Name: chromatin spread preparations for the analysis of mouse oocyte progression from prophase to metaphase ii
Uploaded: 2018-02-26T13:00:00
Description: Watch this Scientific Journal Video about Chromatin Spread Preparations for the Analysis of Mouse Oocyte Progression from Prophase to Metaphase II at JoVE.com

This work was supported by NIGMS (R01GM11755) to P.W.J and by a training grant fellowship from the National Cancer Institute (NIH) (CA009110) to G.H. and J.H.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Johns Hopkins University. Experiments were performed on wild-type C57BL/6J mice.
1. Harvesting Fetal or Neonatal Ovaries and Preparation of Prophase Chromatin Spreads
<ol>
	<li>To extract embryos at 14.5&#8211;19.5 days post-coitum (dpc) sacrifice the pregnant females via cervical dislocation or CO2 asphyxiation according to IACUC guidelines. 
	NOTE: For postnatal day 1...

<ol>
	<li>Morelli, M. A., Cohen, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Not+all+germ+cells+are+created+equal:+aspects+of+sexual+dimorphism+in+mammalian+meiosis.">Not all germ cells are created equal: aspects of sexual dimorphism in mammalian meiosis.</a> Reproduction. 130 (6), 761-781 (2005).</li><li>Keeney, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spo11+and+the+Formation+of+DNA+Double-Strand+Breaks+in+Meiosis.">Spo11 and the Formation of DNA Double-Strand Breaks in Meiosis.</a> Genome Dyn Stab. 2, 81-123 (2008).</li><li>Zickler, D., Kleckner, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombination,+Pairing,+and+Synapsis+of+Homologs+during+Meiosis.">Recombination, Pairing, and Synapsis of Homologs during Meiosis.</a> Cold Spring Harb Perspect Biol. 7 (6), (2015).</li><li>Vries, F. 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=Mouse+Sycp1+functions+in+synaptonemal+complex+assembly,+meiotic+recombination,+and+XY+body+formation.">Mouse Sycp1 functions in synaptonemal complex assembly, meiotic recombination, and XY body formation.</a> Genes Dev. 19 (11), 1376-1389 (2005).</li><li>Baker, S. M., 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=Involvement+of+mouse+Mlh1+in+DNA+mismatch+repair+and+meiotic+crossing+over.">Involvement of mouse Mlh1 in DNA mismatch repair and meiotic crossing over.</a> Nat Genet. 13 (3), 336-342 (1996).</li><li>Lipkin, S. M., 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=Meiotic+arrest+and+aneuploidy+in+MLH3-deficient+mice.">Meiotic arrest and aneuploidy in MLH3-deficient mice.</a> Nat Genet. 31 (4), 385-390 (2002).</li><li>Kolas, N. K., 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=Localization+of+MMR+proteins+on+meiotic+chromosomes+in+mice+indicates+distinct+functions+during+prophase+I.">Localization of MMR proteins on meiotic chromosomes in mice indicates distinct functions during prophase I.</a> J Cell Biol. 171 (3), 447-458 (2005).</li><li>Rankin, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complex+elaboration:+making+sense+of+meiotic+cohesin+dynamics.">Complex elaboration: making sense of meiotic cohesin dynamics.</a> FEBS Journal. 282 (13), 2426-2443 (2015).</li><li>Lee, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Roles+of+Cohesin+and+Condensin+in+Chromosome+Dynamics+During+Mammalian+Meiosis.">Roles of Cohesin and Condensin in Chromosome Dynamics During Mammalian Meiosis.</a> J. Reprod Dev. 59 (5), 431-436 (2013).</li><li>Verver, D. E., Hwang, G. H., Jordan, P. W., Hamer, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resolving+complex+chromosome+structures+during+meiosis:+versatile+deployment+of+Smc5/6.">Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6.</a> Chromosoma. 125 (1), 15-27 (2016).</li><li>Hopkins, 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=Meiosis-specific+cohesin+component,+Stag3+is+essential+for+maintaining+centromere+chromatid+cohesion,+and+required+for+DNA+repair+and+synapsis+between+homologous+chromosomes.">Meiosis-specific cohesin component, Stag3 is essential for maintaining centromere chromatid cohesion, and required for DNA repair and synapsis between homologous chromosomes.</a> PLoS Genet. 10 (7), e1004413 (2014).</li><li>Hwang, G., 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=SMC5/6+is+required+for+the+formation+of+segregation-competent+bivalent+chromosomes+during+meiosis+I+in+mouse+oocytes.">SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes.</a> Development. 144 (9), 1648-1660 (2017).</li><li>Kota, S. K., Feil, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epigenetic+transitions+in+germ+cell+development+and+meiosis.">Epigenetic transitions in germ cell development and meiosis.</a> Dev Cell. 19 (5), 675-686 (2010).</li><li>Taketo, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microspread+ovarian+cell+preparations+for+the+analysis+of+meiotic+prophase+progression+in+oocytes+with+improved+recovery+by+cytospin+centrifugation.">Microspread ovarian cell preparations for the analysis of meiotic prophase progression in oocytes with improved recovery by cytospin centrifugation.</a> Methods Mol Biol. 825 (1), 173-181 (2012).</li><li>Sun, X., Cohen, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studying+recombination+in+mouse+oocytes.">Studying recombination in mouse oocytes.</a> Methods Mol Biol. 957 (1), 1-18 (2013).</li><li>Kim, J. H., Ishiguro, K., Kudo, N., Watanabe, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studying+meiosis-specific+cohesins+in+mouse+embryonic+oocytes.">Studying meiosis-specific cohesins in mouse embryonic oocytes.</a> Methods Mol Biol. 957 (1), 47-57 (2013).</li><li>Susiarjo, M., Rubio, C., Hunt, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+mammalian+female+meiosis.">Analyzing mammalian female meiosis.</a> Methods Mol Biol. 558, 339-354 (2009).</li><li>Hassold, T., Hunt, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=To+err+(meiotically)+is+human:+the+genesis+of+human+aneuploidy.">To err (meiotically) is human: the genesis of human aneuploidy.</a> Nat Rev Genet. 2 (4), 280-291 (2001).</li><li>Hassold, T., Hall, H., Hunt, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+origin+of+human+aneuploidy:+where+we+have+been,+where+we+are+going.">The origin of human aneuploidy: where we have been, where we are going.</a> Hum Mol Genet. 16, R203-R208 (2007).</li><li>Pincus, G., Enzmann, E. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Comparative+Behavior+of+Mammalian+Eggs+In+vivo+and+In+vitro:+I.+The+Activation+of+Ovarian+Eggs.">The Comparative Behavior of Mammalian Eggs In vivo and In vitro: I. The Activation of Ovarian Eggs.</a> J Exp Med. 62 (5), 665-675 (1935).</li><li>Chambon, J. 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Chromatin spread preparations allow researchers to chronologically study female mammalian meiosis and the dynamic localization of proteins involved. The embryonic and neonatal chromatin spreads allow for close analysis of events throughout meiotic prophase. Metaphase I and metaphase II chromatin spreads can be used to distinguish single sister chromatids from paired sisters and paired homologous chromosomes, as well as assess ploidy. By comparison, the protocol described here can be advantageous compared to whole oocyte ...

