Unknown RNAs Research Articles

Identification and functional analysis of a new cold induced LncRNA44154

With the development of high-throughput sequencing technology, numerous unknown long noncoding RNAs (lncRNAs) have been discovered. Preliminary research found that after being subjected to low-temperature enviroment, lncRNA44154 expression in the subcutaneous fat of pigs significantly increased. In order to analyze its biological function and regulatory mechanism, qRT-PCR was used to detect its spatiotemporal expression pattern. The nucleoplasmic isolation and FISH were used to locate it subcellular. Through overexpression or interference assays discussed the effect of lncRNA44154 on adipocyte proliferation and differentiation. RNA-seq was used to screen the biological pathways that lncRNA44154 may be involved in. RNA-pull down was used to find the interaction protein and double luciferase reporter gene detection experiment was used to validate the target gene. It was found that the expression of lncRNA44154 had tissue specificity and played a role in adipocyte proliferation. It was expressed in both cytoplasm and nucleus. After overexpression of lncRNA44154 in adipocytes, the expression level of Cyclins B, D, and E were all up-regulated and the cell proliferation ability was significantly enhanced. The number of positive cells increased significantly and the DNA replication activity was significantly enhanced. LncRNA44154 can promote the proliferation of porcine preadipocytes by encouraging cells to enter the S phase of the cell cycle. The result of interfering with lncRNA44154 is the opposite. Further analysis revealed that lncRNA44154 regulates intracellular lipid metabolism, inhibits the production of intracellular lipid droplets, and inhibits preadipocyte differentiation. RNA-seq results indicate that lncRNA44154 may be involved in biological pathways such as AMPK, PPAR and cAMP signaling pathway. It may work by regulating the RPS4X gene. This research may provide a new perspective for investigating the regulation of adipose metabolism by lncRNAs.

TRNA-derived fragments as new players in regulatory processes in yeast.

For a very long time, RNA molecules were treated as transistory molecules, by which the genetic information flows from DNA to proteins; the model proposed in the 1960s accepted that proteins are boththe products and the regulators of gene expression. Since then, thousands of reports proved that RNAs should be thought about as the factors that do control gene expression. The pervasive transcription has been reported in many eukaryotic organisms, illustrating a highly interwoven transcriptome organization that includes hundreds of previously unknown noncoding RNAs. The key roles of noncoding RNAs (microRNAs and small interferingRNAs) in gene expression regulation are no longer surprising, as are new classes of noncoding RNAs constantly being discovered. TransferRNAs (tRNAs) are the second most abundant type of RNAs in the cell. Advances in high-throughput sequencing technologies exposed the existence of functional, regulatory tRNA-derived RNA fragments (tRFs), generated from precursor and mature tRNAs. These tRF molecules have been found to play central roles during stress and different pathological conditions. Herein, we present the critical assessment of the discoveries made in the field of tRNA-derived fragments in the past 15 years in various pathogenic and nonpathogenic yeast species.

Novel long non-coding RNAs of relevance for ulcerative colitis pathogenesis.

Background and aimsThe study aimed to identify yet unknown and uncharacterized long non-coding RNAs (lncRNAs) in treatment-naïve ulcerative colitis (UC), and to define their possible roles in UC pathogenesis. For that purpose, accurate quantification methods for lncRNA transcript detection, multiple and “stringent” strategies were applied. New insights in the regulation of functional genes and pathways of relevance for UC through expression of lncRNAs are expected.MethodsThe study was based on sequencing data derived from a data set consisting of treatment-naïve UC patients (n = 14) and control subjects (n = 16). Two complementary aligners were used to identify lncRNAs. Several different steps were used to validate differential expression including plotting the reads over the annotation for manual inspection. To help determine potential lncRNA involvement in biological processes, KEGG pathway enrichment was done on protein-coding genes which co-expressed with the lncRNAs.ResultsA total of 99 lncRNAs were identified in UC. The lncRNAs which were not previously characterized (n = 15) in UC or other autoimmune diseases were selected for down-stream analysis. In total, 602 protein-coding genes correlated with the uncharacterized lncRNAs. KEGG pathway enrichment analysis revealed involvement of lncRNAs in two significantly enriched pathways, lipid and atherosclerosis, and T-cell receptor signaling.ConclusionThis study identified a set of 15 yet uncharacterized lncRNAs which may be of importance for UC pathogenesis. These lncRNAs may serve as potential diagnostic biomarkers and might be of use for the development of UC treatment strategies in the future.

Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions.

Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematically particular nucleotides with different nucleotides. Among 347 unknown ESTs, 51 ESTs match mitogenome transcription, 17 and 2 ESTs are from nuclear chromosome non-coding regions, and uncharacterized nuclear genes. Identified ESTs mapped on 205 protein-coding genes, 10 genes had swinger RNAs in several biosamples. Whole cell transcriptome searches for 17 ESTs mapping on non-coding regions confirmed their transcription. The 10 swinger-transcribed genes identified more than once associate with cancer induction and progression, suggesting swinger transformation occurs mainly in highly transcribed genes. Swinger transformation is a unique method to identify noncanonical RNAs obtained from NGS, which identifies putative ncRNA transcribed regions. Results suggest that swinger transcription occurs in highly active genes in normal and genetically unstable cancer cells.

Identification of Noncanonical Transcripts Produced by Systematic Nucleotide Exchanges in HIV-Associated Centroblastic Lymphoma.

Noncanonical transcriptions include transcriptions that systematically exchange nucleotides, also called bijective transformations or swinger transformations. Swinger transformation A↔T+C↔G recovers identities of 8 among 9 unknown RNAs differentially expressed in centroblastic lymphoma, a human immunodeficiency virus (HIV)-associated non-Hodgkin's lymphoma. The identified RNAs align with human genes with known anti-HIV1 or oncogenic activities. Function disruption through swinger-transformed transcription potentially enables avoiding antiviral responses and contributes to cancer induction.

Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.

RNA secondary structure prediction is often used to develop hypotheses about structure-function relationships for newly discovered RNA sequences, to identify unknown functional RNAs, and to design sequences. Secondary structure prediction methods typically use a thermodynamic model that estimates the free energy change of possible structures based on a set of nearest neighbor parameters. These parameters were derived from optical melting experiments of small model oligonucleotides. This work aims to better understand the precision of structure prediction. Here, the experimental errors in optical melting experiments were propagated to errors in the derived nearest neighbor parameter values and then to errors in RNA secondary structure prediction. To perform this analysis, the optical melting experimental values were systematically perturbed within the estimates of experimental error and alternative sets of nearest neighbor parameters were then derived from these error-bounded values. Secondary structure predictions using either the perturbed or reference parameter sets were then compared. This work demonstrated that the precision of RNA secondary structure prediction is more robust than suggested by previous work based on perturbation of the nearest neighbor parameters. This robustness is due to correlations between parameters. Additionally, this work identified weaknesses in the parameter derivation that makes accurate assessment of parameter uncertainty difficult. Considerations for experimental design are provided to mitigate these weaknesses are provided.

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Rhesus macaque was the second non-human primate whose genome has been fully sequenced and is one of the most used model organisms to study human biology and disease, thanks to the close evolutionary relationship between the two species. But compared to human, where several previously unknown RNAs have been uncovered, the macaque transcriptome is less studied. Publicly available RNA expression resources for macaque are limited, even for brain, which is highly relevant to study human cognitive abilities. In an effort to complement those resources, FANTOM5 profiled 15 distinct anatomical regions of the aged macaque central nervous system using Cap Analysis of Gene Expression, a high-resolution, annotation-independent technology that allows monitoring of transcription initiation events with high accuracy. We identified 25,869 CAGE peaks, representing bona fide promoters. For each peak we provide detailed annotation, expanding the landscape of ‘known’ macaque genes, and we show concrete examples on how to use the resulting data. We believe this data represents a useful resource to understand the central nervous system in macaque.

