The authors gratefully acknowledge support by NIH P50GM103297, P30CA100730 and Comprehensive Cancer P01CA16058.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Buffer Compositions</td>
		</tr>
		<tr>
			<td>Wash Buffer:</td>
		</tr>
		<tr>
			<td>50 mM Tris-HCl, pH 7.4</td>
		</tr>
		<tr>
			<td>150 mM NaCl</td>
		</tr>
		<tr>
			<td>3 mM MgCl2</td>
		</tr>
		<tr>
			<td>Low Salt Buffer:</td>
		</tr>
		<tr>
			<td>20 mM Tris-HCl, pH 7.5</td>
		</tr>
		<tr>
			<td>10 mM NaCl</td>
		</tr>
		<tr>
			<td>3 mM MgCl2</td>
		</tr>
		<tr>
			<td>2...

<ol>
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L., Yong, J., Dreyfuss, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-binding+proteins+and+post-transcriptional+gene+regulation.">RNA-binding proteins and post-transcriptional gene regulation.</a> FEBS Lett. 582 (14), 1977-1986 (2008).</li><li>Lunde, B. M., Moore, C., Varani, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-binding+proteins:+modular+design+for+efficient+function.">RNA-binding proteins: modular design for efficient function.</a> Nat.Rev.Mol.Cell Biol. 8 (6), 479-490 (2007).</li><li>Cochrane, A. W., McNally, M. T., Mouland, A. 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+retrovirus+RNA+trafficking+granule:+from+birth+to+maturity.">The retrovirus RNA trafficking granule: from birth to maturity.</a> Retrovirology. 3, 18 (2006).</li><li>Hartman, T. R., Qian, S., Bolinger, C., Fernandez, S., Schoenberg, D. R., Boris-Lawrie, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+helicase+A+is+necessary+for+translation+of+selected+messenger+RNAs.">RNA helicase A is necessary for translation of selected messenger RNAs.</a> Nat.Struct.Mol.Biol. 13 (6), 509-516 (2006).</li><li>Pullmann, 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=Analysis+of+turnover+and+translation+regulatory+RNA-binding+protein+expression+through+binding+to+cognate+mRNAs.">Analysis of turnover and translation regulatory RNA-binding protein expression through binding to cognate mRNAs.</a> Mol.Cell.Biol. 27 (18), 6265-6278 (2007).</li><li>Keene, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+regulons:+coordination+of+post-transcriptional+events.">RNA regulons: coordination of post-transcriptional events.</a> Nat.Rev.Genet. 8 (7), 533-543 (2007).</li><li>Moore, 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=From+birth+to+death:+the+complex+lives+of+eukaryotic+mRNAs.">From birth to death: the complex lives of eukaryotic mRNAs.</a> Science. 309 (5740), 1514-1518 (2005).</li><li>Hassan, M. Q., Gordon, J. A., Lian, J. B., van Wijnen, A. J., Stein, J. L., Stein, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ribonucleoprotein+immunoprecipitation+(RNP-IP):+a+direct+in+vivo+analysis+of+microRNA-targets.">Ribonucleoprotein immunoprecipitation (RNP-IP): a direct in vivo analysis of microRNA-targets.</a> J.Cell.Biochem. 110 (4), 817-822 (2010).</li><li>Selth, L. A., Close, P., Svejstrup, J. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studying+RNA-protein+interactions+in+vivo+by+RNA+immunoprecipitation.">Studying RNA-protein interactions in vivo by RNA immunoprecipitation.</a> Methods Mol.Biol. 791, 253-264 (2011).</li><li>Singh, D., Boeras, I., Singh, G., Boris-Lawrie, K. <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+Cognate+Cellular+and+Viral+Ribonucleoprotein+Complexes+of+HIV-1+RNA+Applicable+to+Proteomic+Discovery+and+Molecular+Investigations.">Isolation of Cognate Cellular and Viral Ribonucleoprotein Complexes of HIV-1 RNA Applicable to Proteomic Discovery and Molecular Investigations.</a> Methods Mol.Biol. 1354, 133-146 (2016).</li><li>Stake, 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=HIV-1+and+two+avian+retroviral+5'+untranslated+regions+bind+orthologous+human+and+chicken+RNA+binding+proteins.">HIV-1 and two avian retroviral 5' untranslated regions bind orthologous human and chicken RNA binding proteins.</a> Virology. 486, 307-320 (2015).</li><li>Sung, F. 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=Genome-wide+expression+analysis+using+microarray+identified+complex+signaling+pathways+modulated+by+hypoxia+in+nasopharyngeal+carcinoma.">Genome-wide expression analysis using microarray identified complex signaling pathways modulated by hypoxia in nasopharyngeal carcinoma.