During spermatogenesis, large semi-synchronous waves of meiotic germ cells are rapidly and continuously replenished in the testis at the onset of puberty and throughout adulthood1. In contrast to males, meiosis in females is initiated solely during fetal development. Following birth, oocytes remain arrested in a prolonged dictyate stage of prophase I with an intact germinal vesicle (GV; nuclear envelope) until puberty. At the onset of puberty, a subset of oocytes are cyclically selected to undergo growth and maturation, marking the initiation of meiotic resumption. Meiotic resumption in fully-grown oocytes is manifested by the disappearance of the GV in a process known as germinal vesicle breakdown (GVBD). The oocyte then undergoes chromosome condensation and segregation, followed by polar body extrusion. Oocytes become arrested upon progression to MII and are stimulated to complete the second and final meiotic division only after fertilization.
Female fertility is highly dependent on the success of meiotic prophase I progression. Key to this is formation of a physical linkage between homologous chromosomes known as the chiasmata, which is mediated by repair of induced DNA double strand breaks (DSBs) via crossover recombination2. This process occurs within the context of a dynamic protein-rich scaffold known as the synaptonemal complex (SC) that forms between homologous chromosomes to facilitate their synapsis3. The SC is a zipper-like tripartite structure that consists of two parallel lateral elements connected by central region proteins that holds homologs together throughout ongoing DNA repair. Prior to synapsis, precursors of the lateral elements, called axial elements, form between sister chromatids. Synaptonemal complex proteins such as SYCP2 and SYCP3 form axial elements that colocalize to the sister-chromatid cohesion axes during early prophase. These later serve as binding sites for the transverse filament protein, SYCP1, which facilitates central element assembly and synapsis between aligned homologs4. In mouse oocytes, complete synapsis is indicated by the presence of 20 completely overlapping SYCP3 and SYCP1 stretches, which can be visualized by using chromatin spread preparations. Synapsis is completed upon entry into the pachytene substage, whereby mature crossovers that are destined to form chiasmata between homologs are decorated with mutL homolog (MLH1/3) dimers to promote their accurate processing5,6,7. The structural maintenance of chromosomes (SMC) complexes, including cohesin, condensin, and the SMC5/6 complex, are important for the regulation of chromosome dynamics and structure throughout meiosis8,9,10,11,12. Collectively, these events ensure proper bi-orientation of homologous chromosomes to opposing spindle poles following disassembly of the SC.
The meiotic cell cycle is a powerful model to examine the roles of various proteins in genome maintenance due to the programmed induction and subsequent repair of DNA DSBs. Furthermore, mammalian meiosis is also a relevant model for the study of epigenetic modifications and imprinting13. However, it is technically difficult to assess these events during female meiosis, which takes place in fetal and neonatal ovaries in mammals (Figure 1). Prophase I can be divided into 5 substages: leptonema, zygonema, pachynema, diplonema and dictyate. Herein, we describe how to isolate and distinguish between fetal and neonatal ovaries and testes (Figure 2). Adapted from previously described methods, this manuscript also outlines a protocol (step 1) with video demonstration for preparation of female meiotic prophase I chromatin spreads14,15,16,17. When coupled with immunolabelling, as described in steps 6-7, this protocol enables detailed microscopic analysis of prophase I events in oocytes.
Oogenesis is error-prone, and chromosome missegregation events during the first meiotic division represent the most common source of genetic disease in progeny18,19. In this manuscript (protocol step 2), we describe a protocol in which mature GV-staged oocytes are extracted from primed ovaries of adult female mice. Under supportive conditions, fully-grown oocytes undergo luteinizing hormone-independent resumption of meiosis following isolation and culture20. Following meiotic resumption, oocytes progress through meiosis I, then arrest at metaphase II. Oocytes remain arrested at metaphase II, unless fertilized. In steps 2&#8211;5, we adapt previously reported protocols with video demonstration to describe how to collect, culture and prepare MI and MII oocytes for chromatin spread preparations21. This chromatin spreading technique allows for clear immunolabelling of proteins associated with chromosomes. Furthermore, this protocol can also be used to distinguish between bivalent and univalent chromosomes, and can further resolve single sister chromatids to facilitate assessment of oocyte ploidy. Therefore, in addition to revealing localization patterns of meiotic proteins, this protocol can also serve as an invaluable tool for elucidating potential causes of chromosome missegregation during MI and MII.