TRid, an enabling method to isolate previously inaccessible small RNA fractions

Detection of rare small RNA species whose sizes are overlapping with tRNAs often suffers from insufficient sensitivity due to the overwhelming abundance of tRNAs. We here report a method, named tRid (tRNA rid), for removing abundant tRNAs from small RNA fractions regardless of tRNA sequence species. By means of tRid, we are able to selectively enrich small RNAs which have been previously difficult to access due to mass existence of tRNAs in such fractions. A flexible tRNA-acylation ribozyme, known as flexizyme, is a key tool where the total tRNAs are aminoacylated with N-biotinylated phenylalanine regardless of tRNA sequences, and therefore the biotin-tagged tRNAs could be readily removed from the small RNA fractions by the use of streptavidin-immobilized magnetic beads. Next generation sequencing of the isolated small RNA fraction revealed that small RNAs with less than 200nt were effectively enriched, allowing us to identify previously unknown small RNAs in HeLa and E. coli.

RNA Systems Biology for Cancer: From Diagnosis to Therapy.

It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with various but primarily regulatory roles. Many of these are linked to the emergence and progression of human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers. These efforts led to the identification of a new tool-kit for cancer diagnosis, monitoring, and treatment, which is now starting to enter and impact on clinical practice. This chapter is to elaborate on the state of the art in RNA systems biology, including a review and perspective on clinical applications toward an integrative RNA systems medicine approach. The focus is on the role of ncRNAs in cancer.

Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages.

To elucidate the transcriptional landscape that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitors spanning the earliest stages of B and T lymphoid specification. Over 3000 novel long non-coding RNA genes (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage-specific and more lineage-specific than protein coding patterns. Protein-coding genes co-expressed with neighboring lncRNA genes were enriched for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships between the earliest progenitors in the human bone marrow and thymus.

Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling.

Clear cell renal cell carcinoma (ccRCC) is a common human malignancy. Despite numerous efforts, there is still no reliable biomarker or combination of biomarkers available for daily practice. Our study was designed to explore the expression profile of messenger RNA (mRNA) and long non-coding RNA (lncRNA) transcripts in ccRCC in order to identify potential diagnostic biomarkers for patients with ccRCC. Total RNA from corresponding normal and malignant tissue of 15 patients with ccRCC was isolated. Expression profiling was performed using a custom Agilent gene expression microarray which allowed the analysis of 34,144 mRNA and 32,183 lncRNA transcripts. We observed that a subset of mRNA (n = 1064; 3.1%) and lncRNA (n = 1308; 4.1%) transcripts are dysregulated (fold change > 2) in ccRCC tissue. The relative higher number of differentially expressed lncRNAs indicates that lncRNA profiling may be better suited for diagnostic purposes; a number of so far unknown RNAs with potential diagnostic interest in ccRCC are identified by our gene expression profiling study. The data are deposited in the Gene Expression Omnibus (GSE61763).

First report of Dahlia latent viroid and Potato spindle tuber viroid mixed‐infection in commercial ornamental dahlia in Japan