</a> Cancer Lett. 253 (1), 74-88 (2007).</li><li>Wang, Z., Gerstein, M., Snyder, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-Seq:+a+revolutionary+tool+for+transcriptomics.">RNA-Seq: a revolutionary tool for transcriptomics.</a> Nat.Rev.Genet. 10 (1), 57-63 (2009).</li><li>Michlewski, G., Caceres, J. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNase-assisted+RNA+chromatography.">RNase-assisted RNA chromatography.</a> RNA. 16 (8), 1673-1678 (2010).</li><li>Tacheny, A., Dieu, M., Arnould, T., Renard, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+spectrometry-based+identification+of+proteins+interacting+with+nucleic+acids.">Mass spectrometry-based identification of proteins interacting with nucleic acids.</a> J. Proteomics. 94, 89-109 (2013).</li><li>Duan, R., Sharma, S., Xia, Q., Garber, K., Jin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Towards+understanding+RNA-mediated+neurological+disorders.">Towards understanding RNA-mediated neurological disorders.</a> J.Genet.Genomics. 41 (9), 473-484 (2014).</li><li>Butsch, M., Hull, S., Wang, Y., Roberts, T. M., Boris-Lawrie, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+5'+RNA+terminus+of+spleen+necrosis+virus+contains+a+novel+posttranscriptional+control+element+that+facilitates+human+immunodeficiency+virus+Rev/RRE-independent+Gag+production.">The 5' RNA terminus of spleen necrosis virus contains a novel posttranscriptional control element that facilitates human immunodeficiency virus Rev/RRE-independent Gag production.</a> J. Virol. 73 (6), 4847-4855 (1999).</li><li>Bolinger, C., 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=RNA+helicase+A+interacts+with+divergent+lymphotropic+retroviruses+and+promotes+translation+of+human+T-cell+leukemia+virus+type+1.">RNA helicase A interacts with divergent lymphotropic retroviruses and promotes translation of human T-cell leukemia virus type 1.</a> Nucleic Acids Res. 35 (8), 2629-2642 (2007).</li><li>Bolinger, C., Sharma, A., Singh, D., Yu, L., Boris-Lawrie, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+helicase+A+modulates+translation+of+HIV-1+and+infectivity+of+progeny+virions.">RNA helicase A modulates translation of HIV-1 and infectivity of progeny virions.</a> Nucleic Acids Res. 38 (5), 1686-1696 (2010).</li><li>Lee, 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=Suppression+of+the+DHX9+helicase+induces+premature+senescence+in+human+diploid+fibroblasts+in+a+p53-dependent+manner.">Suppression of the DHX9 helicase induces premature senescence in human diploid fibroblasts in a p53-dependent manner.</a> J.Biol.Chem. 289 (33), 22798-22814 (2014).</li><li>Bradford, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+and+sensitive+method+for+the+quantitation+of+microgram+quantities+of+protein+utilizing+the+principle+of+protein-dye+binding.">A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.</a> Anal.Biochem. 72, 248-254 (1976).</li><li>Glenn, G. <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+protein+samples+for+mass+spectrometry+and+N-terminal+sequencing.">Preparation of protein samples for mass spectrometry and N-terminal sequencing.</a> Methods Enzymol. 536, 27-44 (2014).</li><li>Keene, J. D., Komisarow, J. M., Friedersdorf, M. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RIP-Chip:+the+isolation+and+identification+of+mRNAs,+microRNAs+and+protein+components+of+ribonucleoprotein+complexes+from+cell+extracts.">RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.</a> Nat.Protoc. 1 (1), 302-307 (2006).</li><li>Ranji, A., Shkriabai, N., Kvaratskhelia, M., Musier-Forsyth, K., Boris-Lawrie, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Features+of+double-stranded+RNA-binding+domains+of+RNA+helicase+A+are+necessary+for+selective+recognition+and+translation+of+complex+mRNAs.">Features of double-stranded RNA-binding domains of RNA helicase A are necessary for selective recognition and translation of complex mRNAs.</a> J.Biol.Chem. 286 (7), 5328-5337 (2011).</li></ol>

The RNP isolation and cognate RNA identification strategy described here is a selective means of investigating a specific RNA-protein interaction and of discovering candidate proteins co-regulating a specific RNP in cells.