<table>
	<tbody>
		<tr>
			<td>10X Phosphate buffered saline (PBS) pH 7.4</td>
			<td>Quality Biological</td>
			<td>119-069-161</td>
			<td></td>
		</tr>
		<tr>
			<td>60 mm x 15 mm petri dishes</td>
			<td>Denville</td>
			<td>T1106</td>
			<td></td>
		</tr>
		<tr>
			<td>35mm x 12mm petri dishes</td>
			<td>Denville</td>
			<td>T1103</td>
			<td></td>
		</tr>
		<tr>
			<td>Fine forceps</td>
			<td>VWR</td>
			<td>300-050</td>
			<td></td>
		</tr>
		<tr>
			<td>Micro dissection scissors</td>
			<td>Ted Pella</td>
			<td>1340</td>
			<td></td>
		</tr>
		<tr>
			<td>Dissecting&#160;scissors, sharp tip, 41/2&#34;</td>
			<td>VWR</td>
			<td>82027-578</td>
			<td></td>
		</tr>
		<tr>
			<td>Watch glass square 1 5/8</td>
			<td>Carolina Biological Supply Company</td>
			<td>742300</td>
			<td>Autoclave before each use</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sigma</td>
			<td>S8501</td>
			<td></td>
		</tr>
		<tr>
			<td>Trisodium Citrate Dihydrate</td>
			<td>Sigma</td>
			<td>S1804</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma</td>
			<td>E6758</td>
			<td></td>
		</tr>
		<tr>
			<td>Trizma Base</td>
			<td>Sigma</td>
			<td>T1503</td>
			<td></td>
		</tr>
		<tr>
			<td>1,4-Dithiothreitol (DTT)</td>
			<td>Sigma</td>
			<td>646563</td>
			<td>Add to hypotonic buffer immediately before use</td>
		</tr>
		<tr>
			<td>50x Protease Inhibitor</td>
			<td>Roche</td>
			<td>11873580001</td>
			<td>Add to hypotonic buffer immediately before use</td>
		</tr>
		<tr>
			<td>Turberculin syringe with needle (1cc, 27 G x 1/2 in)</td>
			<td>Becton, Dickinson (BD)</td>
			<td>309623</td>
			<td></td>
		</tr>
		<tr>
			<td>Gold seal ultra frost glass slides (25X75mm, 1mm thick)</td>
			<td>Thermo</td>
			<td>3063-002</td>
			<td></td>
		</tr>
		<tr>
			<td>Super PAP pen, large (liquid blocker)</td>
			<td>Electron Microscopy Sciences (EMS)</td>
			<td>71310</td>
			<td></td>
		</tr>
		<tr>
			<td>16% Paraformaldehyde aqueous</td>
			<td>Electron Microscopy Sciences (EMS)</td>
			<td>15710</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma</td>
			<td>T8787</td>
			<td>Detergent in manuscript</td>
		</tr>
		<tr>
			<td>Immuno stain moisture chamber</td>
			<td>Evergreen</td>
			<td>240-9020-Z10</td>
			<td></td>
		</tr>
		<tr>
			<td>Coplin jars</td>
			<td>Fisher</td>
			<td>08-815</td>
			<td></td>
		</tr>
		<tr>
			<td>Photo-flo 200</td>
			<td>Electron Microscopy Sciences (EMS)</td>
			<td>74257</td>
			<td>Wetting agent in manuscript</td>
		</tr>
		<tr>
			<td>Pregnant mare serum gonadotropin (PMSG)</td>
			<td>Sigma</td>
			<td>G4877</td>
			<td>Store aliquots at -20C</td>
		</tr>
		<tr>
			<td>Human chorionic gonadotropin (HCG)</td>
			<td>Sigma</td>
			<td>C0434</td>
			<td>Store aliquots at -20C</td>
		</tr>
		<tr>
			<td>PYREX Spot Plates with nine concave cavities</td>
			<td>Fisher</td>
			<td>13-748B</td>
			<td>Autoclave before each use</td>
		</tr>
		<tr>
			<td>Glass capillary</td>
			<td>Fisher</td>
			<td>22260943</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Brand Parafilm M</td>
			<td>Sigma</td>
			<td>BR701501</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Latex rubber tubing (3.2 mm inner diameter x 6.4 mm outer diameter)</td>
			<td>Fisher</td>
			<td>14-178-5B</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Latex rubber tubing (6.4 mm inner diameter x 11.1 mm outer diameter)</td>
			<td>Fisher</td>
			<td>14-178-5D</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Flexible silicone rubber nosepiece, hard plastic mouthpiece and 15 inches of latex tubing</td>
			<td>Sigma</td>
			<td>A5177-5EA</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Mitutoyo micrometer head</td>
			<td>Mituoyo</td>
			<td>150-208</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Syringe 5 mL</td>
			<td>BD Biosciences</td>
			<td>309646</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Syringe filter 0.45 &#956;m filter</td>
			<td>Corning</td>
