Name: combined immunofluorescence and dna fish on 3d-preserved interphase nuclei to study changes in 3d nuclear organization
Uploaded: 2013-02-03T14:00:00
Description: Watch this Scientific Journal Video about Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization at JoVE.com

Vi vill tacka medlemmarna i Skok labbet, speciellt Susannah Hewitt, för diskussioner och kommentarer. Detta arbete stöds av National Institute of Health bidrag R01GM086852, RC1CA145746 (JAS). JAS är en Leukemia &amp; Lymphoma Society forskare. JC är en Irvington institut kamrat av Cancer Research Institute. MM stöds av National Science Foundation integrativ forskarutbildning och forskning Praktik (NSF IGERT 0.333.389).

1. DNA Probe märkning med Fluoroforer: nicktranslation (~ 6 timmar) <ol><li> Ren BAC-DNA (framställd genom maxi-prep) eller plasmider eller PCR-produkter, alla återsuspenderades i H 2 O, kan användas för märkning. Observera att för en robust FISH signal bör sönder spänna minst 10 kb. </li><li> Inkubera DNA i RNas A under 30 min vid 37 ° C (Alla reagens listas i tabell 1). </li><li> Inkubera nicktranslation reaktionen under 2 timmar vid 16 ° C (se tabelle...

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	<li>Chaumeil, J., Okamoto, I., Heard, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=X-chromosome+inactivation+in+mouse+embryonic+stem+cells:+analysis+of+histone+modifications+and+transcriptional+activity+using+immunofluorescence+and+FISH.">X-chromosome inactivation in mouse embryonic stem cells: analysis of histone modifications and transcriptional activity using immunofluorescence and FISH.</a> Methods in enzymology. , 376-405 (2004).</li><li>Cremer, 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=Multicolor+3D+fluorescence+in+situ+hybridization+for+imaging+interphase+chromosomes.">Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes.</a> Methods Mol. Biol. 463, 205-239 (2008).</li><li>Chaumeil, J., Augui, S., Chow, J. C., Heard, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combined+immunofluorescence,+RNA+fluorescent+in+situ+hybridization,+and+DNA+fluorescent+in+situ+hybridization+to+study+chromatin+changes,+transcriptional+activity,+nuclear+organization,+and+X-chromosome+inactivation.">Combined immunofluorescence, RNA fluorescent in situ hybridization, and DNA fluorescent in situ hybridization to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation.</a> Methods Mol. Biol. 463, 297-308 (2008).</li><li>Solovei, I., Cremer, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D-FISH+on+cultured+cells+combined+with+immunostaining.">3D-FISH on cultured cells combined with immunostaining.</a> Methods Mol. Biol. 659, 117-126 (2010).</li><li>Markaki, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+potential+of+3D-FISH+and+super-resolution+structured+illumination+microscopy+for+studies+of+3D+nuclear+architecture:+3D+structured+illumination+microscopy+of+defined+chromosomal+structures+visualized+by+3D+(immuno)-FISH+opens+new+perspectives+for+studies+of+nuclear+architecture.">The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture.</a> BioEssays : news and reviews in molecular, cellular and developmental biology. 34, 412-426 (2012).</li><li>Heard, E., Bickmore, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ins+and+outs+of+gene+regulation+and+chromosome+territory+organisation.">The ins and outs of gene regulation and chromosome territory organisation.</a> Current opinion in cell biology. 19, 311-316 (2007).</li><li>Misteli, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Beyond+the+sequence:+cellular+organization+of+genome+function.">Beyond the sequence: cellular organization of genome function.</a> Cell. 128, 787-800 (1016).</li><li>Fraser, P., Bickmore, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+organization+of+the+genome+and+the+potential+for+gene+regulation.">Nuclear organization of the genome and the potential for gene regulation.</a> Nature. 447, 413-417 (2007).</li><li>Cremer, T., 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=Chromosome+territories--a+functional+nuclear+landscape.">Chromosome territories--a functional nuclear landscape.</a> Current opinion in cell biology. 18, 307-316 (2006).</li><li>Mao, Y. S., Zhang, B., Spector, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biogenesis+and+function+of+nuclear+bodies.">Biogenesis and function of nuclear bodies.</a> Trends in genetics : TIG. 27, 295-306 (2011).</li><li>Dostie, J., Bickmore, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromosome+organization+in+the+nucleus+-+charting+new+territory+across+the+Hi-Cs.">Chromosome organization in the nucleus - charting new territory across the Hi-Cs.</a> Current opinion in genetics &amp; development. 22, 125-131 (2012).</li><li>van Steensel, B., Dekker, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genomics+tools+for+unraveling+chromosome+architecture.">Genomics tools for unraveling chromosome architecture.</a> Nature. 28, 1089-1095 (2010).</li><li>Massey, F. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Kolmogorov-Smirnov+Test+for+Goodness+of+Fit.">The Kolmogorov-Smirnov Test for Goodness of Fit.</a> Journal of the American Statistical Association. 253, 1951 (1951).</li><li>Collins, 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=RUNX+transcription+factor-mediated+association+of+Cd4+and+Cd8+enables+coordinate+gene+regulation.">RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation.</a> Immunity. 34, 303-314 (2011).</li><li>Fisher, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+interpretation+of+&#967;2+from+contingency+tables,+and+the+calculation+of+P.">On the interpretation of &#967;2 from contingency tables, and the calculation of P.</a> Journal of the Royal Statistical Society. 85, 87-94 (1922).</li><li>Benjamini, Y. H., Yosef, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlling+the+false+discovery+rate:+a+practical+and+powerful+approach+to+multiple+testing.">Controlling the false discovery rate: a practical and powerful approach to multiple testing.</a> Journal of the Royal Statistical Society, Series B (Methodological). 57, 125-133 (1995).</li><li>Fitzsimmons, S. P., Bernstein, R. M., Max, E. E., Skok, J. A., Shapiro, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+changes+in+accessibility,+nuclear+positioning,+recombination,+and+transcription+at+the+Igkappa+locus.">Dynamic changes in accessibility, nuclear positioning, recombination, and transcription at the Igkappa locus.</a> J. Immunol. 179, 5264-5273 (2007).</li><li>Fuxa, 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=Pax5+induces+V-to-DJ+rearrangements+and+locus+contraction+of+the+immunoglobulin+heavy-chain+gene.">Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene.</a> Genes Dev. 18, 411-422 (2004).</li><li>Goldmit, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epigenetic+ontogeny+of+the+Igk+locus+during+B+cell+development.">Epigenetic ontogeny of the Igk locus during B cell development.</a> Nature. 6, 198-203 (2005).</li><li>Hewitt, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Association+between+the+Igk+and+Igh+immunoglobulin+loci+mediated+by+the+3'+Igk+enhancer+induces+'decontraction'+of+the+Igh+locus+in+pre-B+cells.">Association between the Igk and Igh immunoglobulin loci mediated by the 3' Igk enhancer induces 'decontraction' of the Igh locus in pre-B cells.</a> Nature. 9, 396-404 (2008).</li><li>Johnson, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IL-7+Functionally+Segregates+the+Pro-B+Cell+Stage+by+Regulating+Transcription+of+Recombination+Mediators+across+Cell+Cycle.">IL-7 Functionally Segregates the Pro-B Cell Stage by Regulating Transcription of Recombination Mediators across Cell Cycle.</a> Journal of Immunology. , (2012).</li><li>Karnowski, 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=Silencing+and+nuclear+repositioning+of+the+lambda5+gene+locus+at+the+pre-b+cell+stage+requires+Aiolos+and+OBF-1.">Silencing and nuclear repositioning of the lambda5 gene locus at the pre-b cell stage requires Aiolos and OBF-1.</a> PLoS ONE. 3, e3568 (2008).</li><li>Kosak, S. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subnuclear+compartmentalization+of+immunoglobulin+loci+during+lymphocyte+development.">Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development.</a> Science. 296, 158-162 (2002).</li><li>Liu, H., 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=Yin+Yang+1+is+a+critical+regulator+of+B-cell+development.">Yin Yang 1 is a critical regulator of B-cell development.</a> Genes Dev. 21, 1179-1189 (2007).</li><li>Parker, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+pre-B-cell+receptor+induces+silencing+of+VpreB+and+lambda5+transcription.">The pre-B-cell receptor induces silencing of VpreB and lambda5 transcription.