The advantage of using oligonucleotide-directed RNase H cleavage to isolate RNPs is the ability to capture and specifically analyze the RNP cis-acting RNA element over heterogeneous RNPs bound downstream to the cis-acting RNA element of interest. Because the abundance of a c...

Post-transcriptional gene expression is precisely regulated, beginning with DNA transcription in the nucleus. Controlled by RNA binding proteins (RBPs), mRNA biogenesis and metabolism occur in highly dynamic ribonucleoprotein particles (RNPs), which associate and dissociate with a substrate precursor mRNA during the progression of RNA metabolism1-3. Dynamic changes in RNP components affect the post-transcriptional fate of an mRNA and provide quality assurance during the processing of primary transcripts, their nuclear trafficking and localization, their activity as mRNA templates for translation, and the eventual turnover of mature mRNAs.
Numerous proteins are designated as RBPs by virtue of their conserved amino acid domains, including the RNA recognition motif (RRM), the double-stranded RNA binding domain (RBD), and stretches of basic residues (e.g., arginine, lysine, and glycine)4. RBPs are routinely isolated by immunoprecipitation strategies and are screened to identify their cognate RNAs. Some RBPs co-regulate pre-mRNAs that are functionally-related, designated as RNA regulons5-8. These RBPs, their cognate mRNAs, and sometimes non-coding RNA, form catalytic RNPs that vary in composition; their uniqueness is due to various combinations of associated factors, as well as to the temporal sequence, location, and duration of their interactions9.
RNA immunoprecipitation (RIP) is a powerful technique to isolate RNPs from cells and to identify associated transcripts using sequence analysis10-13. Moving from candidate to genome-wide screening is feasible through RIP combined with a microarray analysis14 or high-throughput sequencing (RNAseq)15. Likewise, co-precipitating proteins may be identified by mass spectrometry, if they are sufficiently abundant and separable from the co-precipitating antibody16,17. Here, we address the methodology for isolating RNP components of a specific cognate RNA from cultured human cells, although the approach is alterable for soluble lysates of plant cells, fungi, viruses, and bacteria. Downstream analyses of the material include candidate identification and validation by immunoblot, mass spectrometry, biochemical enzymatic assay, RT-qPCR, microarray, and RNAseq, as summarized in Figure 1.
Given the fundamental role of RNPs in controlling gene expression at the post-transcriptional level, alterations in the expression of component RBPs or their accessibility to cognate RNAs can be detrimental for the cell and are associated with several types of disorders, including neurological disease18. DHX9/RNA helicase A (RHA) is necessary for the translation of selected mRNAs of cellular and retroviral origins6. These cognate RNAs exhibit structurally-related cis-acting elements within their 5&#39; UTR, which is designated as the post-transcriptional control element (PCE)19. RHA-PCE activity is necessary for the efficient cap-dependent translation of many retroviruses, including HIV-1, and of growth regulatory genes, including junD6,20,21. Encoded by an essential gene (dhx9), RHA is essential to cell proliferation and its down-regulation eliminates cell viability22. The molecular analysis of RHA-PCE RNPs is an essential step to understanding why RHA-PCE activity is necessary to control cell proliferation.