			<td>431220</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>Glass Pasteur Pipette 5 3/4&#34;</td>
			<td>Fisher</td>
			<td>13-678-6A</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>83 x 0.5 mm pipette tip</td>
			<td>Denville</td>
			<td>P3080</td>
			<td>For making oocyte collection needles</td>
		</tr>
		<tr>
			<td>&#945;-MEM</td>
			<td>Invitrogen</td>
			<td>11415049</td>
			<td></td>
		</tr>
		<tr>
			<td>Waymouth&#39;s media</td>
			<td>Life Technologies</td>
			<td>11220035</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Fisher</td>
			<td>A3160602</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA)</td>
			<td>Sigma</td>
			<td>A3311</td>
			<td>For oocyte culture media</td>
		</tr>
		<tr>
			<td>500ml filter units 0.22um</td>
			<td>Denville</td>
			<td>F5227</td>
			<td></td>
		</tr>
		<tr>
			<td>Hyaluronidase</td>
			<td>Sigma</td>
			<td>H3506</td>
			<td></td>
		</tr>
		<tr>
			<td>Tyrode&#8217;s solution</td>
			<td>Sigma</td>
			<td>T1788</td>
			<td>Store aliquots at -20C</td>
		</tr>
		<tr>
			<td>Horse serum</td>
			<td>Sigma</td>
			<td>H-1270</td>
			<td>For ADB/wash buffer</td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA)</td>
			<td>Sigma</td>
			<td>A1470</td>
			<td>For ADB/wash buffer</td>
		</tr>
		<tr>
			<td>VECTASHIELD antifade mounting medium with DAPI</td>
			<td>Vector Labs</td>
			<td>H-1200</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope cover slides (22mmx60mm)</td>
			<td>Fisher</td>
			<td>12-544-G</td>
			<td></td>
		</tr>
		<tr>
			<td>Clear nail polish</td>
			<td>Amazon</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Microscopes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SteREO Discovery.V8</td>
			<td>Zeiss</td>
			<td>495015-0001-000</td>
			<td></td>
		</tr>
		<tr>
			<td>Observer Z1</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Primary Antibodies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mouse anti-MLH1</td>
			<td>Life Technologies</td>
			<td>MA5-15431</td>
			<td>Dilution factor- 1:100</td>
		</tr>
		<tr>
			<td>Rabbit anti-SYCP1</td>
			<td>Life Technologies</td>
			<td>PA1-16763</td>
			<td>Dilution factor- 1:1000</td>
		</tr>
		<tr>
			<td>Goat anti-SCP3</td>
			<td>Santa Cruz</td>
			<td>sc-20845</td>
			<td>Dilution factor- 1:50</td>
		</tr>
		<tr>
			<td>Human anti-centromere protein</td>
			<td>Antibodies Incorporated</td>
			<td>15-235</td>
			<td>Dilution factor- 1:100</td>
		</tr>
		<tr>
			<td>Rabbit anti- TOPOII</td>
			<td>Abcam</td>
			<td>ab109524</td>
			<td>Dilution factor- 1:100</td>
		</tr>
		<tr>
			<td>Mouse anti-Histone H4 (di methyl K20, tri methyl K20)</td>
			<td>Abcam</td>
			<td>ab78517</td>
			<td>Dilution factor- 1:500</td>
		</tr>
		<tr>
			<td>Rabbit anti-Rec8</td>
			<td>Courtesy of Dr. Karen Schindler</td>
			<td>N/A</td>
			<td>Dilution factor- 1:10,000</td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Secondary Antibodies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Donkey anti-goat IgG (H+L) Alexa Fluor 568 conjugate</td>
			<td>Thermo-Fisher Scientific</td>
			<td>A-11057</td>
			<td>Dilution factor- 1:500</td>
		</tr>
		<tr>
			<td>Donkey anti-mouse IgG (H+L) Alexa Fluor 488 conjugate</td>
			<td>Thermo-Fisher Scientific</td>
			<td>A-21202</td>
			<td>Dilution factor- 1:500</td>
		</tr>
		<tr>
			<td>Donkey anti-rabbit IgG (H+L) Alexa Fluor 647 conjugate</td>
			<td>Thermo-Fisher Scientific</td>
			<td>A-31573</td>
			<td>Dilution factor- 1:500</td>
		</tr>
		<tr>
			<td>Goat anti-mouse IgG (H+L) Alexa Fluor 568 conjugate</td>
			<td>Thermo-Fisher Scientific</td>
			<td>A-11004</td>
			<td>Dilution factor- 1:500</td>
		</tr>
		<tr>
			<td>Goat anti-Human IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488</td>
			<td>Thermo-Fisher Scientific</td>
			<td>A-11013</td>
			<td>Dilution factor- 1:500</td>
		</tr>
		<tr>
			<td>Goat anti-rabbit IgG (H+L) Alexa Fluor 568 conjugate</td>
			<td>Thermo-Fisher Scientific</td>
			<td>A-11011</td>
			<td>Dilution factor- 1:500</td>
		</tr>
	</tbody>
</table>