Dahlia (Asteraceae) has been cultivated since 1841 in Japan. Two viroids belonging to the family Pospiviroidae, Potato spindle tuber viroid (PSTVd) and Dahlia latent viroid (DLVd), were identified separately from dahlia plants in Japan and in the Netherlands, respectively (Tsushima et al., 2011; Verhoeven et al., 3). Because DLVd was characterised as a novel species, the findings drew attention towards the study of DLVd infection in dahlia and its potential risk in domestic dahlia cultivation. A total of four dahlia samples infected with PSTVd-dahlia (Tsushima et al., 2) were collected, and total RNA was extracted from approximately 200 mg of leaf tissue using TRIzol® reagent (Life Technologies, Carlsbad, USA) according to manufacturer's instructions. RNA was separated in 2-dimensional polyacrylamide gel (2D-PAGE) (Schumacher et al., 1) and two specific bands appeared, one corresponding to PSTVd infection and the other being unknown (Fig. 1). The unknown circular RNA samples were gel-excised and first tested with PSTVd-specific primers using a two-step reverse-transcription-polymerase chain reaction (RT-PCR) (Tsushima et al., 2), with, however, negative results. Therefore, a DLVd-specific primer set, DLVd-P1 (5'-GGGGCTCCTCAGAGAGTCTC-3') and DLVd-P2 (5'-GGGGCAACTCCGAGAGTGCTG-3') (Verhoeven et al., 3), was then used in two-step RT-PCR for the unknown viroid-like circular RNAs. The amplified DNA bands of the expected size (~340 bp) from these positive samples were purified, ligated to pGEM®-T easy vector (Promega, Madison, USA) and sequenced. Identical 342 bp sequences were obtained from all four dahlia isolates (GenBank Accession No. LC036322), corresponding with DLVd reported from the Netherlands (JX263426). Furthermore, a total of 78 dahlia leaf samples were collected from fields around Japan, irrespective of disease symptoms, and verified by two-step RT-PCR using the same DLVd-specific and pospiviroid-specific primers (Tsushima et al., 2). Of these samples, DLVd infection was detected in 38, suggesting that DLVd is widespread in Japan. New PSTVd infection was not found. To evaluate the pathogenicity of DLVd and PSTVd, these viroids were co-inoculated into wild hop (Humulus lupulus var. cordifolius) and dahlia seedlings. DLVd alone was inoculated into members of the Asteraceae family, Chrysanthemum pacificum, Tithonia rotundifolia, Helianthus annuus and Glebionis coronaria. Inoculated dahlia seedlings were positive for both DLVd and PSTVd, but wild hop and the remaining members of Asteraceae were negative. Dahlia seedlings that were positive for DLVd and PSTVd showed mild leaf curling in the early stage of growth (Fig. 2). To the best of our knowledge, this is the first report of DLVd infecting commercial dahlia in Japan and also of the mixed-infection of DLVd and PSTVd in commercial dahlia plants. A possible negative synergistic interaction of DLVd and PSTVd during dahlia cultivation must be considered. This work was supported in part by Japan Society for the Promotion of Science KAKENHI grant no. 24380026. TT received Research Fellowship of the Japan Society for the Promotion of Science.

A simple protocol for the inference of RNA global pairwise alignments.

RNA alignment is an important step in the annotation and characterization of unknown RNAs, and several methods have been developed to meet the need of fast and accurate alignments. Being the performances of the aligning methods affected by the input RNA features, finding the most suitable method is not trivial. Indeed, no available method clearly outperforms the others. Here we present a simple workflow to help choosing the more suitable method for RNA pairwise alignment. We tested the performances of six algorithms, based on different approaches, on datasets created by merging publicly available datasets of known or curated RNA secondary structure annotations with datasets of curated RNA alignments. Then, we simulated the frequent case where the secondary structure is unknown by using the same alignment datasets but ignoring the known structure and instead predicting it. In conclusion, the proposed workflow for pairwise RNA alignment depends on the input RNA primary sequence identity and the availability of reliable secondary structures.

Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software.

BackgroundRNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains.ResultsIn order to fill this gap, an innovative software called ORA (Overlapped Reads Assembler) was developed. This software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. It can also determine the size and the position of the untranslated regions (UTR) and of polycistronic transcripts. As a case study, we analyzed the transcriptional landscape of six S. cerevisiae strains in two different key steps of the fermentation process. This comparative analysis revealed differences in the UTR regions of transcripts. By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional role.ConclusionsBy comparing the results obtained using ORA with previous studies and with the transcriptome structure determined with other software, it was proven that ORA has a remarkable reliability. The results obtained from the training set made it possible to detect the presence of transcripts with variable UTRs between S. cerevisiae strains. Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1045) contains supplementary material, which is available to authorized users.

