We thank Jordan Davis, Yanyan Lin, Eric Schadler and Jimiao Zheng for their technical help with this study. This work was supported by NSF CAREER grant MCB-1054962 to A.L.A.

1. Preparing Large Apple Juice-agar Plates
<ol>
	<li>To make 4 plates, add 375 ml H2O, 11.25 g fly agar and a stir bar to a 1,000&#160;ml flask. This is Mix A. Autoclave Mix A with the flask lid loosely capped on one 30 min-sterilization cycle for liquid goods.</li>
	<li>Add 125 ml apple juice, 12.5 g table sugar and a stir bar to a 500&#160;ml beaker. This is Mix B. Heat Mix B on a heated platform while stirring and maintain the temperature at approximately 70 &#176;C until the autoclaving of Mix A is finis...

<ol>
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E., Ptudor Mahowald, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=a+gene+required+for+assembly+of+the+germ+plasm+in+Drosophila+melanogaster.">a gene required for assembly of the germ plasm in Drosophila melanogaster.</a> Cell. 43, 97-104 (1985).</li><li>Thomson, T., Lasko, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+tudor+is+essential+for+polar+granule+assembly+and+pole+cell+specification,+but+not+for+posterior+patterning.">Drosophila tudor is essential for polar granule assembly and pole cell specification, but not for posterior patterning.</a> Genesis. 40, 164-170 (2004).</li><li>Arkov, A. L., Ramos, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Building+RNA-protein+granules:+insight+from+the+germline.">Building RNA-protein granules: insight from the germline.</a> Trends in cell biology. 20, 482-490 (2010).</li><li>Gao, M., Arkov, A. 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Genes &amp; development. 23, 2742-2752 (2009).</li><li>Matthews, K. A., Goldstein, L. S. B., Fyrberg, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+melanogaster:+Practical+Uses+in+Cell+and+Molecular+Biology.">Drosophila melanogaster: Practical Uses in Cell and Molecular Biology.</a> Methods in Cell Biology. 44, 13-32 (1995).</li><li>Sambrook, J., Russell, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Molecular cloning: A laboratory manual. , (2001).</li><li>Thomson, T., Liu, N., Arkov, A., Lehmann, R., Lasko, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+new+polar+granule+components+in+Drosophila+reveals+P+body+and+ER+associated+proteins.">Isolation of new polar granule components in Drosophila reveals P body and ER associated proteins.</a> Mechanisms of development. 125, 865-873 (2008).</li><li>Vasilescu, J., Guo, X., Kast, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+protein-protein+interactions+using+in+vivo+cross-linking+and+mass+spectrometry.">Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry.</a> Proteomics. 4, 3845-3854 (2004).</li><li>Klockenbusch, C., Kast, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+formaldehyde+cross-linking+for+protein+interaction+analysis+of+non-tagged+integrin+beta1.">Optimization of formaldehyde cross-linking for protein interaction analysis of non-tagged integrin beta1.</a> J Biomed Biotechnol. 2010, 9275-9285 (2010).</li><li>Nowak, D. E., Tian, B., Brasier, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-step+cross-linking+method+for+identification+of+NF-kappaB+gene+network+by+chromatin+immunoprecipitation.">Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation.</a> Biotechniques. 39, 715-725 (2005).</li><li>Zeng, P. Y., Vakoc, C. R., Chen, Z. C., Blobel, G. A., Berger, 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=In+vivo+dual+cross-linking+for+identification+of+indirect+DNA-associated+proteins+by+chromatin+immunoprecipitation.">In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation.</a> Biotechniques. 41, 694 (2006).</li><li>Liu, N., Dansereau, D. A., Lasko, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fat+facets+interacts+with+vasa+in+the+Drosophila+pole+plasm+and+protects+it+from+degradation.">Fat facets interacts with vasa in the Drosophila pole plasm and protects it from degradation.</a> Current biology : CB. 13, 1905-1909 (2003).</li></ol>

Formaldehyde has been commonly used as a crosslinking reagent for identifying protein-protein and protein-nucleic acid interactions. Its good solubility and cell membrane permeability, together with the compatibility with downstream mass spectrometry procedures, make formaldehyde an ideal candidate agent for intracellular crosslinking applications3,15-17. In particular, it was successfully used to identify mRNAs associated with Vasa, a critical germ cell RNA helicase in Drosophila11. In add...