chromatin spread preparations for the analysis of mouse oocyte progression from prophase to metaphase ii

Chromatin spread techniques have been widely used to assess the dynamic localization of various proteins during gametogenesis, particularly for spermatogenesis. These techniques allow for visualization of protein and DNA localization patterns during meiotic events such as homologous chromosome pairing, synapsis and DNA repair. While a few protocols have been described in the literature, general chromatin spread techniques using mammalian prophase oocytes are limited and difficult due to the timing of meiosis initiation in fetal ovaries. In comparison, prophase spermatocytes can be collected from juvenile male mice with higher yields without the need for microdissection. However, it is difficult to obtain a pure synchronized population of cells at specific stages due to the heterogeneity of meiotic and post-meiotic germ cell populations in the juvenile and adult testis. For later stages of meiosis, it is advantageous to assess oocytes undergoing meiosis I (MI) or meiosis II (MII), because groups of mature oocytes can be collected from adult female mice and stimulated to resume meiosis in culture. Here, methods for meiotic chromatin spread preparations using oocytes dissected from fetal, neonatal and adult ovaries are described with accompanying video demonstrations. Chromosome missegregation events in mammalian oocytes are frequent, particularly during MI. These techniques can be used to assess and characterize the effects of different mutations or environmental exposures during various stages of oogenesis. As there are distinct differences between oogenesis and spermatogenesis, the techniques described within are invaluable to increase our understanding of mammalian oogenesis and the sexually dimorphic features of chromosome and protein dynamics during meiosis.

We have described two techniques for visualizing and assessing meiotic chromosomes in oocytes. The first technique is catered toward assessing prophase progression in embryonic and neonatal ovaries. Prophase chromatin spread preparations are incredibly valuable for visualizing numerous dynamic processes during meiosis, including chromosome pairing, synapsis and desynapsis, homologous recombination, and epigenetic chromosome remodeling. Here, we have demonstrated the utility of this method...

Watch this Scientific Journal Video about Chromatin Spread Preparations for the Analysis of Mouse Oocyte Progression from Prophase to Metaphase II at JoVE.com

Chromatin Spread Preparations for the Analysis of Mouse Oocyte Progression from Prophase to Metaphase II

Oogenesis in mammals is known to be error-prone, particularly due to chromosome missegregation. This manuscript describes chromatin spread preparation methods for mouse prophase, metaphase I and II-staged oocytes. These fundamental techniques allow for the study of chromatin-bound proteins and chromosome morphology throughout mammalian oogenesis.

Chromatin spread techniques have been widely used to assess the dynamic localization of various proteins during gametogenesis, particularly for ...

