We thank Marco Antonio Rosales Vega and Abel Segura for taking some of the confocal images, Carmen Mu&#241;oz for media preparation and Dr. Arturo Pimentel, M.C. Andr&#233;s Saralegui, and Dr. Chris Wood from the LMNA for advice on the use of the microscopes.
FUNDING: 
This work was supported by the Consejo Nacional de Ciencia y Tecnolog&#237;a (CONACyT) (A1-S-8239 to VV-G) and Programa de Apoyo a Proyectos de Investigaci&#243;n e Innovaci&#243;n Tecnol&#243;gica (204915 and 200118 to VV-G)

1. Third instar larvae culture
<ol>
	<li>Prepare 1 liter of standard media by adding 100 g of yeast, 100 g of unrefined whole cane sugar, 16 g of agar, 10 mL of propionic acid and 14 g of gelatin. Dissolve all ingredients except the yeast in 800 mL of tap water and then dissolve the yeast. Autoclave immediately for 30 minutes.
	<ol>
		<li>Afterward, let the media cool down to 60 &#176;C and add propionic acid to a final concentration 0.01%. Let the bottle stand until the gelatin is formed.</li>
	</ol>
	</li>
	<li>To optimize the 3&#7506; instar larvae culture, first collect 5-to-10-day old adults and place 50 (25 males and 25 females) in a broad neck bottle of standard media.</li>
	<li>Place the bottle with the flies in a controlled temperature incubator at 25 &#176;C until the number of eggs laid is 50 (approximately 12 hours for the wild-type strain).</li>
	<li>After the incubation time is over, remove the adults and transfer them to a new bottle to repeat the procedure. Let the embryos grow at 18 &#176;C for 72 hours 
	&#8203;NOTE: For more about Drosophila stock maintenance conditions, see Tennessen &#38; Thymmel13.</li>
</ol>
2. Larvae collection
<ol>
	<li>For larvae collection choose the wandering larvae that do not have everted spiracles. After the eversion of the spiracles, the larva enters the prepupal stage, while retaining excellent polytene chromosomes suitable for analysis. Only after 12 hours do the cells of the salivary gland begin to prepare for programmed cell death14,15.</li>
	<li>Take fifteen 3&#176; instar larvae and put them in a watch glass to wash them. Then transfer them to an ice-cold saline solution or PBS (1x PBS: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, adjust pH to 7.4).</li>
	<li>Dissect 15 to 30 pairs of salivary glands (or as many as possible in 30 minutes) in cold PBS with protease inhibitors under the stereoscopic microscope. Transfer the salivary glands to a 1.5 mL tube with ice-cold PBS.</li>
	<li>Wash once with 1 mL of PBS plus protease inhibitors. Wait for the tissue to reach the bottom of the tube.</li>
	<li>After the wash, remove the PBS with a 1000 &#181;L pipette. Take care not to touch the tissue.
	<ol>
		<li>Alternatively, dissect the salivary glands in 5 mL of PBS to eliminate the need for this washing step and proceed to step 3 by transferring the salivary glands to 0.5 mL of the Ruvkun fixing buffer described below.</li>
	</ol>
	</li>
</ol>
3. Salivary gland tissue fixation
<ol>
	<li>After removing the PBS from the last step, directly add 0.5 mL of 1x Ruvkun fixing buffer, with 50% methanol (add 0.5 mL of methanol) and 2% formaldehyde. 
	&#8203;NOTE: 2x Ruvkun solution is 160 mM KCl, 40 mM NaCl, 20 mM EGTA, 30 mM PIPES at pH 7.4.</li>
	<li>Incubate for 2 hours at 4 &#176;C with mild rotation.</li>
</ol>
4. Salivary gland tissue wash
<ol>
	<li>Carry out one 5-minute rotation wash with 1 mL of Tris/Triton buffer (100 mM Tris pH 7.4, 1% Triton X-100 and 1 mM EDTA). 
	&#8203;NOTE: Wait for the tissue to reach the bottom of the tube.</li>