Isolation of multisubunit protein assemblies and DNA- or RNA-protein complexes is performed to identify protein complexes, genomic loci recognized by DNA-binding regulatory proteins or RNA targets of RNA binding proteins. Different methods allow genome-wide identification of DNA sites recognized by transcription factors or chromatin proteins (ChIP-seq)1 and RNA targets associated with a given RNA-binding protein (CLIP-seq)2. The libraries of RNA-derived cDNAs or DNA targets are then deeply sequenced. These methods use chemical or UV-induced cross-linking to stabilize the complexes followed by immunoprecipitation (IP) with an antibody against a protein component of the studied complex.
During development of an organism, many protein complexes form transiently. Therefore, it is crucial to analyze the composition and function of these complexes in vivo to understand the molecular mechanisms that control development. Such an in vivo analysis would be superior to in vitro approach since it is virtually impossible to reproduce native concentrations of the interacting components and cellular biochemical environment in vitro. Here we demonstrate an in vivo approach that we successfully use to isolate large protein complexes from Drosophila embryos. In this method, protein complexes in the living embryos are crosslinked with a low concentration of formaldehyde and subsequently protein complexes of interest are isolated by IP with an antibody against a known component of the complexes followed by gel purification of the complexes and mass spectrometry analysis to identify unknown complex components. Since formaldehyde is able to permeate the cell membrane and has a crosslinking range of 2.3-2.7 &Aring;3, protein complexes can be crosslinked in vivo and the complex components are likely to be close to each other. In this article we describe this method using the isolation of Tudor (Tud) protein complex as an example. Tud is a germline protein which is essential for germline development4-7. This protein contains 11 Tud domains known to interact with methylated arginines or lysines of other polypeptides8-10.
Previously, we have generated a transgenic Drosophila line which expresses HA-tagged functional Tud5 and therefore, specific anti-HA antibody is used to pull down Tud complex after crosslinking.
In addition to protein-protein crosslinks, formaldehyde can generate nucleic acid-protein crosslinks and is used in ChIP-seq experiments. Furthermore, in Drosophila, in vivo crosslinking with formaldehyde has allowed the identification of an RNA target of Vasa RNA helicase protein11.
While in this article we describe a method for in vivo crosslinking and purification of protein complexes from Drosophila embryos, this method can be adapted for other organisms and tissues.