The overall goal of this chromatin spread preparation is to chronologically visualize the dynamic localization patterns of chromatin-bound proteins and chromosome morphology of oocytes throughout mammalian oogenesis. This method can help answer key questions in the field of female reproductive biology, such as homologous chromosome pairing, synapsis, DNA repair, and meiotic chromosome segregation. The main advantage of this technique is that it allows for clear immunolabeling and visualization of proteins associated with chromosomes and assessment of oocyte ploidy.Oogenesis is error-prone, and chromosome missegregation often results in genetic disease. This method can be used to improve our understanding of maternal causes of aneuploidy and infertility. After euthanizing a female mouse that is 14 to 19 days post-coitum, make a V-shaped opening into the abdominopelvic cavity.Then remove the maternal uterine horn. Next separate the embryos from the placenta, and sacrifice the embryos by decapitation. Then transfer them to 35-millimeter Petri dish containing three milliliters of PBS at 37 degrees Celsius.Then move one pup to a separate dish also loaded with warm PBS. After euthanizing the fetus, make a cut along the ventral midline of the posterior half, along the anterior half below the forelimbs, and directly above the hindlimbs and tail. Next open the embryo's abdomen using 3.5-inch scissors.Using fine-tipped forceps, displace or remove the liver and loops of bowel, exposing the gonads. Now determine if the gonads are male or female gonads. The ovaries are located immediately below and behind the kidney, toward the posterior wall of the peritoneal cavity.Remove both ovaries using a pair of fine-tipped forceps, and transfer them into a small container containing PBS that is maintained at 37 degrees Celsius. Proceed quickly to collect the ovaries from all of the fetuses. Next in a new small container, completely immerse each separate set of ovaries in half a milliliter of freshly made hypo-extraction buffer.Let them incubate at 25 degrees Celsius for at least 15 minutes, but not more than 30 minutes. During the incubation, use a hydrophobic barrier PAP pen to draw two 22 by 22 millimeter squares on a clean glass slide. Prepare one slide for each set of ovaries.When the incubation is complete, add a 50-microliter drop of 100 millimolar sucrose to a clean slide, and transfer one pair of ovaries into the drop. Now use two 27-gauge needles to tease the ovaries and release the cells therein. With forceps, remove and discard the large pieces of ovary.Then carefully pipette the sucrose solution to disperse the released cells. Next load each square on a slide with 40 microliters of 1%PFA with 0.2%Triton X-100. Spread the solution around the square using a pipette tip or by rocking the slide back and forth.Then for each pool of sucrose solution with cells, load two fixative puddles with 20 microliters of suspended cells so that each slide has cells from one set of ovaries. For either MI or MII oocyte collections, first prepare and euthanize the donor mouse. Then make a large V-shaped opening in the abdominopelvic cavity, and use forceps to displace the intestines to locate each uterine horn.Find the ovaries proximal to the rib cage. Hold the oviduct with fine forceps, and cut the fat superior to the ovary using dissection scissors. While still holding the oviduct, use fine forceps to release the ovary from the bursa, and transfer the ovaries into a collection dish containing medium maintained at 37 degrees Celsius.To collect GV-stage oocytes, use a one-milliliter syringe with a 27-gauge needle to release the cumulus-oocyte complexes by manually puncturing the large antral follicles. To collect MII stage oocytes, tear a hole in the ampulla of the oviduct to release them rather than simply making a puncture. Now collect the oocytes using a mouth-operated glass pipette or capillary, or use a hand-operated micrometer syringe.Some oocytes may be surrounded with cumulus cells, others not. For the MI oocytes, prepare fresh hyaluronidase in MEM-alpha/BSA to denude the oocytes of the surrounding cumulus cells. For each collection of oocytes, treat them in an incubator with 2.5 milliliters of prepared hyaluronidase for three minutes.Then transfer the MI oocytes to freshly made warm MEM-alpha/BSA medium. There, use a mouth-operated glass pipette to provide the shearing force needed to completely detach the cumulus cells. In general, the success of this procedure requires the mastery of oocyte collection and manipulation using mouth-operated glass pipettes or capillaries.Allow the oocytes to recover in the incubator. Meanwhile, into a heated nine-well glass plate, load 300 microliters of warm Tyrode's solution. Load two wells with 300 microliters of warm MEM-alpha/BSA, and load one well with 300 microliters of warm Waymouth's medium.To remove the zona pellucida, transfer five to 10 MI or MII-stage oocytes into the bath of Tyrode's solution for just 30 to 45 seconds while watching them under a dissection microscope. When the zona pellucida is visibly dissolved, immediately transfer the oocytes to the medium using a pipette pre-wet with MEM-alpha/BSA medium. Then transfer the oocytes to a second bath of warmed medium.After the second bath, transfer the oocytes to warm Waymouth's medium, and let them recover in an incubator for 30 minutes. To prepare for a chromatin spread, use a PAP pen to draw an 11 by 44 millimeter rectangle on a glass slide. Next coat the slide with a thin layer of 1%PFA with 0.2%Triton X-100 in water, and then rock the slide back and forth to spread the solution.Then tap the slide to remove the excess. Now siphon between five and 10 oocytes with a minimal amount of medium. Then transfer the oocytes to the prepared slide by simultaneously dragging a pipette tip through the fixative solution and dropping the oocytes onto the slide from about one centimeter above.The oocytes should burst immediately, spreading chromatin on the slide. Now incubate slides at room temperature in a closed humidified chamber. Let them settle overnight so the chromatin adheres to the slide.The described embryonic chromatin collection was used to quantitatively analyze crossover formation in oocytes harvested from C57 black/6J embryos. Prophase chromatin spread preparations were immunolabeled to detect SYCP3, SYCP1, and MLH1, and stained with DAPI. Pachytene-stage chromosomes had 27 MLH1 foci distributed along 20 fully assembled SC structures.When the spread preparation was suboptimal and individual chromosomes were indistinguishable, the preparation was not included in the assessment. In good preparations, SMC6 was enriched at the pericentromeric heterochromatin region and along the chromosome arms, and the MLH1 foci distributed along the SC at the pachytene stage. The number of MLH1-positive crossovers from 15 good wild-type preparations was about 24.The oocyte collection method was used to assess chromatin morphology in oocytes following meiotic resumption. Protein localization, as well as ploidy, was easily assessed, exposing potential causes of chromosome segregation errors. Topoisomerase II-alpha could be seen along the chromosome arms and the pericentromeric heterochromatin.In MII oocytes, paired sister chromatids could be distinguished by chromosome and centromere morphology. Once mastered, these techniques without or after culturing can be completed within one or two hours per mouse. Following this procedure, other complementary methods, like whole cell oocyte immunolabeling and live cell imaging can be performed to assess homologous chromosomes and sister chromatids within the context of the cell.Collectively, chromatin spread methods described here can be easily applied to assess mammalian oogenesis and the sexually dimorphic features of chromosome and protein dynamics during meiosis.

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Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Elucidation of the binding properties of chromatin-targeting proteins can be very challenging due to the complex nature of chromatin and the heterogeneous nature of most mammalian chromatin-modifying complexes. In order to overcome these hurdles, we have adapted a sequential salt extraction (SSE) assay for evaluating the relative binding affinities of chromatin-bound complexes. This easy and straightforward assay can be used by non-experts to evaluate the relative difference in binding affinity of two related complexes, the changes in affinity of a complex when a subunit is lost or an individual domain is inactivated, and the change in binding affinity after alterations to the chromatin landscape. By sequentially re-suspending bulk chromatin in increasing amounts of salt, we are able to profile the elution of a particular protein from chromatin. Using these profiles, we are able to determine how alterations in a chromatin-modifying complex or alterations to the chromatin environment affect binding interactions. Coupling SSE with other in vitro and in vivo assays, we can determine the roles of individual domains and proteins on the functionality of a complex in a variety of chromatin environments.

Sequential salt extraction of chromatin bound proteins is a useful tool for determining the binding properties of large protein complexes. This method can be employed to evaluate the role of individual subunits or domains in the overall affinity of a protein complex to bulk chromatin.

Elucidation of the binding properties of chromatin-targeting proteins can be very challenging due to the complex nature of chromatin and the heterogeneous ...