</a> Embo J. 24, 3895-3905 (2005).</li><li>Roldan, E., 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=Locus+'decontraction'+and+centromeric+recruitment+contribute+to+allelic+exclusion+of+the+immunoglobulin+heavy-chain+gene.">Locus 'decontraction' and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene.</a> Nature immunology. 6, 31-41 (2005).</li><li>Skok, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nonequivalent+nuclear+location+of+immunoglobulin+alleles+in+B+lymphocytes.">Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes.</a> Nature. 2, 848-854 (2001).</li><li>Skok, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reversible+contraction+by+looping+of+the+Tcra+and+Tcrb+loci+in+rearranging+thymocytes.">Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes.</a> Nature immunology. 8, 378-387 (2007).</li><li>Xiang, Y., Zhou, X., Hewitt, S. L., Skok, J. A., Garrard, W. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+multifunctional+element+in+the+mouse+Igkappa+locus+that+specifies+repertoire+and+Ig+loci+subnuclear+location.">A multifunctional element in the mouse Igkappa locus that specifies repertoire and Ig loci subnuclear location.</a> Journal of Immunology. 186, 5356-5366 (2011).</li><li>Hewitt, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RAG-1+and+ATM+coordinate+monoallelic+recombination+and+nuclear+positioning+of+immunoglobulin+loci.">RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci.</a> Nature immunology. 10, 655-664 (2009).</li><li>Deriano, 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=The+RAG2+C+terminus+suppresses+genomic+instability+and+lymphomagenesis.">The RAG2 C terminus suppresses genomic instability and lymphomagenesis.</a> Nature. 471, 119-123 (2011).</li><li>Brown, K. E., Baxter, J., Graf, D., Merkenschlager, M., Fisher, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+repositioning+of+genes+in+the+nucleus+of+lymphocytes+preparing+for+cell+division.">Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division.</a> Molecular cell. 3, 207-217 (1999).</li><li>Fernandez-Capetillo, O., Lee, A., Nussenzweig, M., Nussenzweig, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=H2AX:+the+histone+guardian+of+the+genome.">H2AX: the histone guardian of the genome.</a> DNA repair. 3, 959-967 (2004).</li><li>Croft, J. 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=Differences+in+the+localization+and+morphology+of+chromosomes+in+the+human+nucleus.">Differences in the localization and morphology of chromosomes in the human nucleus.</a> The Journal of cell biology. 145, 1119-1131 (1999).</li><li>Chaumeil, J., Le Baccon, P., Wutz, A., Heard, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+role+for+Xist+RNA+in+the+formation+of+a+repressive+nuclear+compartment+into+which+genes+are+recruited+when+silenced.">A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced.</a> Genes Dev. 20, 2223-2237 (2006).</li><li>Walter, 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=Towards+many+colors+in+FISH+on+3D-preserved+interphase+nuclei.">Towards many colors in FISH on 3D-preserved interphase nuclei.</a> Cytogenetic and genome research. 114, 367-378 (2006).</li><li>Toomre, D., Bewersdorf, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+wave+of+cellular+imaging.">A new wave of cellular imaging.</a> Annual review of cell and developmental biology. 26, 285-314 (2010).</li><li>Schermelleh, L., Heintzmann, R., Leonhardt, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guide+to+super-resolution+fluorescence+microscopy.">A guide to super-resolution fluorescence microscopy.</a> The Journal of cell biology. 190, 165-175 (2010).</li><li>Dobbie, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=OMX:+a+new+platform+for+multimodal,+multichannel+wide-field+imaging.">OMX: a new platform for multimodal, multichannel wide-field imaging.</a> Cold Spring Harbor protocols. , 899-909 (2011).</li><li>Boyle, S., Rodesch, M. J., Halvensleben, H. A., Jeddeloh, J. A., Bickmore, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+in+situ+hybridization+with+high-complexity+repeat-free+oligonucleotide+probes+generated+by+massively+parallel+synthesis.">Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis.</a> Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 19, 901-909 (2011).</li></ol>

De tekniker som beskrivs ovan användes i vårt labb för att analysera regleringen av V (D) J-rekombination av immunglobulin och Tcra / d loci utveckla lymfocyter 30,31. Vi är övertygade om att denna teknik kan anpassas för detektion av olika nukleära proteiner, nukleära fack och loci i olika celltyper. Ändringar av protokollet kan vara nödvändigt, och i detta fall de viktigaste stegen för att fokusera på är följande. Först, kan längden på permeabilisering justeras beroende p...

Epigenetiska mekanismer utlöser etablering och arv av utvecklings-och celltyp specifika transkriptionella profiler. På en nivå handlar det modulering av kromatin förpackningar som definierar aktiva eller tysta genomiska regioner. På en större skala, den globala 3D organisation av genomet och nukleära arkitektur spelar också en roll i kontrollen av transkriptionella mönster. Således är dissektion av dessa epigenomic funktioner nödvändiga för en fullständig förståelse av hur gener regleras 6-11. Kombinerad immunofluorescens och 3D-DNA FISH ger en unik möjlighet att komplettera molekylära och biokemiska analyser genom att bedöma specifika interaktioner / sammanslutningar av DNA-sekvenser och / eller proteiner i kärnan. Vidare, medan genomet hela hög kapacitet tekniker såsom kromatin immunoprecipitation (chip-seq) eller kromosom fånga konformation i kombination med djup sekvensering (4C-seq, 5C, Hi-C) ger den globala data på cellpopulationer 12, immunofluorescens / DNA FISH teknik möjliggör analyser på en enda cell nivå. Här beskriver vi ett protokoll för samtidig detektion av histon ändringar av immunofluorescens och DNA-sekvenser med DNA-FISK följt av 3D mikroskopi och analyser (3D immuno-FISH). Fördelen med detta protokoll är den kombinerade visualisering av DNA och bevarande av proteinstrukturer. Vår erfarenhet på detta område har gjort det möjligt för oss att förbättra och förenkla existerande protokoll. Även om vi har använt detta protokoll för att upptäcka DNA dubbelsträngade avbrott i lymfocyter som genomgår rekombination, kan denna metod tillämpas på andra proteiner och andra celltyper.

<table border="1"><tbody><tr><td> Namn på reagens / material </td><td> Företag </td><td> Katalognummer </td><td> Kommentarer </td></tr><tr><td> H 2 O </td><td> Fisher </td><td> # BP2470 </td><td></td></tr><tr><td> RNas A </td><td> Sigma </td><td> # R4642 </td><td></td></tr><tr><td> dNTP </td><td> Sigma </td><td> # DNTP100 </td><td></td></tr><tr><td> Alexa dUTP </td><td> Invitrogen </td><td> # C11397 till C-11.401 </td><td></td></tr><tr><td> Cy3 eller Cy5 dUTP </td><td> Fisher </td><td> # 45-001-xxx </td><td></td></tr><tr><td> DNas I </td><td> Roche </td><td> # 04536282001 </td><td></td></tr><tr><td> DNA-Pol I </td><td> Biolabs </td><td> # M0209 </td><td></td></tr><tr><td> 0,025 im filter </td><td> Millipore </td><td> # VSWP02500 </td><td></td></tr><tr><td> Barnsäng-1-DNA 1 mg / ml </td><td> Invitrogen </td><td> # 18440 </td><td></td></tr><tr><td> Hybloc DNA 1 mg / ml </td><td> Tillämpad genetik </td><td> # MHB </td><td></td></tr><tr><td> Laxsperma </td><td> Sigma </td><td> # D1626 </td><td> pulver som skall återsuspenderas vid 10 mg / ml i H 2 O </td></tr><tr><td> NaAc (natriumacetat, pH 5,2, buffertlösning) </td><td> Sigma </td><td> # S7899 </td><td></td></tr><tr><td> Ficoll 400 (Mol Biol kvalitet) </td><td> Fisher </td><td> # 525 </td><td></td></tr><tr><td> Polyvinylpyrrolidon (Mol Biol kvalitet) </td><td> Fisher </td><td> # BP431 </td><td></td></tr><tr><td> Dextransulfat pulver </td><td> Sigma </td><td> # D8906 </td><td></td></tr><tr><td> SSPE (saltlösning-natriumfosfat-EDTA) 20x lösning </td&gt; <td> Fisher </td><td> # BP1328 </td><td></td></tr><tr><td> Formamid </td><td> Fisher </td><td> # BP227 </td><td></td></tr><tr><td> Täckglas </td><td> Fisher </td><td> # 12-548-B </td><td></td></tr><tr><td> Diabilder </td><td> Fisher </td><td> # 12-550 </td><td></td></tr><tr><td> 6-brunnsplattor </td><td> Fisher </td><td> # 0720080 </td><td></td></tr><tr><td> PBS, 10x </td><td> Fisher </td><td> # MT-46-013-CM </td><td></td></tr><tr><td> Poly-L-lysin-lösning </td><td> Sigma </td><td> # P8920 </td><td></td></tr><tr><td> Paraformaldehyd, pellets, 95% </td><td> Sigma </td><td> # 441244 </td><td></td></tr><tr><td> Triton-X-100, Mol Biol grad </td><td> Sigma </td><td> # T8787 </td><td></td></tr><tr><td> BSA (bovint serumalbumin) fraktion V </td><td> Fisher </td><td> # BP 1600 </td><td></td></tr><tr><td> Normalt getserum </td><td> Vector Labs </td><td> # S-1000 </td><td></td></tr><tr><td> Tween-20, Mol Biol grad </td><td> Sigma </td><td> # P9416 </td><td></td></tr><tr><td> SSC (saltlösning natriumcitrat) 20x lösning </td><td> Fisher </td><td> # BP1325 </td><td></td></tr><tr><td> Förlänga guld antifad reagens </td><td> Invitrogen </td><td> # P36930 </td><td></td></tr><tr><td> DAPI (4 &#39;,6-diamidino-2-fenylindol) </td><td> Sigma </td><td> # D9542 </td><td></td></tr><tr><td> Bästa testet en päls gummi cement </td><td> Konst eller kontor leverans butiker </td><td></td><td></td></tr><tr><td></td><td></td><td></td><td> Tabell 1. Särskilda reagenser och mindre utrustning. </td></tr></tbody></table>

combined immunofluorescence and dna fish on 3d-preserved interphase nuclei to study changes in 3d nuclear organization

Fluorescent in situ hybridisering med DNA-sonder på 3-dimensionellt bevarade kärnor följt av 3D konfokalmikroskopi (3D-DNA FISH) är det mest direkta sättet att visualisera placeringen av genloci, kromosomal delregioner eller hela territorier i enskilda celler. Denna typ av analys ger en inblick i den globala arkitekturen i kärnan samt uppförande av specifika genomiska loci och regioner inom den nukleära utrymmet. Immunofluorescens, å andra sidan, för detektering av nukleära proteiner (modifierade histoner, histon varianter och modifieringsmedel, transkription maskiner och faktorer, nukleära sub-fack, etc). Den stora utmaningen att kombinera immunofluorescens och 3D-DNA FISK är, å ena sidan för att bevara den epitop som detekteras av antikroppen såväl som 3D-arkitektur av kärnan, och å andra sidan, för att tillåta penetrering av DNA-prob för att detektera genloci eller territorier kromosom 1-5. Här erbjuder vi ett protokoll som kombinerar visualisering av kromatin ändringar med genomiska loci i 3D bevarade kärnor.

DNA och immuno-FISH används i Skok labbet för att studera förändringar i kärn organisation i samband med processen för V (D) J-rekombination av loci antigenreceptor under B-och T-lymfocyter utveckling. De tekniker som beskrivs ovan gör att vi kan i) mäta avstånd mellan de två ändarna av ett lokus (kontraktion) ii) mäta avstånd mellan alleler eller loci (parning), iii) analysera DNA-skador som inträffar inom lokus, iv) bedöma placeringen av alleler och loci relativt nukleära sub-fack (repressiva pericentr...

Watch this Scientific Journal Video about Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization at JoVE.com

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Här beskriver vi ett protokoll för samtidig detektion av histon ändringar genom immunofluorescens och DNA-sekvenser med DNA-FISK följt av 3D mikroskopi och analyser (3D immuno-DNA FISH).

Kombinerad Immunfluorescens och DNA FISH på 3D bevarade interfaskärnorna att studera förändringar i 3D Nuclear organisation

Fluorescent in situ hybridization using DNA probes  on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA  FISH) represents the ...

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Biology

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testa Visual Känsligheten för hastighet och rörelseriktning i Ödlor

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of ...

DNA-based Fish Species Identification Protocol

DNA-baserade Fiskarter Identification protokoll

We have developed a fast, simple, and accurate DNA-based screening method to identify the fish species present in fresh and processed seafood samples. ...

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISK Använda Direkt märkta prober

3D DNA FISH has become a major tool for  analyzing three-dimensional organization of the nucleus, and several variations  of the technique have been ...

Assessing Species-specific Contributions To Craniofacial Development Using Quail-duck Chimeras

Bedöma Artspecifika Bidrag Till Kraniofaciala utveckling Använda Quail-anka chimärer

The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to ...

Combined DNA-RNA Fluorescent In situ Hybridization (FISH) to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells

Combined DNA-RNA Fluorescent In situ Hybridization FISH to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells

Kombinerad DNA-RNA Fluorescent<em&gt; In situ</em&gt; Hybridisering (FISH) för att studera X-kromosom inaktivering i Differentierade Kvinna Mouse embryonala stamceller

Fluorescent in situ hybridization (FISH) is a molecular technique which enables the detection of nucleic acids in cells. DNA FISH is often used in ...

Measuring DNA Damage and Repair in Mouse Splenocytes After Chronic In Vivo Exposure to Very Low Doses of Beta- and Gamma-Radiation

Measuring DNA Damage and Repair in Mouse Splenocytes After Chronic In Vivo Exposure to Very Low Doses of Beta- and Gamma-Radiation

Att mäta DNA-skador och reparation i mussplenocyter Efter kronisk<em&gt; In Vivo</em&gt; Exponering för mycket låga doser av beta- och gamma-strålning

Low dose radiation exposure may produce a variety of biological effects that are different in quantity and quality from the effects produced by high ...

Experimental Approaches to Study Mitochondrial Localization and Function of a Nuclear Cell Cycle Kinase, Cdk1

Experimentella metoder för att studera mitokondrie Lokalisering och funktion av en kärnteknisk Cell Cycle kinas, Cdk1

Although mitochondria possess their own transcriptional machinery, merely 1% of mitochondrial proteins are synthesized inside the organelle. The ...

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP

Isolering av specifika genomregioner och Identifiering av associerade molekyler av enChIP

The identification of molecules associated with specific genomic regions of interest is required to understand the mechanisms of regulation of the ...

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

Metoder för att studera förändringar i inneboende Protein aggregering med åldern i Caenorhabditis elegans

In the last decades, the prevalence of neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson's disease (PD), has grown. These ...

Sequential Immunofluorescence and Immunohistochemistry on Cryosectioned Zebrafish Embryos

Sekventiell immunofluorescens och immunohistokemi på Kryosektionerade Zebrafiskembryon

Investigation of intercellular interactions often requires discrete labeling of specific cell populations and precise protein localization. The zebrafish ...