</ol>
5. Permeabilization
<ol>
	<li>Incubate the salivary glands in 1 mL of Tris/Triton X-100 (the same as above). For some proteins it might be necessary to add 1% &#946;-mercaptoethanol.</li>
	<li>Incubate for 2 hours at 37 &#176; C with mild shaking (300 rpm).</li>
</ol>
6. Preservation step (optional)
NOTE: If not proceeding immediately to the incubation with the antibody, preserve the tissue as follows.
<ol>
	<li>Wash with 1 mL of BO3 buffer (0.01 M H3BO3 pH 9.2 + 0.01 M NaOH) and then incubate in BO3/10 mM DTT at 37 &#176; C with mild shaking (300 rpm) for 15 minutes.</li>
	<li>At the end of the incubation period, perform a wash with 1 mL of BO3 buffer alone. 
	NOTE: Wait for the tissue to reach the bottom of the tube.</li>
	<li>Add 1 mL of PBS. Preserve the tissue in this solution at 4 &#176;C for up to 72 hours and then proceed with the next step. This step is particularly helpful when working with different mutant strains that may present a delayed life cycle, so the immunodetection can be performed at the same time along with the controls.</li>
</ol>
7. Tissue blocking
<ol>
	<li>Incubate the salivary glands in 1 mL of Buffer B (PBS + 0.1% BSA + 0.5% Triton X-100 + 1 mM EDTA) for 2 hours at room temperature with rotation.</li>
</ol>
8. Immunostaining
<ol>
	<li>Remove all buffer B and add buffer A (PBS + 0.1% BSA) plus antibody of interest. 
	&#8203;NOTE: We use the HP1a C1A9c (concentrated antibody) from Hybridoma Bank up to 1:3000. When using the C1A9s (supernatant) we have tried from 1:100 to a 1:500 dilution and any dilution between this rank works well) overnight at 4 &#7506;C with rotation. At this point it is important that the shaking does not raise bubbles which might damage the antibody.</li>
</ol>
9. Immunostaining washing
<ol>
	<li>Perform 3 x 15-minute washes with buffer B under stirring at room temperature using 1 mL each time.</li>
	<li>Transfer the glands to buffer B together with the secondary antibody coupled to a fluorophore for 2 hours under rotation at 4 &#7506;C (secondary antibody Alexa fluor 568 Invitrogen were used 1:3000).
	<ol>
		<li>Cover the tube with aluminum paper foil to protect the secondary antibody from the light.</li>
	</ol>
	</li>
	<li>Carry out 2 x 15-minute washes at room temperature while rotation with 1 mL of Buffer B.</li>
	<li>Incubate with a DNA marker such as Sytox (take 2 &#181;L of 5 mM stock and dissolve in 1 mL of Buffer B) or Hoechst (take 1 &#181;L of 10 mg/mL stock and dissolve in 1 mL of Buffer B) for 10 minutes at room temperature with rotation.</li>
	<li>Carry out one wash with Buffer B and once with PBS, each wash lasting 10 minutes while rotating at room temperature. 
	&#8203;NOTE: Remember to protect it from the light.</li>
</ol>
10. Imaging
<ol>
	<li>Mount the salivary glands on a slide, making a pool with a coverslip.</li>
	<li>Put the salivary glands in the middle of the pool and cover with AF1 citifluor to avoid the formation of bubbles extending the viscous liquid all over the place. Then seal all the sides with clear nail polish.</li>
	<li>Observe under a fluorescence or confocal microscope. If the sample is not going to be observed on the same day, store away from light at 4 &#176;C.</li>
	<li>Use GraphPad Prism 6 to generate all graphs and statistical analyses.</li>
	<li>Analyze the data from HP1a distribution in salivary glands using the Kruskal-Wallis test. Statistical significance was set at (p &#60; 0.05*, &#60; 0.01 **, &#60; 0.001***, &#60; 0.0001****).</li>
</ol>

<ol>
	<li>Berger, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emil+Heitz,+a+true+epigenetics+pioneer.">Emil Heitz, a true epigenetics pioneer.</a> Nature Reviews Molecular Cell Biology. 20 (10), 572 (2019).</li><li>Irick, 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+new+function+for+heterochromatin.">A new function for heterochromatin.</a> Chromosoma. 103 (1), 1-3 (1994).</li><li>Kasinathan, B., 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=Innovation+of+heterochromatin+functions+drives+rapid+evolution+of+essential+ZAD-ZNF+genes+in+Drosophila.">Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila.</a> Elife. , 1-31 (2020).</li><li>Lifschytz, E., Hareven, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Heterochromatin+markers:+Arrangement+of+obligatory+heterochromatin,+histone+genes+and+multisite+gene+families+in+the+interphase+nucleus+of+D.+melanogaster.">Heterochromatin markers: Arrangement of obligatory heterochromatin, histone genes and multisite gene families in the interphase nucleus of D. melanogaster.</a> Chromosoma. 86 (4), 443-455 (1982).</li><li>Eissenberg, J. C., Elgin, S. C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HP1a:+A+structural+chromosomal+protein+regulating+transcription.">HP1a: A structural chromosomal protein regulating transcription.</a> Trends in Genetics. 30 (3), 103-110 (2014).</li><li>Lee, Y. C. 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=Pericentromeric+heterochromatin+is+hierarchically+organized+and+spatially+contacts+H3K9me2+islands+in+euchromatin.">Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin.</a> PLoS Genetics. 16 (3), 1-27 (2020).</li><li>Koryakov, D. 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=The+SUUR+protein+is+involved+in+binding+of+SU+(VAR)3-9+and+methylation+of+H3K9+and+H3K27+in+chromosomes+of+Drosophila+melanogaster.">The SUUR protein is involved in binding of SU (VAR)3-9 and methylation of H3K9 and H3K27 in chromosomes of Drosophila melanogaster.</a> Chromosome Research. 19 (2), 235-249 (2011).</li><li>Cao, 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=Role+of+Histone+H3+Lysine+27+Methylation+in+Polycomb-Group+Silencing.">Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing.</a> Science. 298 (5595), 1039 (2002).</li><li>Hines, K. 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=Domains+of+heterochromatin+protein+1+required+for+Drosophila+melanogaster+heterochromatin+spreading.">Domains of heterochromatin protein 1 required for Drosophila melanogaster heterochromatin spreading.</a> Genetics. 182 (4), 967-977 (2009).</li><li>Elgin, S. C. R., Reuter, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Position-effect+variegation,+heterochromatin+formation,+and+gene+silencing+in+Drosophila.">Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila.</a> Cold Spring Harbor Perspectives in Biology. 5 (8), 1-26 (2013).</li><li>Eissenberg, J. C., Elgin, S. C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HP1a:+A+structural+chromosomal+protein+regulating+transcription.">HP1a: A structural chromosomal protein regulating transcription.</a> Trends in Genetics. 30 (3), 103-110 (2014).</li><li>Meyer-Nava, S., Torres, A., Zurita, M., Valadez-graham, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+effects+of+dADD1+misexpression+in+chromatin+organization+and+transcription.">Molecular effects of dADD1 misexpression in chromatin organization and transcription.</a> BMC Molecular and Cell Biology. 2, 1-17 (2020).</li><li>Tennessen, J. M., Thummel, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordinating+growth+and+maturation+-+Insights+from+drosophila.">Coordinating growth and maturation - Insights from drosophila.</a> Current Biology. 21 (18), 750-757 (2011).</li><li>Cai, W., Jin, Y., Girton, J., Johansen, J., Johansen, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+drosophila+polytene+chromosome+squashes+for+antibody+labeling.">Preparation of drosophila polytene chromosome squashes for antibody labeling.</a> Journal of Visualized Experiments. (36), 1-4 (2010).</li><li>Bainbridge, S. P., Bownes, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Staging+the+metamorphosis+of+Drosophila+melanogaster.">Staging the metamorphosis of Drosophila melanogaster.</a> Journal of Embryology and Experimental Morphology. 66 (1967), 57-80 (1981).</li><li>Larson, A. 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=Liquid+droplet+formation+by+HP1&#945;+suggests+a+role+for+phase+separation+in+heterochromatin.">Liquid droplet formation by HP1&#945; suggests a role for phase separation in heterochromatin.</a> Nature. 547 (7662), 236-240 (2017).</li><li>Larson, A. G., Narlikar, G. 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+Role+of+Phase+Separation+in+Heterochromatin+Formation,+Function,+and+Regulation.">The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation.</a> Biochemistry. 57 (17), 2540-2548 (2018).</li><li>Keenen, M. M., Larson, A. G., Narlikar, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+and+Quantitation+of+Phase-Separated+Droplet+Formation+by+Human+HP1&#945;.">Visualization and Quantitation of Phase-Separated Droplet Formation by Human HP1&#945;.</a> Methods in Enzymology. , (2018).</li><li>Lu, B. Y., Emtage, P. C., Duyf, B. J., Hilliker, a. J., Eissenberg, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Heterochromatin+protein+1+is+required+for+the+normal+expression+of+two+heterochromatin+genes+in+Drosophila.">Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila.</a> Genetics. 155 (2), 699-708 (2000).</li><li>Marsano, R. M., Giordano, E., Messina, G., Dimitri, P. <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+Portrait+of+Constitutive+Heterochromatin:+Lessons+from+Drosophila+melanogaster.">A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster.</a> Trends in Genetics. , (2019).</li><li>Strom, A. 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=Phase+separation+drives+heterochromatin+domain+formation.">Phase separation drives heterochromatin domain formation.</a> Nature. 547 (7662), 241-245 (2017).</li><li>Sanulli, 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=HP1+reshapes+nucleosome+core+to+promote+phase+separation+of+heterochromatin.">HP1 reshapes nucleosome core to promote phase separation of heterochromatin.</a> Nature. 575 (7782), 390-394 (2019).</li><li>Dialynas, G., Delabaere, L., Chiolo, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arp2/3+and+Unc45+maintain+heterochromatin+stability+in+Drosophila+polytene+chromosomes.">Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes.</a> Experimental Biology and Medicine. 244 (15), 1362-1371 (2019).</li><li>Kolesnikova, T. D., 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=Induced+decondensation+of+heterochromatin+in+drosophila+melanogaster+polytene+chromosomes+under+condition+of+ectopic+expression+of+the+supressor+of+underreplication+gene.">Induced decondensation of heterochromatin in drosophila melanogaster polytene chromosomes under condition of ectopic expression of the supressor of underreplication gene.</a> Fly. 5 (3), 181-190 (2011).</li><li>Bettinger, J. C., Lee, K., Rougvie, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stage-specific+accumulation+of+the+terminal+differentiation+factor+LIN-29+during+Caenorhabditis+elegans+development.">Stage-specific accumulation of the terminal differentiation factor LIN-29 during Caenorhabditis elegans development.</a> Development. 122 (8), 2517-2527 (1996).</li><li>Messina, 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=Yeti,+an+essential+Drosophila+melanogaster+gene,+encodes+a+protein+required+for+chromatin+organization.">Yeti, an essential Drosophila melanogaster gene, encodes a protein required for chromatin organization.</a> Journal of Cell Science. 127 (11), 2577-2588 (2014).</li><li>Aguilar-Fuentes, 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=p8/TTDA+overexpression+enhances+UV-irradiation+resistance+and+suppresses+TFIIH+mutations+in+a+Drosophila+trichothiodystrophy+model.">p8/TTDA overexpression enhances UV-irradiation resistance and suppresses TFIIH mutations in a Drosophila trichothiodystrophy model.</a> PLOS Genetics. 4 (11), 1-9 (2008).</li><li>Reynaud, E., Lomeli, H., Vazquez, M., Zurita, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Drosophila+melanogaster+Homologue+of+the+Xeroderma+Pigmentosum+D+Gene+Product+Is+Located+in+Euchromatic+Regions+and+Has+a+Dynamic+Response+to+UV+Light-induced+Lesions+in+Polytene+Chromosomes.">The Drosophila melanogaster Homologue of the Xeroderma Pigmentosum D Gene Product Is Located in Euchromatic Regions and Has a Dynamic Response to UV Light-induced Lesions in Polytene Chromosomes.</a> Molecular Biology of the Cell. 10 (4), 1191-1203 (1999).</li><li>Farka&#353;, R., Mechler, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+timing+of+Drosophila+salivary+gland+apoptosis+displays+an+I+(2)gl-dose+response.">The timing of Drosophila salivary gland apoptosis displays an I (2)gl-dose response.</a> Cell Death &amp; Differentiation. 7 (1), 89-101 (2000).</li><li>Zhang, P., Spradling, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Drosophila+salivary+gland+chromocenter+contains+highly+polytenized+subdomains+of+mitotic+heterochromatin.">The Drosophila salivary gland chromocenter contains highly polytenized subdomains of mitotic heterochromatin.</a> Genetics. 139 (2), 659-670 (1995).</li><li>Stormo, B. M., Fox, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polyteny:+still+a+giant+player+in+chromosome+research.">Polyteny: still a giant player in chromosome research.</a> Chromosome Research. 25 (3-4), 201-214 (2017).</li></ol>

The authors declare that they have no competing interests.

The cellular function of eukaryotic organisms can define the 3D structure within the nucleus, which is supported by interactions between different proteins with chromatin and various molecules including RNA. In the last three years, the biological condensates that have had relevance, including heterochromatin, have taken a fundamental role in the determination of the phase separation promoting the distinct nuclear spatial organization of active and repressive chromatin 16,<sup class="xr...

Since the early studies of Emil Heitz1, heterochromatin has been considered an important regulator of cellular processes such as gene expression, meiotic and mitotic separation of chromosomes, and the maintenance of genome stability2,3,4.
Heterochromatin is mainly divided into two types: constitutive heterochromatin that characteristically defines repetitive sequences, and transposable elements that are present at specific chromosome sites such as the telomeres and centromeres. This type of heterochromatin is mainly defined epigenetically by specific histone marks such as the di or tri-methylation of lysine 9 of histone H3 (H3K9me3) and the binding of the Heterochromatin protein 1a (HP1a)5,6. On the other hand, facultative heterochromatin localizes through the chromosome&#39;s arms and consists mainly of developmentally silenced genes7,8. Immunostaining of heterochromatin blocks in metaphase cells, or the observation of heterochromatin aggregates in interphase cells, has unveiled much light in the understanding of the formation and function of heterochromatic regions9.
The use of Drosophila as a model system has allowed the development of essential tools to study heterochromatin without the use of electron microscopy10. Since the description of position effect variegation and the discovery of heterochromatin-associated proteins, such as HP1a, and histone post-translational modifications, many groups have developed several immunohistochemical techniques that allow visualization of these heterochromatic regions10,11.
These techniques are based on the use of specific antibodies that recognize heterochromatin-associated proteins or histone marks. For every cell type and antibody, the fixation and permeabilization conditions must be determined empirically. Also, conditions may vary if additional mechanical processes such as squashing techniques are used. In this protocol, we describe the use of Drosophila salivary glands to study heterochromatic foci. Salivary glands have polytenized cells that contain more than 1,000 copies of the genome, thus providing an amplified view of most of the chromatin features, with the exception of satellite DNA and some heterochromatic regions which are under replicated. Nevertheless, heterochromatin regions are easily visualized in polytene chromosome preparations, but the squashing techniques may sometimes disrupt characteristic chromatin-bound complexes or the chromatin architecture. Therefore, immunolocalization of proteins in whole salivary gland tissue can surpass these undesired effects. We have used this protocol to detect several chromatin bound proteins, and we have demonstrated that this protocol combined with mutant Drosophila stocks can be used to study heterochromatin disruption12.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.5 mL microcentrifuge tubes</td>
			<td>Axygen MCT-150-C</td>
			<td>11351904</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>16% formaldehyde</td>
			<td>Thermo Scientific</td>
			<td>28908</td>
			<td></td>
		</tr>
		<tr>
			<td>AF1 Citifluor</td>
			<td>Ted pella</td>
			<td>19470</td>
			<td>25 mL</td>
		</tr>
		<tr>
			<td>BSA, Molecular Biology Grade</td>
			<td>Roche</td>
			<td>10735078001</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>Complete, protease inhibitors Ultra EDTA-free 
			protease inhibitors</td>
			<td>Merck</td>
			<td>5892953001</td>
			<td></td>
		</tr>
		<tr>
			<td>Coverslip</td>
			<td>Corning</td>
			<td>CLS285022-200EA</td>
			<td>22x22, brand not critical</td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Sigma</td>
			<td>d9779</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma</td>
			<td>E5134</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td></td>
			<td></td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>Glass slide</td>
			<td>Gold seal</td>
			<td>3011</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>H3BO3</td>
			<td>Baker</td>
			<td>0084-01</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>H3K9me3</td>
			<td>Abcam</td>
			<td>8889</td>
			<td></td>
		</tr>
		<tr>
			<td>HP1a</td>
			<td>Hybridoma Bank</td>
			<td>C1A9</td>
			<td>Product Form&#160;Concentrate 0.1 mL</td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Baker</td>
			<td>3040-01</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Baker</td>
			<td>9070-03</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma</td>
			<td>71376</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td></td>
			<td></td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>PIPES</td>
			<td></td>
			<td></td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>Rotator</td>
			<td>Thermo Scientific</td>
			<td>13-687-12Q</td>
			<td>&#160;Labquake Tube Shaker</td>
		</tr>
		<tr>
			<td>Thermo Mixer C</td>
			<td>Eppendorf</td>
			<td>13527550</td>
			<td>SmartBlock 1.5 mL</td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Milipore</td>
			<td>648311</td>
			<td>brand not critical</td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma</td>
			<td>T8787</td>
			<td>100 mL, brand not critical</td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>Bio-Rad</td>
			<td>1610710</td>
			<td>25 mL, brand not critical</td>
		</tr>
	</tbody>
</table>

immunofluorescent staining for visualization of heterochromatin associated proteins in drosophila salivary glands

Visualization of heterochromatin aggregates by immunostaining can be challenging. Many mammalian components of chromatin are conserved in Drosophila melanogaster. Therefore, it is an excellent model to study heterochromatin formation and maintenance. Polytenized cells, such as the ones found in salivary glands of third instar D. melanogaster larvae, provide an excellent tool to observe the chromatin amplified nearly a thousand times and have allowed researchers to study changes in the distribution of heterochromatin in the nucleus. Although the observation of heterochromatin components can be carried out directly in polytene chromosome preparations, the localization of some proteins can be altered by the severity of the treatment. Therefore, the direct visualization of heterochromatin in cells complements this type of study. In this protocol, we describe the immunostaining techniques used for this tissue, the use of secondary fluorescent antibodies, and confocal microscopy to observe these heterochromatin aggregates with greater precision and detail.

Representative results of HP1a immunostaining in Drosophila salivary glands are shown in Figure 1. A positive result is to observe one focal point (Figure 1a) (heterochromatic aggregate or condensate). A negative result is no signal or a dispersed signal. Sometimes a double signal can be observed, that is, with a double point (Figure 1c), but it usually occurs in smaller quantities.
Data analysis...

Watch this Scientific Journal Video about Immunofluorescent Staining for Visualization of Heterochromatin Associated Proteins in Drosophila Salivary Glands at JoVE.com

Immunofluorescent Staining for Visualization of Heterochromatin Associated Proteins in Drosophila Salivary Glands

This protocol aims to visualize heterochromatin aggregates in Drosophila polytene cells.

Immunofluorescent Staining for Visualization of Heterochromatin Associated Proteins in Drosophila Salivary Glands

Visualization of heterochromatin aggregates by immunostaining can be challenging. Many mammalian components of chromatin are conserved in Drosophila ...

immunofluorescent-staining-for-visualization-heterochromatin

Research

JoVE Journal

Biology

3.6K Views.  Universidad Nacional Autónoma de México. This protocol aims to visualize heterochromatin aggregates in Drosophila polytene cells.

Video: Immunofluorescent Staining for Visualization of Heterochromatin Associated Proteins in Drosophila Salivary Glands

Dissection of Midgut and Salivary Glands from Ae. aegypti Mosquitoes

The mosquito midgut and salivary glands are key entry and exit points for pathogens such as Plasmodium parasites and Dengue viruses. This video protocol demonstrates dissection techniques for removal of the midgut and salivary glands from Aedes aegypti mosquitoes. 



The mosquito midgut and salivary glands are key entry and exit points for vector pathogens like Plasmodium falciparum and the dengue virus. This video demonstrates the dissection techniques for removing the midgut and salivary glands from Aedes aegypti mosquitoes.

The mosquito midgut and salivary glands are key entry and exit points for pathogens such as Plasmodium parasites and Dengue viruses. This video protocol ...

Staining Proteins in Gels

Following separation by electrophoretic methods, proteins in a gel can be detected by several staining methods. This unit describes protocols for detecting proteins by four popular methods. Coomassie blue staining is an easy and rapid method. Silver staining, while more time consuming, is considerably more sensitive and can thus be used to detect smaller amounts of protein. Fluorescent staining is a popular alternative to traditional staining procedures, mainly because it is more sensitive than Coomassie staining, and is often as sensitive as silver staining. Staining of proteins with SYPRO Orange and SYPRO Ruby are also demonstrated here.

Following separation by electrophoretic methods, proteins in a gel can be detected by several staining methods. Staining of proteins with Coomassie Blue, Silver Staining, SYPRO Orange, SYPRO Ruby are demonstrated in this video.

Following separation by electrophoretic methods, proteins in a gel can be detected by several staining methods. This unit describes protocols for ...

A Novel RFP Reporter to Aid in the Visualization of the Eye Imaginal Disc in Drosophila

The Drosophila eye is a powerful model system for studying areas such as neurogenesis, signal transduction and neurodegeneration. Many of the discoveries made using this system have taken advantage of the spatiotemporal nature of photoreceptor differentiation in the developing eye imaginal disc. To use this system it is first necessary for the researcher to learn to identify and dissect the eye disc. We describe a novel RFP reporter to aid in the identification of the eye disc and the visualization of specific cell types in the developing eye. We detail a methodology for dissection of the eye imaginal disc from third instar larvae and describe how the eye-RFP reporter can aid in this dissection. This eye-RFP reporter is only expressed in the eye and can be visualized using fluorescence microscopy either in live tissue or after fixation without the need for signal amplification. We also show how this reporter can be used to identify specific cells types within the eye disc. This protocol and the use of the eye-RFP reporter will aid researchers using the Drosophila eye to address fundamentally important biological questions.

A Novel RFP Reporter to Aid in the Visualization of the Eye Imaginal Disc in Drosophila

We describe a novel red fluorescent protein (RFP) reporter that is expressed specifically in the Drosophila eye. We detail a methodology for dissection of the eye imaginal disc and how this reporter can be used to aid in the dissection and identification of specific cell types in the developing eye.

The Drosophila eye is a powerful model system for studying areas such as neurogenesis, signal transduction and neurodegeneration. Many of the discoveries ...

Dissection and Staining of Drosophila Larval Ovaries

Many organs depend on stem cells for their development during embryogenesis and for maintenance or repair during adult life. Understanding how stem cells form, and how they interact with their environment is therefore crucial for understanding development, homeostasis and disease. The ovary of the fruit fly Drosophila melanogaster has served as an influential model for the interaction of germ line stem cells (GSCs) with their somatic support cells (niche) 1, 2. The known location of the niche and the GSCs, coupled to the ability to genetically manipulate them, has allowed researchers to elucidate a variety of interactions between stem cells and their niches 3-12.
Despite the wealth of information about mechanisms controlling GSC maintenance and differentiation, relatively little is known about how GSCs and their somatic niches form during development. About 18 somatic niches, whose cellular components include terminal filament and cap cells (Figure 1), form during the third larval instar 13-17. GSCs originate from primordial germ cells (PGCs). PGCs proliferate at early larval stages, but following the formation of the niche a subgroup of PGCs becomes GSCs 7, 16, 18, 19. Together, the somatic niche cells and the GSCs make a functional unit that produces eggs throughout the lifetime of the organism.
Many questions regarding the formation of the GSC unit remain unanswered. Processes such as coordination between precursor cells for niches and stem cell precursors, or the generation of asymmetry within PGCs as they become GSCs, can best be studied in the larva. However, a methodical study of larval ovary development is physically challenging. First, larval ovaries are small. Even at late larval stages they are only 100&mu;m across. In addition, the ovaries are transparent and are embedded in a white fat body. Here we describe a step-by-step protocol for isolating ovaries from late third instar (LL3) Drosophila larvae, followed by staining with fluorescent antibodies. We offer some technical solutions to problems such as locating the ovaries, staining and washing tissues that do not sink, and making sure that antibodies penetrate into the tissue. This protocol can be applied to earlier larval stages and to larval testes as well.

Dissection and Staining of Drosophila Larval Ovaries

How niches and stem cells form during development is an important question with practical implications. In the Drosophila ovary, germ line stem cells and their somatic niches form during larval development. This video demonstrates how to dissect, stain and mount female gonads from late third instar (LL3) Drosophila larvae.

Many organs depend on stem cells for their development during embryogenesis and for maintenance or repair during adult life. Understanding how stem cells ...

Live Imaging of GFP-labeled Proteins in Drosophila Oocytes

The Drosophila oocyte has been established as a versatile system for investigating fundamental questions such as cytoskeletal function, cell organization, and organelle structure and function. The availability of various GFP-tagged proteins means that many cellular processes can be monitored in living cells over the course of minutes or hours, and using this technique, processes such as RNP transport, epithelial morphogenesis, and tissue remodeling have been described in great detail in Drosophila oocytes1,2.
The ability to perform video imaging combined with a rich repertoire of mutants allows an enormous variety of genes and processes to be examined in incredible detail. One such example is the process of ooplasmic streaming, which initiates at mid-oogenesis3,4. This vigorous movement of cytoplasmic vesicles is microtubule and kinesin-dependent5 and provides a useful system for investigating cytoskeleton function at these stages.
Here I present a protocol for time lapse imaging of living oocytes using virtually any confocal microscopy setup.

Live Imaging of GFP-labeled Proteins in Drosophila Oocytes

A protocol for live imaging of GFP-tagged proteins or autofluorescent structures in individual Drosophila oocytes is described.

The  Drosophila oocyte has been established as a versatile system for investigating  fundamental questions such as cytoskeletal function, cell ...

In Situ Immunofluorescent Staining of Autophagy in Muscle Stem Cells

Increasing evidence points to autophagy as a crucial regulatory process to preserve tissue homeostasis. It is known that autophagy is involved in skeletal muscle development and regeneration, and the autophagic process has been described in several muscular pathologies and age-related muscle disorders. A recently described block of the autophagic process that correlates with the functional exhaustion of satellite cells during muscle repair supports the notion that active autophagy is coupled with productive muscle regeneration. These data uncover the crucial role of autophagy in satellite cell activation during muscle regeneration in both normal and pathological conditions, such as muscular dystrophies. Here, we provide a protocol to monitor the autophagic process in the adult Muscle Stem Cell (MuSC) compartment during muscle regenerative conditions. This protocol describes the setup methodology to perform in situ immunofluorescence imaging of LC3, an autophagy marker, and MyoD, a myogenic lineage marker, in muscle tissue sections from control and injured mice. The methodology reported allows for monitoring the autophagic process in one specific cell compartment, the MuSC compartment, which plays a central role in orchestrating muscle regeneration.

In Situ Immunofluorescent Staining of Autophagy in Muscle Stem Cells

Active autophagy is associated with productive muscle regeneration, which is essential for Muscle Stem Cell (MuSC) activation. Here, we provide a protocol for the in situ detection of LC3, an autophagy marker in MyoD-positive MuSCs of muscle tissue sections from control and injured mice.

Increasing evidence points to autophagy as a crucial regulatory process to preserve tissue homeostasis. It is known that autophagy is involved in skeletal ...

Determination of Plasma Membrane Partitioning for Peripherally-associated Proteins

This method provides a fast approach for the determination of plasma membrane partitioning of any fluorescently-tagged peripherally-associated protein using the profiles of fluorescence intensity across the plasma membrane. Measured fluorescence profiles are fitted by a model for membrane and cytoplasm fluorescence distribution along a line applied perpendicularly to the cell periphery. This model is constructed from the fluorescence intensity values in reference cells expressing a fluorescently-tagged marker for cytoplasm and with FM 4-64-labeled plasma membrane. The method can be applied to various cell types and organisms; however, only plasma membranes of non-neighboring cells can be evaluated. This fast microscopy-based method is suitable for experiments, where subtle and dynamic changes of plasma membrane-associated markers are expected and need to be quantified, e.g., in the analysis of mutant versions of proteins, inhibitor treatments, and signal transduction observations. The method is implemented in a multi-platform R package that is coupled with an ImageJ macro that serves as a user-friendly interface.

Here, we present a protocol to perform a quantitative analysis of the level of plasma-membrane association for fluorescently-tagged peripherally-associated protein. The method is based on the computational decomposition of membrane and cytoplasmic component of signal observed in cells labeled with plasma membrane fluorescent marker.

This method provides a fast approach for the determination of plasma membrane partitioning of any fluorescently-tagged peripherally-associated protein ...

Visualization of 3D White Adipose Tissue Structure Using Whole-mount Staining

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various techniques have been developed to study the morphology and biology of adipose tissue. However, conventional visualization methods are limited to studying the tissue in 2D sections, failing to capture the 3D architecture of the whole organ. Here we present whole-mount staining, an immunohistochemistry method that preserves intact adipose tissue morphology with minimal processing steps. Hence, the structures of adipocytes and other cellular components are maintained without distortion, achieving the most representative 3D visualization of the tissue. In addition, whole-mount staining can be combined with lineage tracing methods to determine cell fate decisions. However, this technique has some limitations to providing accurate information regarding deeper parts of adipose tissue. To overcome this limitation, whole-mount staining can be further combined with tissue clearing techniques to remove the opaqueness of tissue and allow for complete visualization of entire adipose tissue anatomy using light-sheet fluorescent microscopy. Therefore, a higher resolution and more accurate representation of adipose tissue structures can be captured with the combination of these techniques.

The focus of the present study is to demonstrate the whole-mount immunostaining and visualization technique as an ideal method for 3D imaging of adipose tissue architecture and cellular component.

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various ...

Visualization of DNA Repair Proteins Interaction by Immunofluorescence

Mammalian cells are constantly exposed to chemicals, radiations, and naturally occurring metabolic by-products, which create specific types of DNA insults. Genotoxic agents can damage the DNA backbone, break it, or modify the chemical nature of individual bases. Following DNA insult, DNA damage response (DDR) pathways are activated and proteins involved in the repair are recruited. A plethora of factors are involved in sensing the type of damage and activating the appropriate repair response. Failure to correctly activate and recruit DDR factors can lead to genomic instability, which underlies many human pathologies including cancer. Studies of DDR proteins can provide insights into genotoxic drug response and cellular mechanisms of drug resistance.
There are two major ways of visualizing&#160;proteins in vivo: direct observation, by tagging the protein of interest with a fluorescent protein and following it by live imaging, or indirect immunofluorescence on fixed samples. While visualization of fluorescently tagged proteins allows precise monitoring over time, direct tagging in N- or C-terminus can interfere with the protein localization or function. Observation of proteins in their unmodified, endogenous version is preferred. When DNA repair proteins are recruited to the DNA insult, their concentration increases locally and they form groups, or &#8220;foci&#8221;, that can be visualized by indirect immunofluorescence using specific antibodies.
Although detection of protein foci does not provide a definitive proof of direct interaction, co-localization of proteins in cells indicates that they regroup to the site of damage and can inform of the sequence of events required for complex formation. Careful analysis of foci spatial overlap in cells expressing wild type or mutant versions of a protein can provide precious clues on functional domains important for DNA repair function. Last, co-localization of proteins indicates possible direct interactions that can be verified by co-immunoprecipitation in cells, or direct pulldown using purified proteins.

Following DNA damage, human cells activate essential repair pathways to restore the integrity of their genome. Here, we describe the method of indirect immunofluorescence as a means to detect DNA repair proteins, analyze their spatial and temporal recruitment, and help interrogate protein-protein interaction at the sites of DNA damage.

Mammalian cells are constantly exposed to chemicals, radiations, and naturally occurring metabolic by-products, which create specific types of DNA ...

In Vitro Analysis of E3 Ubiquitin Ligase Function

The covalent attachment of ubiquitin (Ub) to internal lysine residue(s) of a substrate protein, a process termed ubiquitylation, represents one of the most important post-translational modifications in eukaryotic organisms. Ubiquitylation is mediated by a sequential cascade of three enzyme classes including ubiquitin-activating enzymes (E1 enzymes), ubiquitin-conjugating enzymes (E2 enzymes), and ubiquitin ligases (E3 enzymes), and sometimes, ubiquitin-chain elongation factors (E4 enzymes). Here, in vitro protocols for ubiquitylation assays are provided, which allow the assessment of E3 ubiquitin ligase activity, the cooperation between E2-E3 pairs, and substrate selection. Cooperating E2-E3 pairs can be screened by monitoring the generation of free poly-ubiquitin chains and/or auto-ubiquitylation of the E3 ligase. Substrate ubiquitylation is defined by selective binding of the E3 ligase and can be detected by western blotting of the in vitro reaction. Furthermore, an E2~Ub discharge assay is described, which is a useful tool for the direct assessment of functional E2-E3 cooperation. Here, the E3-dependent transfer of ubiquitin is followed from the corresponding E2 enzyme onto free lysine amino acids (mimicking substrate ubiquitylation) or internal lysines of the E3 ligase itself (auto-ubiquitylation). In conclusion, three different in vitro protocols are provided that are fast and easy to perform to address E3 ligase catalytic functionality.

In Vitro Analysis of E3 Ubiquitin Ligase Function

The present study provides detailed in vitro ubiquitylation assay protocols for the analysis of E3 ubiquitin ligase catalytic activity. Recombinant proteins were expressed using prokaryotic systems such as Escherichia coli culture.

The covalent attachment of ubiquitin (Ub) to internal lysine residue(s) of a substrate protein, a process termed ubiquitylation, represents one of the ...