<table border="0" cellpadding="0" cellspacing="0" width="858">
	<tbody>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">Drosophila agar</td>
			<td style="width:235px;">Lab Scientific (http://www.labscientific.com/)</td>
			<td style="width:119px;">FLY-8020-1</td>
			<td style="width:289px;">Do not autoclave the water and agar mix for prolonged period of time as it will cause the apple juice plates to become fragile</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Methyl 4-hydroxybenzoate</td>
			<td style="width:235px;">Sigma (http://www.sigmaaldrich.com/united-states.html)</td>
			<td style="width:119px;">H5501</td>
			<td style="width:289px;">Other name: TEGOSEPT</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Population cage</td>
			<td style="width:235px;">Flystuff (http://www.flystuff.com/)</td>
			<td style="width:119px;">59-104</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">Fine nylon mesh</td>
			<td style="width:235px;">Flystuff (http://www.flystuff.com/)</td>
			<td style="width:119px;">57-102</td>
			<td style="width:289px;">When making the collection basket, cut the mesh slightly larger than the opening of the falcon tube cap to ensure a tight seal</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Dounce homogenizer</td>
			<td style="width:235px;">Sigma (http://www.sigmaaldrich.com/united-states.html)</td>
			<td style="width:119px;">D8938-1SET</td>
			<td style="width:289px;">Chill the homogenizer on ice and prerinse with cold lysis buffer before use to prevent protein degradation</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Protease inhibitor cocktail&#160;</td>
			<td style="width:235px;">Roche (http://www.rocheusa.com/portal/usa)</td>
			<td style="width:119px;">4693132001</td>
			<td style="width:289px;">PBS could be used to prepare concentrated protease inhibitor stock solution</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Anti-HA agarose beads</td>
			<td style="width:235px;">MBL international (http://www.mblintl.com/)</td>
			<td style="width:119px;">561-8</td>
			<td style="width:289px;">The kit also includes HA-peptide and spin columns</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">HA-peptide</td>
			<td style="width:235px;">MBL international (http://www.mblintl.com/)</td>
			<td style="width:119px;">561-8</td>
			<td style="width:289px;">Prepare to 2 mg/ml with PBS&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Spin Column</td>
			<td style="width:235px;">MBL international (http://www.mblintl.com/)</td>
			<td style="width:119px;">561-8</td>
			<td style="width:289px;">Spin columns are included as part of the kit</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Isopropanol</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">BP26324</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Triton X-100</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">BP151-500</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Heptane</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">H350-4</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">PBS</td>
			<td style="width:235px;">Invitrogen (https://www.lifetechnologies.com/us/en/home.html)</td>
			<td style="width:119px;">AM9625</td>
			<td style="width:289px;">Dilute from 10 X to 1 X with nanopure water before use</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Formaldehyde</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">BP531-500</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Glycine</td>
			<td style="width:235px;">BioRad (www.bio-rad.com/&#8206;)</td>
			<td style="width:119px;">161-0724</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">SDS</td>
			<td style="width:235px;">BioRad (www.bio-rad.com/&#8206;)</td>
			<td style="width:119px;">161-0301</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Urea</td>
			<td style="width:235px;">BioRad (www.bio-rad.com/&#8206;)</td>
			<td style="width:119px;">161-0730</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Phenylmethanesulfonyl fluoride</td>
			<td style="width:235px;">Sigma (http://www.sigmaaldrich.com/united-states.html)</td>
			<td style="width:119px;">P7626-1G</td>
			<td style="width:289px;">Prepare 200 mM stock solution in isopropanol then dilute to working concentration of 2 mM in lysis buffer</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">IGEPAL CA-630</td>
			<td style="width:235px;">Sigma (http://www.sigmaaldrich.com/united-states.html)</td>
			<td style="width:119px;">I8896-50ML</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Tween 20</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">BP337-100</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">15-ml tubes</td>
			<td style="width:235px;">USA Scientific (http://www.usascientific.com/)</td>
			<td style="width:119px;">1475-0511</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Bleach</td>
			<td style="width:235px;">Clorox brand</td>
			<td style="width:119px;"></td>
			<td style="width:289px;">Dilute with equal volume of nanopure water to make 50% bleach</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">50-ml tubes</td>
			<td style="width:235px;">BD Biosciences (http://www.bdbiosciences.com/home.jsp)</td>
			<td style="width:119px;">352098</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Top layer sieve</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">04-884-1AK</td>
			<td style="width:289px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Bottom layer sieve</td>
			<td style="width:235px;">Fisher Scientific (www.fishersci.com/&#8206;)</td>
			<td style="width:119px;">04-884-1BA</td>
			<td style="width:289px;"></td>
		</tr>
	</tbody>
</table>

an in vivo crosslinking approach to isolate protein complexes from drosophila embryos

Many cellular processes are controlled by multisubunit protein complexes. Frequently these complexes form transiently and require native environment to assemble. Therefore, to identify these functional protein complexes, it is important to stabilize them in vivo before cell lysis and subsequent purification. Here we describe a method used to isolate large bona fide protein complexes from Drosophila embryos. This method is based on embryo permeabilization and stabilization of the complexes inside the embryos by in vivo crosslinking using a low concentration of formaldehyde, which can easily cross the cell membrane. Subsequently, the protein complex of interest is immunopurified followed by gel purification and analyzed by mass spectrometry. We illustrate this method using purification of a Tudor protein complex, which is essential for germline development. Tudor is a large protein, which contains multiple Tudor domains - small modules that interact with methylated arginines or lysines of target proteins. This method can be adapted for isolation of native protein complexes from different organisms and tissues.

The effectiveness of the crosslinking and the successful purification of the crosslinked Tud protein complex were analyzed by SDS-PAGE on a 3% - 7% step gel (illustrated in Figure 1) followed by western blot (Figure 2).
The purpose of using the 3% - 7% step gel is based on the effective separation of crosslinked Tud protein complex from the remaining uncrosslinked Tud protein and concentration of the complex. Under our in vivo crosslinking conditions ...

Watch this Scientific Journal Video about An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos at JoVE.com

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos

Multi-component protein complexes play crucial roles during cellular function and development. Here we describe a method used to isolate native protein complexes from Drosophila embryos after in vivo crosslinking followed by purification of the crosslinked complexes for subsequent structure-function analysis.

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos

Many cellular processes are controlled by multisubunit protein complexes. Frequently these complexes form transiently and require native environment to ...

an-vivo-crosslinking-approach-to-isolate-protein-complexes-from

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16.6K Views.  Murray State University. Multi-component protein complexes play crucial roles during cellular function and development. Here we describe a method used to isolate native protein complexes from Drosophila embryos after in vivo crosslinking followed by purification of the crosslinked complexes for subsequent structure-function analysis. 