Analysis of the c-KIT Ligand Promoter Using Chromatin Immunoprecipitation

Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. Therefore, DNA-protein interactions regulate multiple physiological, pathophysiological, and biological functions, such as cell differentiation, cell proliferation, cell cycle control, chromosome stability, epigenetic gene regulation, and cell transformation. In eukaryotic cells, the DNA interacts with histone and nonhistone proteins and is condensed into chromatin. Several technical tools can be used to analyze DNA-protein interactions, such as the Electrophoresis (gel) Mobility Shift Assay (EMSA) and DNase I footprinting. However, these techniques analyze the protein-DNA interaction in vitro, not within the cellular context. Chromatin immunoprecipitation (ChIP) is a technique that captures proteins at their specific DNA binding sites, thereby allowing for the identification of DNA-protein interactions within their chromatin context. It is done by fixation&#160;of the DNA-protein interaction, followed by&#160;immunoprecipitation of the protein of interest. Subsequently, the genomic site that the protein was bound to is characterized. Here, we describe and discuss ChIP and demonstrate its analytical value for the identification of the Transforming Growth Factor-&#946; (TGF-&#946;)-induced binding of the transcription factor SMAD2 to SMAD Binding Elements (SBE) within the promoter region of the tyrosine-protein kinase Kit (c-KIT) receptor ligand Stem Cell Factor (SCF).

DNA-protein interactions are essential for multiple biological processes. During the evaluation of cellular functions, the analysis of DNA-protein interactions is indispensable for understanding gene regulation. Chromatin immunoprecipitation (ChIP) is a powerful tool to analyze such interactions in vivo.

Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. ...

Chromatin Immunoprecipitation (ChIP) in Mouse T-cell Lines

Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational modifications (PTMs) of histone tails, the exchange of canonical histones with histone variants, and nucleosome eviction. Such regulation requires the binding of signal-sensitive transcription factors (TFs) that recruit chromatin-modifying enzymes at regulatory elements defined as enhancers. Understanding how signaling cascades regulate enhancer activity requires a comprehensive analysis of the binding of TFs, chromatin modifying enzymes, and the occupancy of specific histone marks and histone variants. Chromatin immunoprecipitation (ChIP) assays utilize highly specific antibodies to immunoprecipitate specific protein/DNA complexes. The subsequent analysis of the purified DNA allows for the identification the region occupied by the protein recognized by the antibody. This work describes a protocol to efficiently perform ChIP of histone proteins in a mature mouse T-cell line. The presented protocol allows for the performance of ChIP assays in a reasonable timeframe and with high reproducibility.

Chromatin Immunoprecipitation ChIP in Mouse T-cell Lines

This work describes a protocol for chromatin immunoprecipitation (ChIP) using a mature mouse T-cell line. This protocol is suitable to investigate the distribution of specific histone marks at specific promoter sites or genome-wide.

Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational ...

Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions

Moloney murine leukemia (MLV) virus-based retroviral vectors integrate predominantly in acetylated enhancers and promoters. For this reason, mLV integration sites can be used as functional markers of active regulatory elements. Here, we present a retroviral scanning tool, which allows the genome-wide identification of cell-specific enhancers and promoters. Briefly, the target cell population is transduced with an mLV-derived vector and genomic DNA is digested with a frequently cutting restriction enzyme. After ligation of genomic fragments with a compatible DNA linker, linker-mediated polymerase chain reaction (LM-PCR) allows the amplification of the virus-host genome junctions. Massive sequencing of the amplicons is used to define the mLV integration profile genome-wide. Finally, clusters of recurrent integrations are defined to identify cell-specific regulatory regions, responsible for the activation of cell-type specific transcriptional programs.
The retroviral scanning tool allows the genome-wide identification of cell-specific promoters and enhancers in prospectively isolated target cell populations. Notably, retroviral scanning represents an instrumental technique for the retrospective identification of rare populations (e.g. somatic stem cells) that lack robust markers for prospective isolation.

Here, we describe a protocol for genome-wide mapping of the integration sites of Moloney murine leukemia virus-based retroviral vectors in human cells.

Moloney murine leukemia (MLV) virus-based retroviral vectors integrate predominantly in acetylated enhancers and promoters. For this reason, mLV ...

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states. Combinatorial measurements of nucleosome accessibility with histone modification generated by ndChIP-seq allows for the simultaneous interrogation of these features. The ndChIP-seq methodology is applicable to small numbers of primary cells inaccessible to cross-linking based ChIP-seq protocols. Taken together, ndChIP-seq enables the measurement of histone modification in combination with local nucleosome density to obtain new insights into shared mechanisms that regulate RNA transcription within rare primary cell populations.

We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) methodology for the generation of sequence datasets suitable for a nucleosome density ChIP-seq analytical framework integrating micrococcal nuclease (MNase) accessibility with histone modification measurements.

We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution ...

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 104 - 5 x 105 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

Here, we describe a chromatin immunoprecipitation (ChIP) and ChIP-seq library preparation protocol to generate global epigenomic profiles from low-abundance chicken embryonic samples.

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, ...

Constitutive and Inducible Systems for Genetic In Vivo Modification of Mouse Hepatocytes Using Hydrodynamic Tail Vein Injection

In research models of liver cancer, regeneration, inflammation, and fibrosis, flexible systems for in vivo gene expression and silencing are highly useful. Hydrodynamic tail vein injection of transposon-based constructs is an efficient method for genetic manipulation of hepatocytes in adult mice. In addition to constitutive transgene expression, this system can be used for more advanced applications, such as shRNA-mediated gene knock-down, implication of the CRISPR/Cas9 system to induce gene mutations, or inducible systems. Here, the combination of constitutive CreER expression together with inducible expression of a transgene or miR-shRNA of choice is presented as an example of this technique. We cover the multi-step procedure starting from the preparation of sleeping beauty-transposon constructs, to the injection and treatment of mice, and the preparation of liver tissue for analysis by immunostaining. The system presented is a reliable and efficient approach to achieve complex genetic manipulations in hepatocytes. It is specifically useful in combination with Cre/loxP-based mouse strains and can be applied to a variety of models in the research of liver disease.

