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. 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.
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' 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' terminal of the 5' 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' 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.
Buffer Compositions |
Wash Buffer: |
50 mM Tris-HCl, pH 7.4 |
150 mM NaCl |
3 mM MgCl2 |
Low Salt Buffer: |
20 mM Tris-HCl, pH 7.5 |
10 mM NaCl |
3 mM MgCl2 |
2 mM DTT |
1x protease inhibitor cocktail EDTA-free |
RNase Out 5 µl/ml (RNase inhibitor) |
Cytoplasmic Lysis Buffer: |
0.2 M Sucrose |
1.2% Triton X-100 |
NETN-150 Wash Buffer: |
20 mM Tris-HCl, pH 7.4 |
150 mM NaCl |
0.5% NP-40 |
3 mM MgCl2 |
10% Glycerol |
Binding Buffer: |
10 mM HEPES pH 7.6 |
40 mM KCl |
3 mM MgCl2 |
2 mM DTT |
5% glycerol |
Table 2: Buffer compositions.
1. Preparation of the Cells and the Affinity Matrix
2. Harvesting the RNPs
NOTE: Prepare the RNPs during the incubation time after step 1.8.
3. Immunoprecipitation
4. Elution
5. Protein Electrophoresis and Western Blot Analysis
6. Collection of the Immunoprecipitated RNA
NOTE: RNA isolation can be done by Trizol method or following the described protocol.
7. RNA Reverse Transcription and Amplification of cDNA by PCR
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' 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 ribonucleoprotein complexes (RNPs) formed in proliferating cells, we performed FLAG-MS2 RNP immunoprecipitation in transfected HEK293 cell lysates. The results show efficient precipitation of the FLAG-MS2 protein. Notably, DHX9/RHA is identified within this RNP complex and not within the IgG isotype control, nor within the negative-control HEK293 cell lysate (Figure 2A). The matrix containing the RNPs was incubated with a complementary 30-nt oligonucleotide, and then an RNase H cleavage of the RNA-DNA hybrid was performed. Upon RNase H digestion, the eluates were analyzed by Western blotting. The demonstrated RNase H cleavage of PCEgag RNA at the RNA-DNA hybrid position released the RNP complex specifically bound to the 5' UTR. The DHX9/RHA-associated RNPs were determined to be enriched in the eluents. Importantly, the FLAG-MS2-bound RNPs remained with the antibody-conjugated beads (Figure 2B). The co-immunoprecipitation of the MS2 stem-loop containing retroviral PCEgag RNA in cells and in eluents was validated by RT-PCR and qRTPCR (Figure 2C). The results confirmed a select association between DHX9/RHA and the retroviral 5' UTR, which has been highlighted as a unique RNP important for targeted translation control6.
Figure 1: RNP isolation and the enrichment of specific RNPs associated with the 5' UTR of PCEgag by RNase H cleavage. Workflow showing the steps to isolate a selected ribonucleoprotein formed de novo in cells, its collection by oligonucleotide-guided RNaseH cleavage, and the downstream analysis of RNA and protein components. Summary of affinity chromatography using a high-affinity interaction between multimers for the MS2 RNA stem-loop and the MS2 coat protein-FLAG fusion protein to capture PCE RNA on FLAG beads. Please click here to view a larger version of this figure.
Figure 2: A PCEgag RNA containing 6 MS2 RNA binding sites was captured by an immobilized FLAG-tagged MS2 coat protein, and specific RNPs associated with the 5' UTR were released by oligonucleotide-directed RNase H cleavage. HEK293 cells were co-transfected with pAR200 (a plasmid containing the PCEgag and 6x MS2 loops in the HIV intron) and a plasmid expressing the FLAG epitope-tagged MS2 protein with a nuclear localization sequence (NLS). Cells were collected and the cytoplasm was isolated at 48 hr post-transfection. The cytoplasmic lysates were subjected to immunoprecipitation with either FLAG antibody or an IgG control. (A) The IP efficiency was determined by immunoblot using an anti-FLAG antibody. DHX9/RHA, a PCE binding protein, served as a positive control; PCE-containing RNA immunoprecipitated with the MS2 protein. Lanes 1-3: Input proteins used for IP. Lanes 4-5: FLAG IP of FLAG MS2 overexpressed lysate and HEK293 cytoplasmic cell lysate. Lane 6: IgG IP of FLAG MS2 overexpressed lysate. Lanes 7-9: Flow-through of the IPs. (B) 5' UTR-bound RNPs were enriched by RNase H cleavage. Lanes 1-3: Eluates of the 5' UTR-bound protein by RNase H. Lanes 4-6: proteins bound to antibody-conjugated beads. (C) Reverse transcriptase PCR and real-time quantitative PCR of specific RNA bound to different fractions of RNPs. Please click here to view a larger version of this figure.
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 cognate RNA in a given RNP is a minor fraction of the collected RNPs isolated without RNase H cleavage, the major disadvantage to this workflow is the scarcity of the cognate RNP. In our experience, this limitation necessitated 5- to 10-fold more starting material than conventional RNA IP for detection in sensitive immunoblot and proteomics analyses. Another advantage provided by immobilizing the RNP is the convenience of repeating the RNase H treatment and collecting additional eluate. In our experience, 2-4 rounds of RNase H treatment were advisable to collect additional eluate.
