by homologous recombination (HR). In addition, HR represents an important mechanism of replication fork rescue following stalling or collapse. The regulation of the many reversible and irreversible steps of this complex pathway promotes its fidelity. The physical analysis of the recombination intermediates formed during HR enables the characterization of these controls by various nucleoprotein factors and their interactors. Though there are well-established methods to assay specific events and intermediates in the recombination pathway, the detection of D-loop formation and extension, two critical steps in this pathway, has proved challenging until recently. Here, efficient methods for detecting key events in the HR pathway, namely DNA double-stranded break formation, D-loop formation, D-loop extension, and the formation of products via break-induced replication (BIR) in Saccharomyces cerevisiae are described. These assays detect their relevant recombination intermediates and products with high sensitivity and are independent of cellular viability. The detection of D-loops, D-loop extension, and the BIR product is based on proximity ligation. Together, these assays allow for the study of the kinetics of HR at the population level to finely address the functions of HR proteins and regulators at significant steps in the pathway.

DLC assay 
The DLC assay detects both nascent and extended D-loops formed by the invasion of a site-specific DSB into a single donor (Figure 2). Psoralen crosslinking physically links the broken strand and the donor via the heteroduplex DNA within the D-loop. Restriction enzyme site restoration with a long, hybridizing oligo on the resected strand of the break allows for restriction enzyme cleavage, followed by ligation of the broken strand to the proximal dono...

Watch this Scientific Journal Video about Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae at JoVE.com

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

The D-loop capture (DLC) and D-loop extension (DLE) assays utilize the principle of proximity ligation together with quantitative PCR to quantify D-loop formation, D-loop extension, and product formation at the site of an inducible double-stranded break in Saccharomyces cerevisiae.

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

DNA damage, including DNA double-stranded breaks and inter-strand cross-links, incurred during the S and G2 phases of the cell cycle can be repaired by ...

The D-loop capture and extension assays are the first to allow unbiased and direct quantitation of the D-loop formation and extension steps during homologous recombination in mitotically growing yeast cells. This viability independent technique allows the studying of proteins in D-loop metabolism that would not otherwise be possible to disentangle from later roles, just looking at BIR products. In the future, we envision transitioning these assays to human cells to better understand the role of key proteins, including BRCA2 and the bloom and Warner kilo cases in homologous recombination.Begin by centrifuging the samples for five minutes. Resuspend the pellet in 2.5 milliliters of 1x psoralen solution and transfer it to a 60 by 15 millimeter Petri dish. For no crosslinking control, resuspend the pellet in 2.5 milliliters of TE1 solution.Next, set the UV light source the top in orbital shaker, set at 50 RPM. To cross-link the samples using a UV cross-linker with 365 nanometer long wave bulbs. Position the Petri dishes one to two centimeters below the UV light source for 10 minutes with gentle shaking on a pre chilled plastic or plexiglass plate.Then transfer the sample into a new 15 milliliter tube. Rinse the Petri dish with 2.5 milliliters of TE1 solution and add this to the tube. Centrifuge the samples for five minutes.Discard the supernatant and store the pellet at minus 20 degrees Celsius. Place the samples on ice for thawing. Simultaneously, preheat a dry bath to 30 degrees Celsius.Resuspend the samples in one milliliter of spheroplasting buffer and transfer them to 1.5 milliliter micro centrifuge tubes. Then add 3.5 microliters of zymolyase solution and mix gently by tapping. Incubate at 30 degrees Celsius for 15 minutes.And then place the tubes on ice. Centrifuge for three minutes and place the samples on ice. Wash the samples thrice in one milliliter spheroplasting buffer and centrifuge the samples for three minutes.Resuspend the samples in one milliliter of cold restriction enzyme buffer. Centrifuge for three minutes and place the samples on ice. Repeat the wash once.Resuspend the samples in one milliliter of cold 1x restriction enzyme buffer. Split the sample equally into two. Centrifuge the samples for three minutes at 16, 000 G at four degree Celsius.Resuspend one tube from each sample in 180 microliters of 1.4x restriction enzyme buffer with hybridizing oligos and another tube in 180 microliters of 1.4x restriction enzyme buffer without hybridizing oligos. Snap freeze the samples in liquid nitrogen. Thaw the samples on ice.Preheat one dry bath to 65 and another to 37 degrees Celsius. Aliquot 36 microliters of the sample into a new micro centrifuge tube and four microliters of 1%SDS and mixed by gently tapping the side of the tube. Incubate at 65 degrees Celsius for 15 minutes with gentle tapping every five minutes.Place samples on ice immediately following the incubation. Add 4.5 microliters of 10%Triton X-100 and mixed by pipetting. Add 20 to 50 units of high fidelity EcoR1 or HindIII restriction enzyme to each sample.And incubate at 37 degrees Celsius for one hour with gentle agitation every 20 to 30 minutes. During this time, preheated dry bath to 55 degrees Celsius and a water bath to 16 degrees Celsius. Add 8.6 microliters of 10%SDS to each sample and mix by pipetting and tapping.Incubate at 55 degree Celsius for 10 minutes. Add 80 microliters of 10%Triton X-100 to each sample and mix by pipetting. Add 660 microliters of 1x ligation buffer without ATP, One millimolar ATP at pH 8.0 and eight units of T4 DNA ligase to each sample, and mix gently by inversion.Incubate 16 degrees Celsius for 1.5 hours with an inversion every 30 minutes. Place the samples on ice immediately following the incubation. Following DNA purification as described in the protocol, use two microliters of purified DNA to set up a 20 microliter qPCR reaction according to the manufacturer's instructions.For each sample, set up five control reactions and one quantification reaction and run them in duplicate. DLC assay analysis two hours after double stranded break or DSB induction showed that psoralen cross-linking is critical and efficiency depends on the time between sample collection and qPCR. ARG4 Cp values values were similar between the cross-linked samples but lower for the without cross-linking sample since DNA without cross-links amplifies more efficiently.For all samples, the intermolecular ligation qPCR control was within the range. Robust DSB induction was evidenced by a low qPCR signal for the control that amplifies across the HO endonuclease recognition site. Similar results were observed for the EcoR1 qPCR control.DLC signal with hybridizing oligo was calculated by normalizing to the intermolecular ligation control. DLE assay analysis performed at six hours post DSB induction showed that ARG4 CP values were similar between the with and without hybridizing oligos sample. The intermolecular ligation qPCR control revealed an acceptable signal for the with and without hybridizing oligos sample but a lower signal for the failed sample.In all three samples, there was robust DSB induction. Since HindIII cleavage depends on restriction enzyme site restoration by the hybridizing oligo. There was a significant difference in amplification across the HindIII cleavage site on the resected strand between the width and without oligo samples.A smaller difference in amplification across the site on the extended strand was observed because here HindIII cleavage also depends on extension. The samples and buffer need to be kept cold at all times. Samples must be flash frozen following resuspension in 1.4x cold restriction enzyme buffer with or without hybridizing oligos.The effects downstream of D-loop formation and extension on product formation may be studied using Southern blotting or genetic endpoint assays. Effects on homology search may be investigated using high CP.Chromatin-immunoprecipitation can provide information on recruitment of a protein of interest.

Research

JoVE Journal

Genetics

Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts

Human signal transducer and activator of transcription 3 (STAT3) is one of many genes containing a tandem splicing site. Alternative donor splice sites 3 ...

Detection of microRNA Expression in Peritoneal Membrane of Rats Using Quantitative Real-time PCR

MicroRNAs (miRNAs) are small noncoding RNAs that regulate messenger RNA expression post-transcriptionally. The miRNA expression profile has been ...

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral ...

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide mapping of protein-DNA interactions is critical for understanding gene regulation, chromatin remodeling, and other chromatin-resident ...

Chromatin Immunoprecipitation (ChIP) of Histone Modifications from Saccharomyces cerevisiae

Chromatin Immunoprecipitation ChIP of Histone Modifications from Saccharomyces cerevisiae

Histone post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation, are dynamically regulated by a series of enzymes ...

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene ...

Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity

Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity

Global defects in RNA polymerase II transcription might be overlooked by transcriptomic studies analyzing steady-state RNA. Indeed, the global decrease in ...

Identification of Homologous Recombination Events in Mouse Embryonic Stem Cells Using Southern Blotting and Polymerase Chain Reaction

Relative to the issues of off-target effects and the difficulty of inserting a long DNA fragment in the application of designer nucleases for genome ...

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

A central goal of modern genetics is to understand how and why organisms in the wild differ in phenotype. To date, the field has advanced largely on the ...

Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Antisense Protein (ASP) RNA Transcripts in Patients by Strand-Specific RT-PCR

Detection of Human Immunodeficiency Virus Type 1 HIV-1 Antisense Protein ASP RNA Transcripts in Patients by Strand-Specific RT-PCR

In retroviruses, antisense transcription has been described in both human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus 1 (HTLV-1). ...