Constitutive and Inducible Systems for Genetic In Vivo Modification of Mouse Hepatocytes Using Hydrodynamic Tail Vein Injection

Hydrodynamic tail vein injection of transposon-based integration vectors enables stable transfection of murine hepatocytes in vivo. Here, we present a practical protocol for transfection systems that enables the long-term constitutive expression of a single transgene or combined constitutive and doxycycline-inducible expression of a transgene or miR-shRNA in the liver.

In research models of liver cancer, regeneration, inflammation, and fibrosis, flexible systems for in vivo gene expression and silencing are highly ...

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Investigating the three-dimensional architecture of chromatin offers invaluable insight into the mechanisms of gene regulation. Here, we describe a protocol for performing the chromatin conformation capture technique in situ Hi-C on staged Drosophila melanogaster embryo populations. The result is a sequencing library that allows the mapping of all chromatin interactions that occur in the nucleus in a single experiment. Embryo sorting is done manually using a fluorescent stereo microscope and a transgenic fly line containing a nuclear marker. Using this technique, embryo populations from each nuclear division cycle, and with defined cell cycle status, can be obtained with very high purity. The protocol may also be adapted to sort older embryos beyond gastrulation. Sorted embryos are used as inputs for in situ Hi-C. All experiments, including sequencing library preparation, can be completed in five days. The protocol has low input requirements and works reliably using 20 blastoderm stage embryos as input material. The end result is a sequencing library for next generation sequencing. After sequencing, the data can be processed into genome-wide chromatin interaction maps that can be analyzed using a wide range of available tools to gain information about topologically associating domain (TAD) structure, chromatin loops, and chromatin compartments during Drosophila development.

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

This work describes a protocol for the generation of high resolution in situ Hi-C libraries from tightly staged pre-gastrulation Drosophila melanogaster embryos.

Investigating the three-dimensional architecture of chromatin offers invaluable insight into the mechanisms of gene regulation. Here, we describe a ...

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 that add or remove these marks in response to signals received by the cell. These PTMS are key contributors to the regulation of processes such as gene expression control and DNA repair. Chromatin immunoprecipitation (chIP) has been an instrumental approach for dissecting the abundance and localization of many histone PTMs throughout the genome in response to diverse perturbations to the cell. Here, a versatile method for performing chIP of post-translationally modified histones from the budding yeast Saccharomyces cerevisiae (S. cerevisiae) is described. This method relies on crosslinking of proteins and DNA using formaldehyde treatment of yeast cultures, generation of yeast lysates by bead beating, solubilization of chromatin fragments by micrococcal nuclease, and immunoprecipitation of histone-DNA complexes. DNA associated with the histone mark of interest is purified and subjected to quantitative PCR analysis to evaluate its enrichment at multiple loci throughout the genome. Representative experiments probing the localization of the histone marks H3K4me2 and H4K16ac in wildtype and mutant yeast are discussed to demonstrate data analysis and interpretation. This method is suitable for a variety of histone PTMs and can be performed with different mutant strains or in the presence of diverse environmental stresses, making it an excellent tool for investigating changes in chromatin dynamics under different conditions.

Chromatin Immunoprecipitation ChIP of Histone Modifications from Saccharomyces cerevisiae

Here, we describe a protocol for chromatin immunoprecipitation of modified histones from the budding yeast Saccharomyces cerevisiae. Immunoprecipitated DNA is subsequently used for quantitative PCR to interrogate the abundance and localization of histone post-translational modifications throughout the genome.

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

Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells

The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein interactions in yeast. It allows analysis of a target region of interest without the need for prior knowledge about likely proteins bound to the target region. This, in theory, allows HyCCAPP to be used to analyze any genomic region of interest, and it provides sufficient flexibility to work in different cell systems. This method is not meant to study binding sites of known transcription factors, a task better suited for Chromatin Immunoprecipitation (ChIP) and ChIP-like methods. The strength of HyCCAPP lies in its ability to explore DNA regions for which there is limited or no knowledge about the proteins bound to it. It can also be a convenient method to avoid biases (present in ChIP-like methods) introduced by protein-based chromatin enrichment using antibodies. Potentially, HyCCAPP can be a powerful tool to uncover truly novel DNA-protein interactions. To date, the technology has been predominantly applied to yeast cells or to high copy repeat sequences in mammalian cells. In order to become the powerful tool we envision, HyCCAPP approaches need to be optimized to efficiently capture single-copy loci in mammalian cells. Here, we present our adaptation of the initial yeast HyCCAPP capture protocol to human cell lines, and show that single-copy chromatin regions can be efficiently isolated with this modified protocol.

This is a method to identify novel DNA-interacting proteins at specific target loci, relying on sequence-specific capture of crosslinked chromatin for subsequent proteomic analyses. No prior knowledge about potential binding proteins, nor cell modifications are required. Initially developed for yeast, the technology has now been adapted for mammalian cells.

The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein ...