Full-length cDNA Synthesis Research Articles

Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein.

Eukaryotic retrotransposons encode a reverse transcriptase that binds RNA to template DNA synthesis. The ancestral non-long terminal repeat (non-LTR) retrotransposons encode a protein that performs target-primed reverse transcription (TPRT), in which the nicked genomic target site initiates complementary DNA (cDNA)synthesis directly into the genome. The best understood model system for biochemical studies of TPRT is the R2 protein from the silk moth Bombyx mori. The R2 protein selectively binds the 3' untranslated region of its encoding RNA as template for DNA insertion to its target site in 28S ribosomal DNA. Here, binding and TPRT assays define RNA contributions to RNA-protein interaction, template use for TPRT and the fidelity of template positioning for TPRT cDNA synthesis. We quantify both sequence and structure contributions to protein-RNA interaction. RNA determinants of binding affinity overlap but are not equivalent to RNA features required for TPRT and its fidelity of template positioning for full-length TPRT cDNA synthesis. Additionally, we show that a previously implicated RNA-binding protein surface of R2 protein makes RNA binding affinity dependent on the presence of two stem-loops. Our findings inform evolutionary relationships across R2 retrotransposon RNAs and are a step toward understanding the mechanism and template specificity of non-LTR retrotransposon mobility.

Sanger Sequencing to Determine the Full-Length Sequence of Circular RNAs.

The pre-existing theory of pre-mRNA splicing into linear mature RNA was questioned with the introduction of circular RNAs (circRNAs). Hundreds of studies using high throughput RNA-sequencing (RNA-seq) techniques and novel computational programs reported the abundant and ubiquitous expression of circRNAs originating by pre-mRNA backsplicing. CircRNAs are mostly involved in gene expression by regulating functions of interacting microRNAs (miRNAs) and RNA-binding proteins (RBPs) or translating into functional polypeptides. Although all circRNA annotation tools identify circRNAs based on the backsplice junction (BSJ) sequences, only a few identify the internal sequences of circRNAs. However, the full-length sequence of circRNAs from RNA-seq data could be error-prone due to its similarity with the counterpart linear RNA. Since circRNA function depends on the mature sequence, validation of the mature sequence is the prerequisite for their further characterization. In this chapter, we discuss the validation of circRNA BSJ sequence by RT-PCR using divergent primer followed by Sanger sequencing. Furthermore, we describe the circRNA-rolling circle amplification (circRNA-RCA; circRNA enrichment by RNase R treatment, full-length cDNA synthesis, rolling circle PCR amplification using full-length primers, and Sanger sequencing of the PCR product) to validate the mature splice sequence of circRNAs. This chapter highlights the basic guidelines for designing divergent and full-length primers for PCR amplification and Sanger sequencing to validate circRNA sequences.

PBMC fixation and processing for Chromium single-cell RNA sequencing

BackgroundInterest in single-cell transcriptomic analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In almost all reported works investigators have used live cells, which introduces cell stress during preparation and hinders complex study designs. Recent studies have indicated that cells fixed by denaturing fixative can be used in single-cell sequencing, however they did not usually work with most types of primary cells including immune cells.MethodsThe methanol-fixation and new processing method was introduced to preserve human peripheral blood mononuclear cells (PBMCs) for single-cell RNA sequencing (scRNA-Seq) analysis on 10× Chromium platform.ResultsWhen methanol fixation protocol was broken up into three steps: fixation, storage and rehydration, we found that PBMC RNA was degraded during rehydration with PBS, not at cell fixation and up to 3-month storage steps. Resuspension but not rehydration in 3× saline sodium citrate (SSC) buffer instead of PBS preserved PBMC RNA integrity and prevented RNA leakage. Diluted SSC buffer did not interfere with full-length cDNA synthesis. The methanol-fixed PBMCs resuspended in 3× SSC were successfully implemented into 10× Chromium standard scRNA-seq workflows with no elevated low quality cells and cell doublets. The fixation process did not alter the single-cell transcriptional profiles and gene expression levels. Major subpopulations classified by marker genes could be identified in fixed PBMCs at a similar proportion as in live PBMCs. This new fixation processing protocol also worked in several other fixed primary cell types and cell lines as in live ones.ConclusionsWe expect that the methanol-based cell fixation procedure presented here will allow better and more effective batching schemes for a complex single cell experimental design with primary cells or tissues.

Decreased Km to dNTPs is an essential M-MuLV reverse transcriptase adoption required to perform efficient cDNA synthesis in One-Step RT-PCR assay.

Personalized medicine and advanced diagnostic tools based on RNA analysis are focusing on fast and direct One-Step RT-PCR assays. First strand complementary DNA (cDNA) synthesized by the reverse transcriptase (RT) is exponentially amplified in the end-point or real-time PCR. Even a minor discrepancy in PCR conditions would result in big deviations during the data analysis. Thus, One-Step RT-PCR composition is typically based on the PCR buffer. In this study, we have used compartmentalized ribosome display technique for in vitro evolution of the Moloney Murine Leukemia Virus reverse transcriptase (M-MuLV RT) that would be able to perform efficient full-length cDNA synthesis in PCR buffer optimized for Thermus aquaticus DNA polymerase. The most frequent mutations found in a selected library were analyzed. Aside from the mutations, which switch off RNase H activity of RT and are beneficial for the full-length cDNA synthesis, we have identified several mutations in the active center of the enzyme (Q221R and V223A/M), which result in 4-5-fold decrease of Km for dNTPs (<0.2 mM). The selected mutations are in surprising agreement with the natural evolution process because they transformed the active center from the oncoretroviral M-MuLV RT-type to the lenitiviral enzyme-type. We believe that this was the major and essential phenotypic adjustment required to perform fast and efficient cDNA synthesis in PCR buffer at 0.2-mM concentration of each dNTP.

Transcript Profiling Using Long-Read Sequencing Technologies.

RNA sequencing using next-generation sequencing (NGS, RNA-Seq) technologies is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise short-read RNA-Seq (dominated by Illumina) and long-read RNA-Seq technologies provided by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Although short-read sequencing technologies are the most widely used, long-read technologies are increasingly becoming the standard approach for de novo transcriptome assembly and isoform expression quantification due to the complex nature of the transcriptome which consists of variable lengths of transcripts and multiple alternatively spliced isoforms for most genes. In this chapter, we describe experimental procedures for library preparation, sequencing, and associated data analysis approaches for PacBio and ONT with a major focus on full length cDNA synthesis, de novo transcriptome assembly, and isoform quantification.

Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells.

RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived from cultured human cells after crosslinking and immunoprecipitation (CLIP). Here, we report a method for obtaining strand-specific small RNA libraries for RNA sequencing that requires picograms of RNA. We employ an intramolecular circularization step that increases the efficiency of library preparation and avoids the need for intermolecular ligations of adaptor sequences. Other key features include random priming for full-length cDNA synthesis and gel-free library purification. Using our method, we generated CLIP-Seq libraries from nuclear RNA that had been UV-crosslinked and immunoprecipitated with anti-Argonaute 2 (Ago2) antibody. Computational protocols were developed to enable analysis of raw sequencing data and we observe substantial differences between recognition by Ago2 of RNA species in the nucleus relative to the cytoplasm. This RNA self-circularization approach to RNA sequencing (RC-Seq) allows data to be obtained using small amounts of input RNA that cannot be sequenced by standard methods.

Foamy Virus Gag p71-p68 Cleavage Is Required for Template Switch of the Reverse Transcriptase

In contrast to orthoretroviruses, processing of foamy viral p71 Gag is limited to a single cleavage site. Nevertheless, Gag maturation is essential for infectivity, but deletion of p3 results in a modest drop in infectivity. Here, we show that Gag processing of p71 to p68 and p3 is essential for full-length cDNA synthesis, while inactivation of Gag cleavage results in cDNAs containing only the RU5 region; cDNAs encompassing the U3 region were almost undetectable.

Isolation and characterization of a mannose-binding insecticidal lectin gene from Allium sativum (garlic) and its putative role in insect resistance using bioinformatics tools

Monocot mannose-binding lectins (MMBLs) or agglutinins are an extended superfamily of structurally and evolutionarily related proteins. They play important roles in plant defenses. Here we describe the synthesis of full-length cDNA of monocot mannose-binding insecticidal agglutinin isolated from Allium sativum, a traditional herb known to be of great applications in Africa, using reverse transcription polymerase chain reaction (RT–PCR) with specific primers designed based on the insecticidal sequence (NCBI primary accession no. AY866499.1). Sequence analysis revealed a 327bp open reading frame (ORF) encoding a putative 108-aa agglutinin precursor with a C-terminal domain. Multiple alignments of BLEC1 amino acids with those of eight other MMBLs revealed three highly conserved domains among them, indicating BLEC1 belongs to a member of the MMBL superfamily. Tertiary structure analysis showed that BLEC1 had three potential equal mannose-binding sites. Phylogenetic analysis indicated that 20 MMBLs including BLEC1 belonged to an extended superfamily. Gene ontology analyses indicate one biological process with GO ID: 0006952 representing defense response, with two secondary IDs GO: 0002217 GO: 0042829. The child terms has both negative and positive regulation some of which include GO: 0002242 defense response to parasitic plant and GO: 0002213 defense response to insect. The cloning and characterization of BLEC1 will enable us to study its potential use in plant genetic engineering in the development of insect resistance plant.

Full length cDNA synthesis of differentially displayed ESTs during lactation in the Indian buffalo (Bubalus bubalis)

In the present study, antisense primers were designed from 7 differentially displayed expressed sequence tags (ESTs) previously identified at our laboratory. Total RNA was isolated from the mammary gland tissue of lactating buffalo to carry out 5' rapid amplification cDNA ends (RACE) PCR. 5' RACE PCR amplicons, ranging from 161 bp to 336 bp, were cloned and sequenced. These 5' RACE sequences were analyzed using the blastn (Megablast) bioinformatics tool available from NCBI. Of these 7, only one 5' mRNA sequence did not show a match in the available database and another 1 failed to show a match with any specific gene due to the unavailability of buffalo genome information. Two other 5' mRNA sequences showed 82% to 100% homology with the 18S rRNA gene and the remaining 3 showed homology to the Talin-1, \beta-casein, and 28S rRNA genes. Full length cDNA were synthesized using primers designed from 5' mRNA sequences and ranged from 345 bp to 1030 bp. Finally, we conclude that the ESTs identified may act as markers for lactogenesis in other animals.

Cloning and heterologous expression of new xANO2 from Xenopus laevis

We have successfully isolated a novel anoctamin (xANO2), Ca2+-activated chloride channel (ANO1, TMEM16A), from Xenopus laevis. The cDNA sequence was determined to belong to the anoctamin family by comparison with the xTMEM16A sequence in a previous report. Full length cDNA synthesis was performed by repeating 5′- and 3′-rapid amplification of cDNA end (RACE). We successfully completed the entire cDNA sequence and transiently named this sequence xANO2. The xANO2 cDNA is 3884 base pair (bp) long and codes 980 amino acid (aa) proteins. According to an aa homology search using the Basic Local Alignment Search Tool (BLAST), xANO2 showed an overall identity of 92% to xTMEM16A (xANO1) independently sub-cloned in our laboratory. A primary sequence of xANO2 revealed typical characteristics of transmembrane proteins. In tissue distribution analysis, the gene products of anoctamins were ubiquitously detected by real-time PCR (RT-PCR). The expression profiles of each anoctamin were different among brain, oocytes, and digestive organs with relatively weak expression. To clarify the anoctamin activity, physiological studies were performed using the whole cell patch-clamp technique with HEK293T cells, enhanced green fluorescent protein (EGFP), and expression vectors carrying anoctamins. Characteristics typical of voltage-dependent chloride currents were detected in cells expressing both xANO2 and xTMEM16A but not with EGFP alone. Sensitive reactions to the anion channel blocker niflumic acid (NFA) were also revealed. Considering these results, xANO2 was regarded as a new TMEM16A belonging to the Xenopus anoctamin family.

Purification of M-MLVH- RT on a 9-Aminoethyladenine-(1,6-diamine-hexane)-triazine Selected from a Combinatorial Library of dNTP-Mimetic Ligands

Reverse transcriptase (RT) catalyzes the formation of dsDNA from single-stranded retroviral RNA genome. This enzyme is unique among DNA polymerases in its ability to use either RNA or DNA as a template. Moloney Murine Leukemia virus reverse transcriptase lacking RNase H activity (M-MLVH- RT) especially holds particular interest because of its ability to eliminate the deleterious effect of RNase H, which results in more efficient synthesis of full-length cDNA from mRNA. Therefore, the development of a simple purification method attracts the attention of retroviral drug and enzyme researchers and manufacturers. The present work is the first purification example of a non-tagged (native) RT by affinity chromatography using synthetic affinity ligands. In this study, the ligand was selected from a structure-biased combinatorial library of dNTP-mimetic ligands, and it was evaluated for its ability to bind and purify M-MLVH- RT from inclusion bodies of recombinant E. coli. The selected ligand (AEAd), bearing 9-aminoethyladenine and 1,6-diamine-hexane both linked on the same triazine scaffold, displayed the highest enzyme purifying ability after applying mild desorption conditions (6 mM MnCl(2) in 20 mM Tris-HCl buffer, pH 7.5). The binding capacity of immobilized AEAd with M-MLVH- RT was determined to be equal to approximately 1 mg enzyme/g moist weight gel. Adsorption studies with immobilized AEAd and soluble M-MLVH- RT demonstrated that the formation of the respective complex was perturbed by ATP. Quality control tests of the purified M-MLVH- RT essentially showed a single band (sodium dodecyl sulfate polyacrylamide gel electrophoresis) and absence of nucleic acids and contaminating nuclease activities.

PCR-suppression effect: Kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples

In the present study, we analyzed the kinetics of the PCR-suppression effect (PS-effect) and firstly demonstrate that lower annealing temperature enhances PS-effect. Furthermore, we controlled the average size of complex PCR products over a wide range, and simultaneously amplified targets from 0.25 to 10kb by regulating the degree of suppression in a single-primer PCR. In addition, we describe an improved template-switching full-length cDNA synthesis method that greatly reduces truncated cDNA. This study provides a general guide for the design of PS-effect related PCR and is useful for representative or long-transcript enriched cDNA library construction, especially when only a small amount of total RNA is available.

Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom

Tomato genome sequencing projects have started to become an internationally coordinated program. To accelerate tomato functional genomics studies in coordination with the complete sequencing of the tomato genome, we prepared a full-length cDNA library from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom, which has attracted attention as a laboratory-grown model plant. Total RNA from maturing fruits was subjected to a vector-capping protocol for full-length cDNA synthesis. We generated 8,046 expressed sequence tags (ESTs), which comprised 3,484 contigs. We calculated that 80.7% of the cDNA clones in the library met the criteria for full-length clones, and 1,920 non- redundant full-length clones were identified. As a pilot experiment, we chose seven clones, whose encoded proteins shared low homology with Arabidopsis proteins, for full sequencing. Of these, three genes had no or very low homology with Arabidopsis genes, indicating the usefulness of the library for analyses of not-found-in-Arabidopsis genes.

Aptamer-dependent full-length cDNA synthesis by overlap extension PCR.

Sequencing of the human genome in combination with computational annotation has provided tremendous data on predicted genes. However, for most of them, no corresponding cDNAs are available yet. Furthermore, even where cDNA clones were obtained, gene transcripts often have many different splice variants that are not covered by current gene collections. For direct synthesis of cDNA clones corresponding to predicted genes, new splice variants, or any other gene of interest, we established optimal PCR conditions for the direct amplification of exons from genomic DNA, which require a specific Taq aptamer. PCR products comprising differently tagged exons were concatenated by overlap extension into full-length cDNAs. To prove the effectiveness of the approach, the 1900-bp full-length open reading frame of the human mitochondrial aldehyde dehydrogenase (ALDH2) gene was synthesized in a two-step reaction comprising all 13 exons. Thus, our conditions are of general value for in vitro synthesis of cDNAs and alternative splice variants from genomic DNA.

Functional domains of APOBEC3G required for antiviral activity.

The viral protein, Vif, is essential for the production of infectious progeny virions in natural target cells of human immunodeficiency virus type 1 (HIV-1). Several recent reports indicate that Vif acts by antagonizing the activity of an endogenous human antiviral protein, APOBEC3G. To investigate this route to restrict HIV-1 infection, we employed mutagenesis to assess APOBEC3G function during HIV-1 infection including interaction with Vif, localization, and activity in virions. We found that APOBEC3G binds Vif in infected cells and the C'-terminal region is required for this interaction. APOBEC3G was only incorporated into virions in the absence of Vif and deletion of either the N'-terminal or C'-terminal regions of APOBEC3G abrogated virion localization. Assaying endogenous reverse transcription we found that APOBEC3G and its C'-terminal deletion mutant inhibited full-length cDNA synthesis, possibly through binding to viral RNA, a function revealed through gel-shift assays. Taken together, our studies suggest that APOBEC3G inhibits HIV-1 infection through interference with reverse transcription and that Vif counteracts APOBEC3G by impeding its entry into virions.

Laser capture microdissection and analysis of amplified antisense RNA from distinct cell populations of the young and aged rat brain: effect of traumatic brain injury on hippocampal gene expression

To explore the molecular mechanisms underlying the increased vulnerability of the aged brain to traumatic brain injury (TBI), we compared the expression of several age-related genes in the CA1, CA3 and dentate gyrus subfields of the young and aged rat hippocampus before and after lateral fluid percussion TBI. Using laser capture microdissection (LCM), we obtained hippocampal neurons and glia from the neuropil adjacent to the pyramidal and granule cell layers. Subsequently, we linearly amplified and analyzed the antisense mRNA using Northern blot and ribonuclease protection assays (RPA). Our procedures, which have not been previously applied to quantitative analysis of LCM mRNA from neural tissue, included a modified reverse transcription step to enhance full-length cDNA synthesis, thus enhancing the yield of larger components of in vitro-transcribed mRNA for downstream analysis. Northern analysis showed greater expression of two aging-associated genes, p21 and brain-derived neurotrophic factor (BDNF) in the aged hippocampus. The age-related differences in p21 and BDNF expression were particularly prominent after TBI. By quantitative RPA analysis, we found that the expression of p21, known to be induced in senescent cells, was significantly greater in the CA3 region of aged rats, an area that is selectively vulnerable to TBI. However, expression of genes associated with regenerative and repair functions was significantly decreased in aged hippocampus. Our RPA results indicate that substantial age-dependent differences in the transcriptional profile of distinct regions of the hippocampal formation may account, in part, for their differential susceptibility to brain injury.

Thermal effects on reverse transcription: improvement of accuracy and processivity in cDNA synthesis.

Reverse transcription, coupled with DNA amplification, has been widely used for molecular analysis of RNAs. Reverse transcriptases are retroviral DNA polymerases that can synthesize DNA from both RNA and DNA. In general, because of the lack of 3'-->5' exonuclease activity in retroviral reverse transcriptases, the reverse transcription step is error prone. Mutations created during the reverse transcription step of cDNA synthesis or RT-PCR are delivered to the final products to be analyzed, interfering with accurate analysis of the RNAs. In addition, because reverse transcription uses RNA as a template, processive DNA synthesis by reverse transcriptase is frequently interrupted by secondary structures of the RNA templates, causing difficulties in full-length cDNA synthesis. Here, we report that an increase in reaction temperature greatly enhances both the accuracy and the processivity of reverse transcription catalyzed by murine leukemia virus (MuLV) and human immunodeficiency virus type 1 (HIV-1) reverse transcriptases.

Involvement of HIV-I Nucleocapsid Protein in the Recruitment of Reverse Transcriptase into Nucleoprotein Complexes Formedin Vitro

Retroviral reverse transcription takes place within the virion core, where nucleocapsid (NC) protein (NCp) molecules cover the dimeric RNA genome. NCp thus has structural roles in the virion core but is also extensively involved in viral DNA synthesis and virion assembly. To further characterize the role of human immunodeficiency virus type 1 NCp7 during replication of the viral genome, we investigated the relationship between NCp7 and reverse transcriptase (RT) either directly or within nucleoprotein complexes in vitro. We show that NCp7 interacts directly with RT and enhances synthesis of full-length cDNA by increasing RT processivity. Using NCp7 mutants, we show that the complete amino acid sequence of NCp7 is required for functional interactions with RT. Our results suggest that NCp7 plays a role in recruitment of RT into stable and functional nucleoprotein complexes during viral DNA synthesis.

Sequence-independent amplification and cloning of large dsRNA virus genome segments by poly(dA)-oligonucleotide ligation

A strategy was developed for sequence-independent synthesis and amplification of full-length cDNA of 3–4 kb genes of dsRNA viruses. The method of single primer amplification ( Lambden et al., 1992) was adapted by the inclusion of a 3′ poly(A) tail to an oligonucleotide ligated to dsRNA genome segments as a template for oligo(dT)-primed cDNA synthesis. Full-length copies of the largest genome segments, 1 (4 kb) and 2 (3 kb), of African horse sickness virus (AHSV) have been cloned, terminally sequenced and expressed in vitro.

Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA.

The advent of thermostable enzymes has led to great advances in molecular biology, such as the development of PCR and ligase chain reaction. However, isolation of naturally thermostable enzymes has been restricted to those existing in thermophylic bacteria. Here, we show that the disaccharide trehalose enables enzymes to maintain their normal activity (thermostabilization) or even to increase activity at high temperatures (thermoactivation) at which they are normally inactive. We also demonstrate how enzyme thermoactivation can improve the reverse transcriptase, reaction. In fact, thermoactivated reverse transcriptase, which displays full activity even at 60 degrees C, was powerful enough to synthesize full length cDNA without the early termination usually induced by stable secondary structures of mRNA.