RNA

About: RNA is a research topic. Over the lifetime, 111695 publications have been published within this topic receiving 5475262 citations. The topic is also known as: ribonucleic acid.

Divergent Transcription from Active Promoters

Abstract: Transcription initiation by RNA polymerase II (RNAPII) is thought to occur unidirectionally from most genes. Here, we present evidence of widespread divergent transcription at protein-encoding gene promoters. Transcription start site-associated RNAs (TSSa-RNAs) nonrandomly flank active promoters, with peaks of antisense and sense short RNAs at 250 nucleotides upstream and 50 nucleotides downstream of TSSs, respectively. Northern analysis shows that TSSa-RNAs are subsets of an RNA population 20 to 90 nucleotides in length. Promoter-associated RNAPII and H3K4-trimethylated histones, transcription initiation hallmarks, colocalize at sense and antisense TSSa-RNA positions; however, H3K79-dimethylated histones, characteristic of elongating RNAPII, are only present downstream of TSSs. These results suggest that divergent transcription over short distances is common for active promoters and may help promoter regions maintain a state poised for subsequent regulation.

Characterization of human plasma-derived exosomal RNAs by deep sequencing

Abstract: Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using three human plasma samples and evaluated the efficacies of small RNA library preparation protocols from three manufacturers. In all we evaluated 14 libraries (7 replicates). From the 14 size-selected sequencing libraries, we obtained a total of 101.8 million raw single-end reads, an average of about 7.27 million reads per library. Sequence analysis showed that there was a diverse collection of the exosomal RNA species among which microRNAs (miRNAs) were the most abundant, making up over 42.32% of all raw reads and 76.20% of all mappable reads. At the current read depth, 593 miRNAs were detectable. The five most common miRNAs (miR-99a-5p, miR-128, miR-124-3p, miR-22-3p, and miR-99b-5p) collectively accounted for 48.99% of all mappable miRNA sequences. MiRNA target gene enrichment analysis suggested that the highly abundant miRNAs may play an important role in biological functions such as protein phosphorylation, RNA splicing, chromosomal abnormality, and angiogenesis. From the unknown RNA sequences, we predicted 185 potential miRNA candidates. Furthermore, we detected significant fractions of other RNA species including ribosomal RNA (9.16% of all mappable counts), long non-coding RNA (3.36%), piwi-interacting RNA (1.31%), transfer RNA (1.24%), small nuclear RNA (0.18%), and small nucleolar RNA (0.01%); fragments of coding sequence (1.36%), 5′ untranslated region (0.21%), and 3′ untranslated region (0.54%) were also present. In addition to the RNA composition of the libraries, we found that the three tested commercial kits generated a sufficient number of DNA fragments for sequencing but each had significant bias toward capturing specific RNAs. This study demonstrated that a wide variety of RNA species are embedded in the circulating vesicles. To our knowledge, this is the first report that applied deep sequencing to discover and characterize profiles of plasma-derived exosomal RNAs. Further characterization of these extracellular RNAs in diverse human populations will provide reference profiles and open new doors for the development of blood-based biomarkers for human diseases.

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

Abstract: INTRODUCTION Recently, a special class of RNAs has excited researchers and triggered hundreds of now-published studies. Known as circular RNAs (circRNAs), these RNAs are produced by regular transcription from genomic DNA, but the two ends of the (usually) exonic transcripts are covalently closed, probably in most cases by noncanonical splice reactions. Most circRNAs are expressed in the cytoplasm and are unusually stable, suggesting that they may have functions that diverge from those of canonical messenger RNAs (mRNAs) or long noncoding RNAs (lncRNAs). CircRNAs tend to be weakly expressed, but there are exceptions in animal brains. For example, in the mouse brain, a few hundred circRNAs are highly expressed, often with developmentally specific expression patterns that are conserved in the human brain. We previously proposed that circRNAs may, at least sometimes, serve as regulatory RNAs. A circRNA discovered by the Kjems laboratory, CDR1as, caught our attention because it was covered with >70 binding sites for the microRNA (miRNA) miR-7. Our data suggested that CDR1as might serve to alter the free concentration of miR-7. But what really is the function of CDR1as? RATIONALE We first determined which miRNAs specifically bind Cdr1as in postmortem human and mouse brains and characterized Cdr1as expression patterns. Once we had that information, we removed Cdr1as from the mouse genome to study the molecular and behavioral consequences. RESULTS We show that Cdr1as is, in the human brain, directly and massively bound by miR-7 and miR-671. In fact, Cdr1as is one of the most common transcripts targeted by miRNAs out of all brain mRNAs or lncRNAs. The expression of miRNAs was generally unperturbed in Cdr1as knockout (KO) mice, with the exception of the two miRNAs that directly interact with Cdr1as, miR-7 and miR-671, which were respectively down-regulated and up-regulated. This perturbation was posttranscriptional, consistent with a model in which Cdr1as interacts with these miRNAs in the cytoplasm. We show that Cdr1as is highly expressed (hundreds of copies within neurons) in somas and neurites, but not in glial cells. The expression of many immediate early genes (IEGs), which are markers of neuronal activity, was consistently up-regulated in KO animals. For example, c-Fos and a few other miR-7 targets were up-regulated, suggesting that IEG up-regulation can in part be explained by miR-7 down-regulation and that Cdr1as modulates neuronal activity. Cdr1as KO mice showed a strong deficit in prepulse inhibition of the startle response, a sensorimotor gating phenotype that is impaired in several human neuropsychiatric disorders. Electrophysiological measurements indicated an increase in spontaneous vesicle release in Cdr1as KO neurons, suggesting that Cdr1as plays a role in regulating synaptic transmission. CONCLUSION Mechanistically, our data indicate that Cdr1as regulates miR-7 stability or transport in neurons, whereas miR-671 regulates Cdr1as levels. Functionally, our data suggest that Cdr1as and its direct interactions with miRNAs are important for sensorimotor gating and synaptic transmission. More generally, because the brain is an organ with exceptionally high and diverse expression of circRNAs, our data suggest the existence of a previously unknown layer of biological functions carried out by circRNAs.

Argonaute proteins: functional insights and emerging roles

Abstract: Small-RNA-guided gene regulation has emerged as one of the fundamental principles in cell function, and the major protein players in this process are members of the Argonaute protein family. Argonaute proteins are highly specialized binding modules that accommodate the small RNA component - such as microRNAs (miRNAs), short interfering RNAs (siRNAs) or PIWI-associated RNAs (piRNAs) - and coordinate downstream gene-silencing events by interacting with other protein factors. Recent work has made progress in our understanding of classical Argonaute-mediated gene-silencing principles, such as the effects on mRNA translation and decay, but has also implicated Argonaute proteins in several other cellular processes, such as transcriptional regulation and splicing.

Modulation of hiv replication by rna interference

Abstract: Disclosed herein are small interfering RNAs (siRNAs), and vectors encoding one or more siRNAs (including short hairpin siRNAs), that are sufficiently homologous to a portion of the HIV genome to mediate RNA interference in vivo. Also disclosed are methods wherein siRNAs, or vectors encoding siRNAs, are administered to prevent or inhibit HIV infection in a subject, cell or tissue. Knockout and/or knockdown cells or organisms are also disclosed that utilize the siRNAs or vectors of the present invention.