In this protocol, key technical concerns are maintaining the optimal temperature and ensuring the sterile handling of the reagents. All reagents should be RNase- and protease-free. The integrity of the RNA sample is a potential pitfall to consider if an RNA-protein interaction is not detectable.
This technique requires the efficient lysis of the cells to access the RNPs in a suitable quantity for detection. While an important caveat is incomplete cell lysis, vigorous treatments may increase non-specific interactions with the RNA. Therefore, the experimental conditions should be measured in order to enrich specific protein-RNA interactions. However, the use of high-stringency washes may eliminate important yet transient interactions. Therefore, the washing conditions are another variable to consider in the specific requirements of a particular experiment.
RIP efficiency is a powerful technique to isolate cognate RNA-protein partners, but some transient or weak interactions that are of physiological importance are lost during the binding or washing steps. Cross-linking of the mRNP complex is an option to consider in an analysis. Moreover, physiological growth conditions should be kept in mind while analyzing regulatory RNPs, as the expression level of the cognate RNA or RBP may be subject to physiological fluctuations under certain conditions. Furthermore, the type of downstream analysis will also play a role in selecting the lysis and washing conditions during the immunoprecipitation.
In addition, the successful immunoprecipitation requires that the cell lysate be significantly dilute (at least 1:1). 1x wash buffer (20 mM Tris-HCl, pH 7.3; 3 mM MgCl2; and 150 mM NaCl) is the selected diluent, as its composition does not affect RNP integrity, solution solubility, or antibody-antigen interactions.
For downstream mass spectrometry, samples should be free from salts, including Na+, Cl–, and Tris, as well as some detergents. If necessary, components of buffers-the ionic compounds-may be reduced by dialysis or ionic exchange filtration, and in some cases, volatile buffers are useful in the final steps. In cases when antiserum is used to isolate an epitope-tagged protein expressed by transfection, Western blot validation of the recombinant protein using initial cell lysate should be executed before further analysis. In case an epitope tag is used (i.e., FLAG, MYC, GFP, etc.), the exposure of the tag is crucial to the success of the antibody binding step. Freeze-thaw of samples should be avoided.
The RIP technique has been widely employed to elucidate diverse mechanisms of post-transcriptional gene control10,25. This includes the identification of novel protein-mRNA, protein-microRNA, and protein-protein interactions10,25. Here, we provide a comprehensive protocol for the determination of RNP composition within a cell culture. Our method allows for the targeted and genome-wide assessment of critical protein-RNA interactions, as well as for the capture of rare and/or transient RNP complexes.
The application of this technique has contributed to our characterization of RNAs bound by DHX9/RNA helicase A and helped us to define the critical post-transcriptional regulation of retroviruses and the cellular proto-oncogenes junD6,26 and huR (Fritz and Boris-Lawrie, unpublished data). We expect the application of this technique in future studies to further our understanding of the critical mechanisms for gene control, including those mediated by long non-coding RNP complexes.
The authors have nothing to disclose.
The authors gratefully acknowledge support by NIH P50GM103297, P30CA100730 and Comprehensive Cancer P01CA16058.
Dynabeads Protein A | Invitrogen | 10002D | |
Dynabeads Protein G | Invitrogen | 10004D | |
Anti- FLAG antibody | Sigma | F3165 | |
Anti- FLAG antibody | Sigma | F7425 | |
Anti-RHA antibody | Vaxron | PA-001 | |
TRizol LS reagent | Life technology | 10296-028 | |
RNase H | Ambion | AM2292 | |
Chloroform | Fisher Scientific | BP1145-1 | |
Isopropanol | Fisher Scientific | BP26184 | |
RNaeasy clean-up column | Qiagen | 74204 | |
Omniscript reverse transcriptase | Qiagen | 205113 | |
RNase Out | Invitrogen | 10777-019 | |
Protease inhibitor cocktail | Roche | 5056489001 | |
Triton X-100 | Sigma | X100 | |
NP-40 | Sigma | 98379 | |
Glycerol | Fisher Scientific | 17904 | |
Random hexamer primers | Invitrogen | N8080127 | |
Oligo-dT primers | Invitrogen | AM5730G | |
PCR primers | IDT | Gene specific primers for PCR amplification | |
Oligonucleotide for RNase H mediated cleavage | IDT | Anti-sense primer for target RNA | |
Trypsin | Gibco Life technology | 25300-054 | |
DMEM tissue culture medium | Gibco Life technology | 11965-092 | |
Fetal bovine serum | Gibco Life technology | 10082-147 | |
Tris base | Fisher Scientific | BP152-5 | |
Sodium chloride | Fisher Scientific | S642-212 | |
Magnesium chloride | Fisher Scientific | BP214 | |
DTT | Fisher Scientific | R0862 | |
Sucrose | Fisher Scientific | BP220-212 | |
Nitrocellulose membrane | Bio-Rad | 1620112 | |
Magnetic stand | 1.7 ml micro-centrifuge tube holding | ||
Laminar hood | For animal tissue culture | ||
CO2 incubator | For animal tissue culture | ||
Protein gel apparatus | Protein sample separation | ||
Protein transfer apparatus | Protein sample transfer | ||
Ready to use protein gels (4-15%) | Protein sample separation | ||
Table top centrifuge | Pellet down the sample | ||
Table top rotator | Mix the sample end to end | ||
Vortex | Mix the samples |