The precise characterization of the RHA-PCE RNP components at steady state or upon physiological perturbation of the cell requires the selective enrichment and capture of the RHA-PCE RNPs in sufficient abundance for downstream analysis. Here, retroviral PCEgag RNA was tagged with 6 copies of the cis-acting RNA binding site for the MS2 coat protein (CP) within the open reading frame. The MS2 coat protein was exogenously co-expressed with PCEgag RNA by plasmid transfection to facilitate the RNP assembly in growing cells. RNPs containing the MS2 coat protein with cognate MS2-tagged PCEgag RNA were immunoprecipitated from the cell extract and captured on magnetic beads (Figure 2a). To selectively capture the RNP components bound to the PCE, the immobilized RNP was incubated with an oligonucleotide complementary to sequences distal to the PCE, forming an RNA-DNA hybrid that is the substrate for RNase H activity. Since PCE is positioned in the 5&#39; terminal of the 5&#39; untranslated region, the oligonucleotide was complementary to the RNA sequences adjacent to the retroviral translation start site (gag start codon). RNase H cleavage near the gag start codon released the 5&#39; UTR complex from the immobilized RNP, which was collected as the eluent. Thereafter, the sample was evaluated by RT-PCR to confirm the capture of PCEgag and by SDS PAGE and immunoblot to confirm the capture of the target MS2 coat protein. A validation of the PCE-associated RNA binding protein, DHX9/RNA helicase A, was then performed.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Dynabeads Protein A</td>
			<td>Invitrogen</td>
			<td>10002D</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads Protein G</td>
			<td>Invitrogen</td>
			<td>10004D</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti- FLAG antibody</td>
			<td>Sigma</td>
			<td>F3165</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti- FLAG antibody</td>
			<td>Sigma</td>
			<td>F7425</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-RHA antibody</td>
			<td>Vaxron</td>
			<td>PA-001</td>
			<td></td>
		</tr>
		<tr>
			<td>TRizol LS reagent</td>
			<td>Life technology</td>
			<td>10296-028</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase H</td>
			<td>Ambion</td>
			<td>AM2292</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Fisher Scientific</td>
			<td>BP1145-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropanol</td>
			<td>Fisher Scientific</td>
			<td>BP26184</td>
			<td></td>
		</tr>
		<tr>
			<td>RNaeasy clean-up column</td>
			<td>Qiagen</td>
			<td>74204</td>
			<td></td>
		</tr>
		<tr>
			<td>Omniscript reverse transcriptase</td>
			<td>Qiagen</td>
			<td>205113</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase Out</td>
			<td>Invitrogen</td>
			<td>10777-019</td>
			<td></td>
		</tr>
		<tr>
			<td>Protease inhibitor cocktail</td>
			<td>Roche</td>
			<td>5056489001</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma</td>
			<td>X100</td>
			<td></td>
		</tr>
		<tr>
			<td>NP-40</td>
			<td>Sigma</td>
			<td>98379</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Fisher Scientific</td>
			<td>17904</td>
			<td></td>
		</tr>
		<tr>
			<td>Random hexamer primers</td>
			<td>Invitrogen</td>
			<td>N8080127</td>
			<td></td>
		</tr>
		<tr>
			<td>Oligo-dT primers</td>
			<td>Invitrogen</td>
			<td>AM5730G</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR primers</td>
			<td>IDT</td>
			<td></td>
			<td>Gene specific primers for&#160; PCR amplification</td>
		</tr>
		<tr>
			<td>Oligonucleotide for RNase H mediated cleavage</td>
			<td>IDT</td>
			<td></td>
			<td>Anti-sense primer for target RNA</td>
		</tr>
		<tr>
			<td>Trypsin</td>
			<td>Gibco Life technology</td>
			<td>25300-054</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM tissue culture medium</td>
			<td>Gibco Life technology</td>
			<td>11965-092</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Gibco Life technology</td>
			<td>10082-147</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris base</td>
			<td>Fisher Scientific</td>
			<td>BP152-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Fisher Scientific</td>
			<td>S642-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium chloride</td>
			<td>Fisher Scientific</td>
			<td>BP214</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Fisher Scientific</td>
			<td>R0862</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Fisher Scientific</td>
			<td>BP220-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Nitrocellulose membrane</td>
			<td>Bio-Rad</td>
			<td>1620112</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic stand</td>
			<td></td>
			<td></td>
			<td>1.7 ml micro-centrifuge tube holding</td>
		</tr>
		<tr>
			<td>Laminar hood</td>
			<td></td>
			<td></td>
			<td>For animal tissue culture</td>
		</tr>
		<tr>
			<td>CO2 incubator</td>
			<td></td>
			<td></td>
			<td>For animal tissue culture</td>
		</tr>
		<tr>
			<td>Protein gel apparatus</td>
			<td></td>
			<td></td>
			<td>Protein sample separation</td>
		</tr>
		<tr>
			<td>Protein transfer apparatus</td>
			<td></td>
			<td></td>
			<td>Protein sample transfer</td>
		</tr>
		<tr>
			<td>Ready to use protein gels (4-15%)</td>
			<td></td>
			<td></td>
			<td>Protein sample separation</td>
		</tr>
		<tr>
			<td>Table top centrifuge</td>
			<td></td>
			<td></td>
			<td>Pellet down the sample</td>
		</tr>
		<tr>
			<td>Table top rotator</td>
			<td></td>
			<td></td>
			<td>Mix the sample end to end</td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td></td>
			<td></td>
			<td>Mix the samples</td>
		</tr>
	</tbody>
</table>

isolation of cognate rna-protein complexes from cells using oligonucleotide-directed elution

Ribonucleoprotein particles direct the biogenesis and post-transcriptional regulation of all mRNAs through distinct combinations of RNA binding proteins. They are composed of position-dependent, cis-acting RNA elements and unique combinations of RNA binding proteins. Defining the composition of a specific RNP is essential to achieving a fundamental understanding of gene regulation. The isolation of a select RNP is akin to finding a needle in a haystack. Here, we demonstrate an approach to isolate RNPs associated at the 5' untranslated region of a select mRNA in asynchronous, transfected cells. This cognate RNP has been demonstrated to be necessary for the translation of select viruses and cellular stress-response genes.
The demonstrated RNA-protein co-precipitation protocol is suitable for the downstream analysis of protein components through proteomic analyses, immunoblots, or suitable biochemical identification assays. This experimental protocol demonstrates that DHX9/RNA helicase A is enriched at the 5' terminus of cognate retroviral RNA and provides preliminary information for the identification of its association with cell stress-associated huR and junD cognate mRNAs.

Prior RIP results identified retroviral gag RNAs and selected cellular RNAs that co-precipitate with DHX9/RHA, including HIV-16, junD6 and huR (Fritz and Boris-Lawrie, unpublished). The retroviral 5&#39; UTR has been demonstrated to co-precipitate with DHX9/RHA in the nucleus and to co-isolate in the cytoplasm on polyribosomes. It is uniquely defined as the cis-acting post-transcriptional control element (PCE)6. To isolate PCEgag RNA-RHA ribonucle...

Watch this Scientific Journal Video about Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution at JoVE.com

Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution

This manuscript describes an approach to isolate select cognate RNPs formed in eukaryotic cells via a specific oligonucleotide-directed enrichment. We demonstrate the applicability of this approach by isolating a cognate RNP bound to the retroviral 5' untranslated region that is composed of DHX9/RNA helicase A.

Ribonucleoprotein particles direct the biogenesis and post-transcriptional regulation of all mRNAs through distinct combinations of RNA binding proteins. ...

The overall goal of this RNA immunoprecipitation technique is to selectively isolate and characterize endogenous RNA protein complexes formed in eukaryotic cells via a specific oligonucleotide directed enrichment. This method can help answer key questions in the post-transcriptional control field, such as the composition of RNA binding proteins that define the five prime UTR of a retroviral transcript to regulate its gene expression. The main advantage of this technique is that it allows a researcher to selectively isolate and characterize a specific RNA protein complex of interest while maintaining the possibility to conduct a more global analysis of the RNP downstream.Well the implications of this technique extend toward fundamental understanding of viral infections and numerous cellular diseases. And provides significant insight into the mechanisms of post-transcriptional control of gene expression. That could mean new viable drug targets.After culturing cells and carrying out immunoprecipitation of a FLAG-tagged protein according to the text protocol, transfer 60 microliters per IP of pro-TG magnetic bead slurry to a 1.7 milliliter microcentrifuge tube. Place the tube on a magnetic rack and remove the storage solution by carefully pipetting. Then remove the tube from the rack.Add 600 microliters of 1x wash buffer. And place the tube on an end over end rotator at room temperature for three minutes, to wash and equilibrate the beads. Place the tube on the magnetic rack and remove the wash buffer.Then add 10 volumes of fresh 1x wash buffer. Add immunoprecipitating FLAG antibody to the equilibrated pro-TG magnetic beads. And then rotate the tube at room temperature for at least 30 minutes, to conjugate the immunoprecipitating antibody.Place the tube on the magnet and remove the supernatant. Then remove the tube from the magnet and add 1x wash buffer to the beads and rotate at room temperature for three minutes. Repeat the wash step twice and remove the final buffer.Remove the culture medium from the cells by aspiration and use 1.5 milliliters of ice-cold PBS to wash the cells twice. With a cell scraper dislodge the wet, adherent cells. Pipette the cell suspension into fresh tubes and then centrifuge the culture at 226 times G in four degrees celsius, for four minutes.Add 375 microliters of ice cold low salt buffer to the cell pellet, and incubate the sample on ice for five minutes to allow swelling. It is important to take care when adding and re-suspending the cell pellet in the low salt lysis buffer, to ensure complete submersion and swelling without premature mechanical disruption. To collect the cytoplasmic cell lysate, add 125 microliters of ice cold lysis buffer, and then use a pre-chilled Dounce homogenizer to perform ten strokes.Dounce homogenize with enough force to enable plasma membrane lysis and contaminants of the released cytoplasmic lysate. But take care to not overextend the mechanical disruption and risk nuclear contaminations, disruption of RNA protein complex, or loss of released Spin the homogenate in a microfuge at top speed for one minute. Then transfer the supernatant to a new 1.7 milliliter tube that has been on ice.Determine the total protein concentration. Reserve 10%for western blot analysis, to be used as input control. To carry out immunoprecipitation, add the desired volume of harvested cell lysate to the target antibody conjugated beads.Using 1x wash buffer, bring the total volume up to 600 microliters and rotate the sample at room temperature. After 90 minutes of incubation, place the IP tube on the magnet rack to collect the beads. Then collect the supernatant and reserve it as flow through.Next, add 10 volumes of ice cold NETN 150 wash buffer to the RNP bound, antibody conjugated beads, and rotate the sample at room temperature for three minutes. After re-suspending the immobilized RNP complexes in 1x binding buffer according to the text protocol, adjust the remaining volume in 100 microliters of ice cold 1x binding buffer. And heat the tube at 70 degrees Celsius for three minutes.To isolate cognate RNA protein complexes, add an approximately 30 nucleotide DNA oligo, complementary to the three prime sequence boundary of the RNA of interest. And incubate for 30 minutes at room temperature with gentle rocking. Add five to ten units or RNase H to the tube and incubate the sample at room temperature for one hour to cleave the RNA from the RNA DNA hybrid.Then transfer the supernatant containing the captured RNP complexes of interest to a sterile 1.7 milliliter microcentrifuge tube. To collect the immunoprecipitated RNA, re-suspend half of the total sample of captured RNA complexes in 750 microliters of acid guanidinium thiocyanate reagent. Add 200 microliters of chloroform to the tube, shake vigorously for 10 seconds an incubate at room temperature for three minutes.After centrifugation, collect the aqueous phase in a fresh tube, and add an equal volume of isopropanol. Mix well and incubate the sample at room temperature for at least ten minutes. Add one microliter of glycol blue to the sample and store it at negative 20 degrees celsius for efficient precipitation or processing at a future date.Centrifuge the tube at 16, 000 times G in four degrees Celsius for ten minutes. The use a P200 micropipette to carefully collect and discard the supernatant so as not to disturb the RNA pellet. Add 500 microliters of 75%ethanol to each tube.Vortex and centrifuge the tubes for five minutes. Carefully collect and discard the supernatant as just demonstrated. Air dry the pellet for two to three minutes and use 100 microliters of RNase free water to re-suspend it.Apply 100 microliters of the RNA sample to an RNA clean up column. And process it according to the manufacturers protocol. Finally, elute the RNA in 30 microliters of RNase free water and store it at negative 80 degrees Celsius for up to three months.To isolate post-transcriptional control elements, or PCE, GAG, RNA, RHA ribonucleoprotein complexes formed in proliferating cells. FLAG-MS2 RNP immunoprecipitation was carried out in transfected HECK293 cell lysates. The results show efficient precipitation of the FLAG-MS2 protein.As DHX9/RHA is found in the RNP complex and not within the IgG isotope control, nor within the negative control. Shown here are western blots from RNase H digested RNA DNA complexes. RNase H cleaved PCE GAG RNA, releasing the RNP complex specifically bound to the five prime UTR.The DHX9/RHA associated RNPs were enriched in the eluents. Importantly, the FLAG-MS2 bound RNPs remained with the antibody conjugated beads. In this experiment, HO immunoprecipitation of the MS2 stem loop, containing retroviral PCE GAG RNA in cells and in eluents, was validated by RT-PCR and QRT-PCR.The results confirmed a select association between DHX9/RHA and the retroviral five prime UTR, which has been highlighted as a unique RNP, important for targeted translation control. Once mastered, this technique can be done in approximately five hours, if it is performed properly. While attempting this procedure, it's important to remember to perform all steps efficiently and with care, to ensure maintenance of intact RNP complexes and the isolation of the specific RNP complex of interest.Following this procedure, other methods like mass spectrometry and RNA-Seq, can be performed in order to answer additional questions, like global protein association with the target RNA. And region or complete analysis of all transcripts engaged within a particular RNP. After its development, this technique paved the way for researcher in the field of post-transcriptional gene control to explore the distinct RNA protein complexes governing pathogenic viral gene expiration and general mechanism of cellular gene expression control.After watching this video, you should have a good understanding of how to harvest intact cellular RNP complexes and determine their composition using selective oligonucleotide directed enrichment. Do not forget too, working with pathogenic viruses and biological samples and hazardous chemicals like acid or phenol, can be extremely hazardous. All precautions, such as appropriate personal protective equipment should always be taken while performing this procedure.

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8.9K vistas.  University of Minnesota. The overall goal of this RNA immunoprecipitation technique is to selectively isolate and characterize endogenous RNA protein complexes formed in eukaryotic cells via a specific oligonucleotide directed enrichment. This method can help answer key questions in the post-transcriptional control field, such as the composition of RNA binding proteins that define the five prime UTR of a retroviral transcript to regulate its gene expression. The main advantage of this technique is that it allows a re...