Single-stranded RNA Transcripts Research Articles

Circular RNAs: implications of signaling pathways and bioinformatics in human cancer.

Circular RNAs (circRNAs) form a class of endogenous single-stranded RNA transcripts that are widely expressed in eukaryotic cells. These RNAs mediate post-transcriptional control of gene expression and have multiple functions in biological processes, such as transcriptional regulation and splicing. They serve predominantly as microRNA sponges, RNA-binding proteins, and templates for translation. More importantly, circRNAs are involved in cancer progression, and may serve as promising biomarkers for tumor diagnosis and therapy. Although traditional experimental methods are usually time-consuming and laborious, substantial progress has been made in exploring potential circRNA-disease associations by using computational models, summarized signaling pathway data, and other databases. Here, we review the biological characteristics and functions of circRNAs, including their roles in cancer. Specifically, we focus on the signaling pathways associated with carcinogenesis, and the status of circRNA-associated bioinformatics databases. Finally, we explore the potential roles of circRNAs as prognostic biomarkers in cancer.

Mitochondrial matrix-localized p53 participates in degradation of mitochondrial RNAs

Mitochondrial RNA degradation plays an important role in maintenance of the mitochondria genetic integrity. Mitochondrial localization of p53 was observed in non-stressed and stressed cells. p53, as an RNA-binding protein, exerts 3′→5′ exoribonuclease activity. The data suggest that in non-stressed cells, mitochondrial matrix-localized p53, with exoribonuclease activity, may play a housekeeping positive role. p53, through restriction the formation of new RNA/DNA hybrid and processing R-loop, might serve as mitochondrial R-loop suppressor. Conversely, stress-induced matrix-p53 decreases the amount of mitochondrial single-stranded RNA transcripts (including polyA- and non-polyA RNAs), thereby leading to the decline in the amount of mitochondria-encoded oxidative phosphorylation components.

A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases.

Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10−8 U μL−1 for hOGG1 and 3.55 × 10−7 U μL−1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.

Electrochemical Detection of Micro-RNAs As Potential Cancer Biomarker

MicroRNAs (miRNAs) are single-stranded RNA transcripts, typically of 19–23 nucleotides in length. Recently, miRNAs have been identified as important biomarkers that hold promise in early cancer diagnosis. Accumulative evidences have proved that abnormal expression of miRNAs is closely related with the occurrence, diagnosis and treatment of cancer [1]. Conventional methods of miRNA detection have some intrinsic drawbacks including the need for tedious and complex procedures, requirement of large amount of samples, highly skilled experts and high-end equipment. To address these shortcomings as well as to provide multiplexing capability, different types of electrochemical cancer biosensors have been developed. Electrochemical biosensors have been widely paid attention due to their merits including high sensitivity, specificity, low-cost, and multiplexing [2]. Herein, a label-free and sensitive biosensor was developed for miRNA-21 detection at femtomolar concentrations. A glassy carbon electrode (GCE) was first modified with carbon nanotube (CNT) which serves as platform for immobilization of probe DNA as well as providing higher surface area. Capture DNA probes were immobilized onto the surface of CNT modified electrode using an established molecular tethering method [3,4]. Electrochemical analyses confirmed the surface modification, immobilization, and hybridization between probe DNA and the target miRNA. Besides, different variables such as probe concentration and hybridization time were investigated and optimized to find the optimal experimental conditions for miRNA detection. The obtained results demonstrated that the proposed biosensor exhibits excellent analytical properties including high sensitivity, low detection limit, selectivity, and reproducibility for miRNA detection. References Lan H, Lu H, Wang X, Jin H (2015) MicroRNAs as potential biomarkers in cancer: opportunities and challenges. BioMed research international 2015Kilic T, Erdem A, Ozsoz M, Carrara S (2018) MicroRNA biosensors: Opportunities and challenges among conventional and commercially available techniques. Biosensors and Bioelectronics 99:525-546Ramasamy RP, Luckarift HR, Ivnitski DM, Atanassov PB, Johnson GR (2010) High electrocatalytic activity of tethered multicopper oxidase–carbon nanotube conjugates. Chemical Communications 46 (33):6045-6047Zhou Y, Fang Y, Ramasamy RP (2019) Non-covalent functionalization of carbon nanotubes for electrochemical biosensor development. Sensors 19 (2):392

Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization.

micro-RNAs (miRNAs) are single-stranded RNA transcripts that bind to messenger RNAs (mRNAs) and inhibit their translation or promote their degradation. To date, miRNAs have been implicated in a large number of biological and disease processes, which has signified the need for the reliable detection methods of miRNA transcripts. Here, we describe a detailed protocol for digoxigenin-labeled (DIG) Locked Nucleic Acid (LNA) probe-based miRNA detection, combined with protein immunostaining on mouse heart sections. First, we performed an in situ hybridization technique using the probe to identify miRNA-182 expression in heart sections from control and cardiac hypertrophy mice. Next, we performed immunostaining for cardiac Troponin T (cTnT) protein, on the same sections, to co-localize miRNA-182 with the cardiomyocyte cells. Using this protocol, we were able to detect miRNA-182 through an alkaline phosphatase based colorimetric assay, and cTnT through fluorescent staining. This protocol can be used to detect the expression of any miRNA of interest through DIG-labeled LNA probes, and relevant protein expression on mouse heart tissue sections.

RNA sequencing and Prediction Tools for Circular RNAs Analysis.

Circular RNAs (circRNAs) are noncoding and single-stranded RNA transcripts able to form covalently circular-closed structures. They are generated through alternative splicing events and widely expressed from human to viruses. CircRNAs have been appointed as potential regulators of microRNAs (miRNAs), RNA-binding proteins (RPBs), and lineal protein-coding transcripts. Although their mechanism of action remains unclear, the deregulation of circular RNAs has been confirmed in different diseases such as Alzheimer or cancer.The introduction of high-throughput next-generation sequencing (NGS) technology provides millions of short RNA sequences at single-nucleotide level, allowing an accurate and proficient method to measure circular RNAs. Novel protocols based on non-polyadenylated RNAs, rRNA-depleted, and RNA exonuclease-based enrichment approaches (RNase R) have taken even further the possibility of detecting circRNAs.Besides, the identification of circRNAs presence requires the development of specific bioinformatics tools to detect junction-spanning sequences from transcriptome deep-sequencing samples. Thus, recently established bioinformatics' approaches have permitted the discovery of an elevated number of different circRNAs in diverse organisms. In that sense, recent studies have compared different methods and advocate the simultaneous use of more than one prediction tool. For that reason, we want to highlight pipelines such as miARma-Seq that is able to execute various circular RNA identification algorithms in an easy way, without the tedious installation of third-party prerequisites.

Molecular characterization of mitochondrial Zucchini and its relation to nuage-piRNA pathway components in Bombyx mori ovary-derived BmN4 cells

Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with PIWI subfamily proteins, which play an important role in transposon silencing in animal germ cell. The piRNAs biogenesis is divided into two major pathways: primary and secondary, and both pathways are independent of double-stranded RNA-processing enzyme Dicer, which processes the single-stranded RNA transcripts in microRNA (miRNA) and siRNA (small interfering RNA) pathway. Primary piRNAs are processed from long non-coding RNA precursors transcribed from piRNA clusters. Zucchini (Zuc), a mitochondrial phospholipase D (PLD) superfamily protein is conserved among the animals and involved in piRNA biogenesis. Recent studies showed that the Zucchini is an endoribonuclease essential for primary piRNA maturation and production of phased piRNA in secondary piRNA biogenesis of drosophila germ cell. Based on these reports, here we identified and studied the silkworm Zucchini (BmZuc) at subcellular level in ovary-derived BmN4 cell. The silkworm Zuc specifically expressed in germ-related tissues and localized on mitochondria and partially co-localized with perinuclear nuage-piRNA pathway components and nuage marker protein BmVasa. Molecular dissection analyses revealed that the conserved mitochondrial localization sequence, RGV motif, PLDc 2 domain and HKD motif are important for the BmZuc mitochondrial localization. Moreover, the knockdown analyses showed that the piRNA pathway components are independent on BmZuc for their nuage localization, whereas BmZuc depend on piRNA pathway components for the proper localization. Our data provides vital information on mitochondrial BmZuc and its relationship to “nuage” in ovary-derived BmN4 cell.

OR45 RNA sequencing of two lymphoblastoid cell lines reveals novel microrna transcripts of the MHC

Aim MicroRNA (miRNA) are short (∼22 bp) single stranded RNA transcripts that bind to and regulate the posttranscriptional expression of targeted mRNA transcripts. There are 12 known miRNA transcribed from within the MHC, which have been previously identified by RNA sequencing of various primary cell types. This approach to identify novel miRNA is however inherently flawed since it relies upon significant sequence concordance between the reference genome and the generated reads, which is particularly problematic for transcripts originating from within the highly polymorphic MHC. To address this gap, we sequenced short RNA transcripts (less than 50 bp) from two homozygous cell lines with fully characterized MHC haplotypes, PGF and COX, in order to identify and characterize novel microRNA (miRNA) transcripts from within the MHC. Methods Total RNA was extracted from two lymphoblastoid cell lines, PGF and COX. Size selected transcripts (less thank 50 bp) were isolated for library construction and sequenced on an Illumina HiSeq 2500. Single-end reads from PGF and COX were mapped to their respective MHC haplotype reference sequence using NovoAlign. Novel miRNA were identified using a custom computational analysis pipeline and validated by qPCR. Results In total, our analysis has identified 67 and 47 high confidence, significantly expressed, novel miRNAs from RNA-Seq data generated from PGF and COX lymphoblastoid cell lines, respectively. Of these, 25 identified novel miRNA were found to be expressed in both PGF and COX cells, while 42 and 22 novel miRNA were found to exhibit haplotype specific expression patterns in PGF and COX, respectively. Conclusions The ability to de novo assemble the MHC is critical to ensure accurate RNA-Seq read mapping within the highly variable MHC. Our results demonstrate the utility of an accurate MHC reference assembly in combination with a custom developed computational analysis pipeline to identify and characterize novel miRNA transcripts from within the MHC of two homozygous cell lines with fully characterized MHC reference sequences. Our analysis revealed haplotype specific as well as commonly expressed novel miRNA transcripts, identifying novel regulatory elements encoded within the MHC.

Isothermal detection of RNA transcription levels using graphene oxide-based SYBR Green I fluorescence platform

Abstract An isothermal graphene oxide (GO)-based SYBR Green I fluorescence platform for sensitive detection of RNA transcription levels is proposed. Briefly, a synthesized T7 DNA template was transcribed by T7 RNA polymerase, to produce many copies of single-stranded (ss) RNA transcripts. The ssRNA transcripts were then hybridized with a label-free ssDNA probe which alone will be adsorbed on the GO surface. The resultant double-stranded (ds) RNA:DNA hybrids were incubated with GO and SYBR Green I. Then the hybrid binding with SYBR Green I emits enhanced fluorescence for detection. Experimental results show that the detection limit of the method is 0.5 pmol/L of T7 DNA template. A calibration curve with a linearity range of 0.5 pmol/L to 5 nmol/L is established, thus, making quantitative analysis feasible. The method may become a powerful tool for RNA transcription detection due to its sensitivity, rapidity and convenience.

The influence of viral RNA secondary structure on interactions with innate host cell defences.

RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-α, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses.

Characterization of Rotavirus RNAs That Activate Innate Immune Signaling through the RIG-I-Like Receptors

In mammalian cells, the first line of defense against viral pathogens is the innate immune response, which is characterized by induction of type I interferons (IFN) and other pro-inflammatory cytokines that establish an antiviral milieu both in infected cells and in neighboring uninfected cells. Rotavirus, a double-stranded RNA virus of the Reoviridae family, is the primary etiological agent of severe diarrhea in young children worldwide. Previous studies demonstrated that rotavirus replication induces a MAVS-dependent type I IFN response that involves both RIG-I and MDA5, two cytoplasmic viral RNA sensors. This study reports the isolation and characterization of rotavirus RNAs that activate IFN signaling. Using an in vitro approach with purified rotavirus double-layer particles, nascent single-stranded RNA (ssRNA) transcripts (termed in vitro ssRNA) were found to be potent IFN inducers. In addition, large RNAs isolated from rotavirus-infected cells six hours post-infection (termed in vivo 6 hr large RNAs), also activated IFN signaling, whereas a comparable large RNA fraction isolated from cells infected for only one hour lacked this stimulatory activity. Experiments using knockout murine embryonic fibroblasts showed that RIG-I is required for and MDA5 partly contributes to innate immune signaling by both in vitro ssRNA and in vivo 6 hr large RNAs. Enzymatic studies demonstrated that in vitro ssRNA and in vivo 6 hr large RNA samples contain uncapped RNAs with exposed 5’ phosphate groups. RNAs lacking 2’-O-methylated 5’ cap structures were also detected in the in vivo 6 hr large RNA sample. Taken together, our data provide strong evidence that the rotavirus VP3 enzyme, which encodes both guanylyltransferase and methyltransferase activities, is not completely efficient at either 5’ capping or 2’-O-methylation of the 5’ cap structures of viral transcripts, and in this way produces RNA patterns that activate innate immune signaling through the RIG-I-like receptors.

Comparative evaluation of a novel TaqMan real-time reverse transcription–polymerase chain reaction assay for hepatitis A virus detection

To develop and evaluate a novel system for detecting and quantifying hepatitis A virus (HAV) nucleic acid. Real-time TaqMan® reverse transcription-polymerase chain reaction (PCR) procedures were established, based on amplification of the highly conserved 5'-non-coding region. Synthetic single-stranded RNA transcripts synthesized in vitro were used as the quantification standard. Ten-fold dilutions were prepared from HAV strain stock suspension to determine precision, accuracy, sensitivity and specificity. In addition, serum specimens from patients with acute HAV underwent clinical evaluation. The novel assay had a detection limit for HAV RNA of 10 TCID50/ml (where TCID50 is median tissue culture infective dose). It was more sensitive and specific than the commercial quantitative PCR kit manufactured by Shanghai Zhijiang Bio-Tech. However, the Artus HAV RT-PCR kit (Qiagen) had the best performance of the three assays and had a detection limit of 5 TCID50/ml. The new HAV real-time PCR detection system was also successfully applied in 90 serum specimens from patients with confirmed acute HAV infection. Considering its high reproducibility, sensitivity, specificity and simplicity, this novel amplification system may be suitable for wide clinical application as a diagnostic tool, and for the surveillance and investigation of infectious diseases in developing countries where HAV is endemic.

Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc

Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the double-stranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conformational changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini's activity.

Intrinsic Nucleic Acid-Binding Activity of Chp1 Chromodomain Is Required for Heterochromatic Gene Silencing

Centromeric heterochromatin assembly in fission yeast requires the RNAi pathway. Chp1, a chromodomain (CD) protein, forms the Ago1-containing RNA-induced transcriptional silencing (RITS) complex and recruits siRNA-bound RITS to methylated histone H3 lysine 9 (H3K9me) via its CD. Here, we show that the CD of Chp1 (Chp1-CD) possesses unique nucleic acid-binding activities that are essential for heterochromatic gene silencing. Detailed electrophoretic-mobility shift analyses demonstrated that Chp1 binds to RNA via the CD in addition to its central RNA-recognition motif. Interestingly, robust RNA- and DNA-binding activity of Chp1-CD was strongly enhanced when it was bound to H3K9me, which was revealed to involve a positively charged domain within the Chp1-CD by structural analyses. These results demonstrate a role for the CD that provides a link between RNA, DNA, and methylated histone tails to ensure heterochromatic gene silencing.

The Open Reading Frame 2 Product of Cacao Swollen Shoot Badnavirus Is a Nucleic Acid-Binding Protein

The function of the open reading frame 2 product (p2) of cacao swollen shoot virus (CSSV) and of other badnaviruses is not yet determined. Their carboxyl-termini are lysine and proline rich and also contain alanine residues, amino acids present at the C-termini of histone-like proteins. Full-length CSSV p2 (132 amino acids) or versions truncated at the C-terminus (128, 113, 103, or 101 amino acids) were expressed inEscherichia coliand partially purified. When assayed in nucleic acid-binding tests, p2 was able to interact with CSSV and other double-stranded DNAs and with CSSV and other single-stranded RNA transcripts in a sequence-nonspecific manner. Moreover, this binding activity was progressively lost as the C-terminus was gradually deleted.

Heterologous recombination in the double-stranded RNA bacteriophage phi 6.

Bacteriophage phi 6 contains three double-stranded RNA genomic segments. We have constructed a virus with an insertion of a kanamycin resistance gene in genomic RNA segment M. The virus forms small, turbid plaques, and its genome is unstable. Virus from a single plaque contained from about 0.1 to 10% large clear-plaque forms of the virus; these were usually missing the kanamycin resistance gene, and in many cases, the resulting segment M was larger or smaller than its normal size. Sequence analysis of the genomic RNA of the apparent deletions showed that they were formed by recombination events between segment M and either segment S or L. These heterologous recombination events resulted in the loss of the kanamycin resistance gene from segment M and the replacement of the 3' end of segment M with the 3' end of segment S or L. Although the 3' ends of the single-stranded RNA transcripts of the genomic segments appear to have extensive secondary structure, the sequences at the 3' ends are not involved in the specificity of genomic packaging.

REPORTS

A new technique for characterizing somatic mutations in very small samples of cellularly heterogeneous human cancer tissue was developed and tested using mutations in the p53 gene in breast carcinomas as a model system. The technique combines touch preparation of specimens to obtain homogeneous clusters of carcinoma cells free of normal cells with a nested pair of polymerase chain reaction (PCR) amplifications of DNA to increase the amount of target gene sequence sufficiently to permit direct sequencing of the p53 gene. Touch preparations of fresh or previously frozen tissue from human adenocarcinomas derived from several organs were stained, and clusters of 10-50 malignant cells were transferred by pipette into microfuge tubes for PCR amplification. Exons 5-9 of the p53 gene, which contain the major mutational hot spots associated with most human cancers, were sequenced by the following steps: 1) two rounds of PCR amplification using DNA Taq polymerase and two sets of oligonucleotide primers, the second set being nested within the segment amplified by the first set and having attached T7 and SP6 phage promoter sequences, 2) transcription of the amplified DNA sequences with T7 and SP6 RNA polymerases, and 3) dideoxy sequencing of single-stranded RNA transcripts with reverse transcriptase and with additional oligonucleotide primers to achieve specificity for this unique region of the genome. The utility of this approach is illustrated by our success in detecting and analyzing point mutations in cell clusters from four of 11 primary adenocarcinomas of the human breast.

RNA polymerase activity in virions from Ustilago maydis.

RNA polymerase activity is associated with the double-stranded RNA virions of Ustilago maydis. The reaction products of the polymerase activity are single-stranded RNA molecules. The RNA molecules synthesized are homologous to the three classes of double-stranded RNA molecules that typify the viral genome. The single-stranded RNA synthesized is released from the virions. The molecular weight of the single-stranded RNA transcripts is about half the size of the double-stranded RNA segments, and thus, it appears that in the in vitro reaction, full-length transcripts can be obtained.

Virion-associated RNA polymerase of bacteriophage Φ6 synthesizes three complete transcripts of double-stranded RNA genome in vitro

Three single-stranded RNA transcripts synthesized in vitro by a virion-associated RNA polymerase of bacteriophage Φ6 were sequenced at their 5′- and 3′-termini. The sequences agreed with those of the + strands of the 3 double-stranded RNA segments [FEBS Lett. (1982) 141,111–115]. The results show that the transcription by Φ6 RNA polymerase initiates exactly at the 3′-ends of the template RNAs (− strands of the genomic RNA) and terminates exactly at the 5′-ends.

Synthesis of message and genome RNAs in vitro by Sendai virus-infected cell nucleocapsids.

Purified Sendai virus nucleocapsids isolated from infected cells were used to programme a transcription system in vitro to study virus-specific RNA synthesis. The RNA products were analysed for size by centrifugation before and after denaturation with formamide or glyoxal. The polarity of the products [message (+) or genome (-) strands] was analysed by RNA-RNA hybridization. The non-denatured RNA products sedimented in three groups: 7S to 22S single-stranded RNA transcripts and two partially ribonuclease-resistant complexes. One complex, representing 12% of the total product, sedimented at 26S to 36S. After denaturing the 26S to 36S complex to single-stranded molecules, about half of the RNAs sedimented at 25S to 54S and about half at 6S to 24S. The second complex, representing about 13% of the total RNA product, sedimented at 42S to 52S. After denaturing, about 10% of the single-stranded RNAs sedimented at 38S to 52S and about 90% sedimented at 6S to 19S. In hybridization studies, single-stranded RNAs that sedimented at less than 19S were predominantly of message sense (+ strand), whereas RNAs that sedimented at 25S to 54S were a mixture of genome and anti-genome type. These results show that transcription and replication activities in vitro were associated with Sendai virus nucleocapsids obtained from infected cells and that some of the reaction products approached genome size.