Name: novel rna-binding proteins isolation by the rapid methodology
Uploaded: 2016-09-30T14:00:00
Description: Watch this Scientific Journal Video about Novel RNA-Binding Proteins Isolation by the RaPID Methodology at JoVE.com

We thank Prof. Jeff Gerst and Boris Slobodin for their helpful advice in setting up the RaPID protocol and providing the necessary plasmids. We also thank Dr. Avigail Atir-Lande for her help in establishing this protocol and Dr. Tamar Ziv from the Smoler Proteomics Center for her help with the LC-MS/MS analysis. We thank Prof. T.G. Kinzy (Rutgers) for the YEF3 antibody. This work was supported by grant 2011013 from the Binational Science Foundation.

Note: Insert a sequence consisting of 12 MS2-binding sites (MS2 loops; MS2L) into the desired genomic locus, usually between the open reading frame (ORF) and the 3&#39; UTR. A detailed protocol for this integration is provided elsewhere22. Verify proper insertion and expression by PCR, northern analysis or RT-PCR20,23. It is important to verify that the integration did not intervene with the synthesis of the 3&#39;UTR. In addition, a plasmid-expressing MS2-CP fused to SBP under the expression of an ...

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Various methods use the isolation of specific mRNAs to identify their associated proteins11,34 35. These methods apply in vitro and in vivo strategies to probe RNA-protein interactions. In vitro methods incubate exogenously transcribed RNA with cell lysate to capture RBPs and isolate RNP complexes36,37. An effective approach of this type was presented recently, which enabled the identification of novel proteins that bind a regulatory RNA motif18. A dr...

RNA-binding proteins (RBPs) represent about 10% of S. cerevisiae proteins1,2 and about 15% of mammalian proteins3-5. They are implicated in many cellular processes such as mRNA post-transcriptional processing and regulation, translation, ribosome biogenesis, tRNA aminoacylation and modification, chromatin remodeling, and more. An important subgroup of RBPs is the mRNA-binding proteins (mRNPs)6,7. In the course of mRNA maturation, different RBPs bind the transcript and mediate its nuclear processing, export out of the nucleus, cellular localization, translation and degradation6-8. Thus, the distinct set of RBPs bound to a particular transcript at any time point determines its processing and ultimately its fate.
The identification of RBPs associated with an mRNA could significantly improve our understanding of processes underlying their post-transcriptional regulation. Diverse genetic, microscopic, biochemical and bioinformatics methods have been used to identify proteins involved in mRNA regulation (reviewed in9-11). However, only a few of these methods enable the identification of proteins associated with a particular target mRNA. Of note is the Yeast Three Hybrid system (Y3H), which utilizes the mRNA of interest as bait to screen an expression library in yeast cells. Positive clones are usually observed through a growth selection or reporter expression12-14. The key advantage of this method is the large number of proteins that can be scanned in a cellular environment and the ability to measure the strength of the RNA-protein interaction. Drawbacks include the relatively large number of false positive results due to non-specific binding, and the high potential for false negative results due, in part, to misfolding of the fusion protein prey or the bait RNA.
An alternative to the genetic approach is affinity purification of RNA with its associated proteins. Poly A-containing mRNAs can be isolated through the use of oligo dT columns, and their associated proteins are detected by mass spectrometry. The RNA-protein interaction is conserved in its cellular context by crosslinking, which makes short-range covalent bonds. The use of the oligo dT column yields a global view of the entire proteome that is associated with any poly A-containing mRNA3,5,15. However, this does not provide a list of proteins that are associated with a particular mRNA. Very few methods are available to accomplish such an identification. The PAIR method entails the transfection of nucleic acid with complementarity to the target mRNA16,17. The nucleic acid is also attached to a peptide, which allows crosslinking to RBPs in close vicinity to the interaction site. After crosslinking, the RBP-peptide-nucleic acid can be isolated and subjected to proteomics analysis. Recently, an aptamer-based methodology was successfully applied to extracts from mammalian cell lines18. An RNA aptamer with improved affinity to streptavidin was developed and fused to a sequence of interest (AU-rich element (ARE) in this case). The aptamer-ARE RNA was attached to streptavidin beads and mixed with cell lysate. Proteins that associated with the ARE sequence were purified and identified by mass spectrometry (MS). Although this method detected associations that occur outside the cellular settings (i.e., in vitro), it is likely to be modified in the future so as to introduce the aptamers into the genome and thus enable the isolation of proteins associated with the mRNA while in the cellular milieu (i.e., in vivo). In yeast, where genetic manipulations are well established, the RaPID method (developed in Prof. Jeff Gerst&#39;s lab) provides a view of in vivo associations19. RaPID combines the specific and strong binding of the MS2 coat protein (MS2-CP) to the MS2 RNA sequence, and of the streptavidin-binding domain (SBP) to streptavidin conjugated beads. This enables efficient purification of MS2-tagged mRNAs through streptavidin beads. Moreover, expression of 12 copies of MS2 loops allows up to six MS2-CPs to bind simultaneously to the RNA and increase the efficiency of its isolation. This protocol was therefore suggested to enable the identification of novel mRNA-associated proteins once the eluted samples are subjected to proteomics analysis by mass spectrometry.
We recently utilized RaPID to identify novel proteins associated with the yeast PMP1 mRNA20. PMP1 mRNA was previously shown to be associated with the ER membrane and its 3&#39; untranslated region (UTR) was found to be a major determinant in this association21. Thus, RBPs that bind PMP1 3&#39; UTR are likely to play an important role in its localization. RaPID followed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) resulted in the identification of many new proteins that interact with PMP120. Herein, we provide a detailed protocol of the RaPID methodology, important controls that need to be done, and technical tips that may improve yield and specificity.

<table border="0" cellpadding="0" cellspacing="0" width="632">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">Tris</td>
			<td style="width:107px;">sigma</td>
			<td style="width:119px;">T1503</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SDS</td>
			<td>bio-lab</td>
			<td align="right">1981232300</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DTT</td>
			<td>sigma</td>
			<td>D9779</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Acidic Phenol (pH 4.3)</td>
			<td>sigma</td>
			<td>P4682</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Acidic Phenol: Chloroform (5:1, pH 4.3)</td>
			<td>sigma</td>
			<td>P1944</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Chloroform</td>
			<td>bio-lab</td>
			<td align="right">3080521</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Formaldehyde</td>
			<td>Frutarom</td>
			<td align="right">5551820</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glycine</td>
			<td>sigma</td>
			<td>G7126</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NP-40</td>
			<td>Calbiochem</td>
			<td align="right">492016</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Heparin</td>
			<td>Sigma</td>
			<td>H3393</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Phenylmethylsulfonyl Flouride (PMSF)</td>
			<td>Sigma</td>
			<td>P7626</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Leupeptin</td>
			<td>Sigma</td>
			<td>L2884</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Aprotinin</td>
			<td>Sigma</td>
			<td>A1153</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Soybean Trypsin Inhibitor</td>
			<td>Sigma</td>
			<td>T9003</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pepstatin</td>
			<td>Sigma</td>
			<td>P5318</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DNase I</td>
			<td>Promega</td>
			<td>M610A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ribonuclease&#160; Inhibitor</td>
			<td>Takara</td>
			<td>2313A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glass Beads</td>
			<td>Sartorius</td>
			<td>BBI-8541701</td>
			<td>0.4-0.6mm diameter&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mini BeadBeater</td>
			<td>BioSpec</td>
			<td colspan="2">Mini BeadBeater 16</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Guanidinium</td>
			<td>Sigma</td>
			<td>G4505</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Avidin</td>
			<td>Sigma</td>
			<td>A9275</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Streptavidin Beads</td>
			<td>GE Healthcare&#160;</td>
			<td>17-5113-01</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bovine serum albumin (BSA)</td>
			<td>Sigma</td>
			<td>A7906</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Yeast tRNA</td>
			<td>Sigma</td>
			<td>R8508</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Biotin</td>
			<td>Sigma</td>
			<td>B4501</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Yeast extract</td>
			<td>Bacto</td>
			<td dir="LTR">288620</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">peptone</td>
			<td>Bacto</td>
			<td dir="LTR">211677</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glucose</td>
			<td>Sigma</td>
			<td>G8270</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1 x Phosphate-Buffered saline (PBS)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.2 M NaOH</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">4 x Laemmli Sample Buffer (LSB)</td>
			<td></td>
			<td></td>
			<td>0.2 M Tris-Hcl pH 6.8, 8% SDS, 0.4 M DTT, 40% glycerol, 0.04% Bromophenol-Blue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hot phenol lysis buffer</td>
			<td></td>
			<td></td>
			<td>10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">3 M Sodium Acetate pH 5.2</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100% and 70% Ethanol (EtOH)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RNase-free water</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">RaPID lysis buffer</td>
			<td></td>
			<td></td>
			<td>20 mM Tris pH 7.5, 150 mM NaCl, 1.8 mM MgCl2, 0.5% NP-40, 5 mg/ml Heparin, 1 mM Dithiothreitol (DTT), 1 mM Phenylmethylsulfonyl Flouride (PMSF), 10 &#181;g/ml Leupeptin, 10 &#181;g/ml Aprotinin, 10 &#181;g/ml Soybean Trypsin Inhibitor, 10 &#181;g/ml Pepstatin, 20 U/ml DNase I, 100 U/ml Ribonuclease&#160; Inhibitor.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">2x Cross-linking reversal buffer</td>
			<td></td>
			<td></td>
			<td dir="LTR">100 mM Tris pH 7.4, 10 mM EDTA, 20 mM DTT, 2 % SDS.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RaPID wash buffer</td>
			<td></td>
			<td></td>
			<td>20 mM Tris-HCl pH 7.5,&#160; 300 mM NaCl, 0.5% NP-40</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.5 M EDTA pH 8</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Silver Stain Plus Kit</td>
			<td>Bio-Rad&#160;</td>
			<td>161-0449</td>
			<td>For detecting proteins in polyacrylamide gels</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SD selective medium&#160;</td>
			<td></td>
			<td></td>
			<td>1.7 g/l Yeast nitrogen base with out amino acids and ammonium sulfate, 5 g/l Ammonium sulfate, 2% glucose, 350 mg/l Threonine, 40 mg/l Methionine, 40 mg/l Adenine, 50 mg/l Lysine, 50 mg/l Tryptophan, 20 mg/l Histidine, 80 mg/l Leucine, 30 mg/l Tyrosine, 40 mg/l Arginine</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Anti-eEF3 (EF3A,YEF3)</td>
			<td colspan="2">Gift from Kinzy TG. (UMDNJ Robert Wood Johnson Medical School)</td>
			<td>1:5,000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Anti GFP antibody</td>
			<td>Santa Cruz</td>
			<td>sc-8334</td>
			<td>1:3,000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Anti rabbit IgG-HRP conjugated</td>
			<td>SIGMA</td>
			<td>A9169</td>
			<td>1:10,000</td>
		</tr>
	</tbody>
</table>

novel rna-binding proteins isolation by the rapid methodology

RNA-binding proteins (RBPs) play important roles in every aspect of RNA metabolism and regulation. Their identification is a major challenge in modern biology. Only a few in vitro and in vivo methods enable the identification of RBPs associated with a particular target mRNA. However, their main limitations are the identification of RBPs in a non-cellular environment (in vitro) or the low efficiency isolation of RNA of interest (in vivo). An RNA-binding protein purification and identification (RaPID) methodology was designed to overcome these limitations in yeast and enable efficient isolation of proteins that are associated in vivo. To achieve this, the RNA of interest is tagged with MS2 loops, and co-expressed with a fusion protein of an MS2-binding protein and a streptavidin-binding protein (SBP). Cells are then subjected to crosslinking and lysed, and complexes are isolated through streptavidin beads. The proteins that co-purify with the tagged RNA can then be determined by mass spectrometry. We recently used this protocol to identify novel proteins associated with the ER-associated PMP1 mRNA. Here, we provide a detailed protocol of RaPID, and discuss some of its limitations and advantages.

RaPID enables the isolation of a specific target RNA with its associated proteins. Critical for its success is keeping the RNA intact as much as possible, thereby obtaining a sufficient amount of proteins. To determine the isolation efficiency and quality of RNA, northern analysis is performed (Figure 1A). Northern analysis has the advantage of directly reporting the efficiency and quality of RaPID. Thus, the relative amounts of full length and degradation products can be...

Watch this Scientific Journal Video about Novel RNA-Binding Proteins Isolation by the RaPID Methodology at JoVE.com

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

RNA-protein interactions lie at the heart of many cellular processes. Here, we describe an in vivo method to isolate specific RNA and identify novel proteins that are associated with it. This could shed new light on how RNAs are regulated in the cell.

RNA-binding proteins (RBPs) play important roles in every aspect of RNA metabolism and regulation. Their identification is a major challenge in modern ...

The overall goal of this procedure is to efficiently isolate specific RNA with proteins that are associated with the RNA in vivo. This method can help answer key questions in RNA metabolism and regulation, such as what is a distinct set of fau-bee-pees bound to a particular transcript. The main advantage of this technique is the high efficiency of isolation, which allows follow up identification of noble mRNA associated proteins.The rapid methodology utilizes a yeast strain that co-expresses MS2-tagged MRNA and a fusion protein of an MS2 binding protein and a streptavadin binding protein. Grow 500 milliliters of yeast cells at 30 degrees Celsius in synthetic dextrose or SD selective medium to an OD600 of 0.8 to 1.0. When the cells are ready, centrifuge at 3000 times G for 4 minutes at room temperature and discard the supernatant.Wash the cells in PBS and centrifuge again. Discard the supernatant and re-suspend the cells in an equal volume of SD without methionine. Incubate for 45 to 60 minutes at 30 degrees celcius to induce expression of the fusion protein.After 45 to 60 minutes, set aside 10 milliliters of the cells for RNA extraction and use the remaining cells for rapid purification. To begin this procedure, add to the cells 1.35 milliliters of 37%formaldehyde, to a final concentration of 0.1%to cross-link the RNA-protein complexes. Continue incubating at 30 degrees Celsius for 10 minutes.To stop cross-linking, add 26.5 milliliters of 2.5 molar glycine, to a final concentration of 0.125 molar, and incubate at 30 degrees Celsius for 3 minutes. From here on, keep everything on ice and work quickly to minimize RNA degradation. Centrifuge the cells at 3000 times G for 4 minutes at 4 degrees Celsius.Discard the supernatant, add 45 milliliters of cold PBS, and centrifuge again. Remove the supernatant and re-suspend the cells in 5 milliliters of rapid lysis buffer that contains a high concentration of Rnase inhibitors. Divide the cell suspension into aliquots of 500 microliters in screw-capped microfuge tubes and add approximately 400 milligrams of chilled glass beads to each aliquot.Lyse the cells in a bead-beater for three minutes. Immediately put the lysate on ice. Transfer the lysate to new microfuge tubes.Cut the top off a 5 milliliter syringe and put it on an empty 15 milliliter tube to serve as an adapter for screw-cap tubes. Use a hot needle to pierce a small hole in the bottom of each tube and place them on top of the adapted 15 milliliter tubes. Centrifuge the tub assemblies at 3000 times G for one minute at 4 degrees Celsius to elute the lysate to the 15 milliliter tubes.Transfer the flowthrough from each 15 milliliter tube to a new 1.5 milliliter tube and centrifuge at 10, 000 times G for 10 minutes at 4 degrees Celsius to clear the cell debris. Pool the supernatant from all 1.5 milliliter tubes into a single 15 milliliter tube. Set aside 1/50th and 1/100th volume of the lysate for RNA and protein isolation respectively.Begin the rapid procedure for isolating RNA protein complexes by adding 300 micrograms of Avidin to the cell lysate. Incubate for 30 minutes at 4 degrees Celsius under constant rolling. While the cell lysate is being incubated with Avidin, pre-wash the streptavidin beads, transfer about 300 microliters of the streptavadin bead slurry to weigh 1.5 milliliters microcentriuge tube, centrifuge the preparation, and then remove the upper supernatant which will result in 250 microliters of beads.Add 1 milliliter of rapid lysis buffer to the beads and centrifuge at 660 times G for 2 minutes at 4 degrees Celsius. Remove the supernatant and wash again with rapid lysis buffer. To block the beads, add 0.5 milliliters of rapid lysis buffer, 0.5 milliliters of BSA, and 10 microliters of yeast TRNA and incubate for 1 hour at 4 degrees Celsius with constant rotation.Wash the beads twice with 1 milliliter of rapid lysis buffer. Add 250 microliters of the pre-washed streptavidin beads to the avidin containing lysate and incubate for 1 hour at 4 degrees Celsius with constant rotation. This incubation time is a compromise between providing sufficient binding time and minimizing the chances for RNA degradation.After one hour, centrifuge at 660 times G for 2 minutes at 4 degrees Celsius to clear the streptavidin beads. Transfer the supernatant to a 15 milliliter tube. Set aside 1/50th and 1/100th volume of the lysate for RNA and protein isolation respectively.Add 1 milliliter of rapid lysis buffer to the beads. Mix by pipetting, transfer to a new 1.5 milliliter microcentrifuge tube and centrifuge at 660 times G for 2 minutes at 4 degrees Celsius. Wash three more times with rapid lysis buffer.After the final wash with rapid lysis buffer, remove the supernatant, add 1 milliliter of rapid wash buffer, and rotate for 5 minutes at 4 degrees Celsius. Centrifuge and wash 2 more times with rapid wash buffer. Wash the beads with 1 milliliter of PBS and centrifuge as before.Remove the supernatant, add to the beads 120 microliters of PBS, and rotate for 5 minutes in a roller. Centrifuge as before and collect all the supernatant for RNA and protein extraction as the wash sample. To elute RNA and RNA-associated proteins, add 120 microliters of 6 millimolar biotin in PBS to the beads, and incubate for 45 minutes at 4 degrees Celsius with constant rotation.Centrifuge the beads and transfer the eluded material to a new 1.5 milliliter tube. Spin the eluted sample again and transfer the upper phase to a new 1.5 milliliter tube to ensure no carry-over of beads. Take samples for RNA or protein extraction.To determine the isolation efficiency and quality of RNA, Northern Analysis was performed for two tagged RNAs. PMP1 and FPR1, from cast cell lysis, rapid cell lysis, and after elution with biotin. Ribosomal RNAs were detected by ethidium bromide staining, and the lack of ribosomal RNAs in the elution sample indicates the stringency of purification.The stringency and specificity of the purification are further demonstrated by the lack of a signal of an untagged MRNA in the elution samples. The apparent signal in the FPR1 lane, which is not of the size of ACT1, is a leftover from previous hybridization with the MS2L probe. Although the input RNA is somewhat more degraded compared to the RNA that was purified by the Hot Phenol protocol, a significant amount of full length tagged RNA is isolated specifically, as revealed by the strong signal in the elution fractions.Protein samples can be analyzed by SDS-PAGE and silverstaining prior to proteomics analysis. The MS2-CP-GFP-SBP fusion protein, indicated by the arrow, demonstrates equal protein loading. The asterisks indicate bands with differential intensities that were later cut out of the gel for mass-spectrometry analysis.While attempting this procedure, it's important to wear gloves, ensure a clean work-area, prepare solution with RNA free water, and work quickly and efficiently to reduce protocol time. Don't forget that working with reagents like phenol and formaldehyde can be extremely hazardous, and precautions such as working in a chemical hood should always be taken while performing this procedure. After watching this video, you should have a good understanding of how to efficiently and effectively purify RNA of fayn-tress and its associated body.Following this procedure, other methods like RNA-Seq can be performed in order to detect RNAs that bind the transcript of interest.

Research

JoVE Journal

Genetics

Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia ...

Kinetics of Lagging-strand DNA Synthesis In Vitro by the Bacteriophage T7 Replication Proteins

Kinetics of Lagging-strand DNA Synthesis In Vitro by the Bacteriophage T7 Replication Proteins

Here we provide protocols for the kinetic examination of lagging-strand DNA synthesis in vitro by the replication proteins of bacteriophage T7. The T7 ...

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral ...

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

Combinatorial gene editing using CRISPR/Cas9 and single-stranded oligonucleotides is an effective strategy for the correction of single-base point ...

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Quantification of DNA methylation can be achieved using bisulfite sequencing, which takes advantage of the property of sodium bisulfite to convert ...

Novel Sequence Discovery by Subtractive Genomics

Subtractive genomics can be used in any research where the goal is to identify the sequence of a gene, protein, or general region that is embedded in a ...

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing in remote locations and resource-poor settings presents unique challenges. Nanopore sequencing can be successfully used under such conditions, ...

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Genome annotation is central to today's proteomic research as it draws the outlines of the proteomic landscape. Traditional models of open reading frame ...

An Assay for Quantifying Protein-RNA Binding in Bacteria

In the initiation step of protein translation, the ribosome binds to the initiation region of the mRNA. Translation initiation can be blocked by binding ...

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Gene regulation plays an important role in all cells. Transcriptional, post-transcriptional (or RNA processing), translational, and post-translational ...