Genomics: Hiding in plain sight.

The latest releases from the ENCODE and modENCODE research consortia more than double the number of data sets on functional elements in the worm, fly and human genomes. See Articles p.393 , p.400 & Letters p.445 , p.449 , p.453 Although all cells in an animal share the same genes, the palette of those transcribed — the transcriptome — varies enormously between different cells and tissues. This manuscript, from the modENCODE consortium, investigates this variation in a range of cultured cell lines and dissected organ systems of the fruitfly, Drosophila melanogaster, with the aim of establishing just how diverse the transcriptome really is. For example, a small set of mostly neural-specific genes has the potential to encode thousands of messenger-RNA transcripts, each through extensive alternative promoter usage and RNA splicing. Furthermore, gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. The fly transcriptome is clearly much more complex than previously recognized.

Detection of RNAs by 3'-end labeling and RNase H digestion.

This protocol describes an extremely sensitive procedure for detecting the presence of known or unknown RNAs in a complex mixture. A selectively enriched population of RNAs is subjected to 3'-end labeling with [(32)P]pCp, and labeled products are separated from unincorporated label. The labeled RNAs are hybridized to sequence-specific complementary oligodeoxynucleotides, treated with RNase H (which cleaves RNA in an RNA-DNA hybrid) and the products analyzed by electrophoresis through denaturing polyacrylamide gels with the appropriate controls. If the RNA of interest was present and hybridized to its complementary oligonucleotide, its digestion with RNase H will result in a shift in its mobility through the gel or, if the RNA was fully degraded, its band will not appear. If the RNA of interest is not cleaved in the presence of any known complementary oligodeoxynucleotides, then its position in the gel will remain unaltered. This result may suggest the presence of a new or unknown RNA that may be identified using a variety of cloning techniques or by direct chemical sequencing methods.

Diversity and dynamics of the Drosophila transcriptome.

Animal transcriptomes are dynamic, each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. We identified new genes, transcripts, and proteins using poly(A)+ RNA sequence from Drosophila melanogaster cultured cell lines, dissected organ systems, and environmental perturbations. We found a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long noncoding RNAs (lncRNAs) some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized arising from combinatorial usage of promoters, splice sites, and polyadenylation sites.

Overview of research on Bombyx mori microRNA.

MicroRNAs (miRNAs) constitute some of the most significant regulatory factors involved at the post-transcriptional level after gene expression, contributing to the modulation of a large number of physiological processes such as development, metabolism, and disease occurrence. This review comprehensively and retrospectively explores the literature investigating silkworm, Bombyx mori L. (Lepidoptera: Bombicidae), miRNAs published to date, including discovery, identification, expression profiling analysis, target gene prediction, and the functional analysis of both miRNAs and their targets. It may provide experimental considerations and approaches for future study of miRNAs and benefit elucidation of the mechanisms of miRNAs involved in silkworm developmental processes and intracellular activities of other unknown non-coding RNAs.

Identification of MIWI-associated Poly(A) RNAs by immunoprecipitation with an anti-MIWI monoclonal antibody

MIWI is one of the PIWI subfamily of proteins mainly expressed in mouse germ cells, and associates with pachytene piRNAs. MIWI has been thought to play an essential role in spermatogenesis and spermiogenesis via biogenesis and/or stability of pachytene piRNAs, retrotransposon silencing, and post-transcriptional regulation of target mRNAs. However, MIWI's detailed role and function are not well understood. In this study, we produced an anti-MIWI mouse monoclonal antibody and identified MIWI-associated poly(A) RNAs by immunoprecipitation from adult mouse testes lysates. Approximately 70% of the MIWI-associated poly(A) RNAs were known mRNAs and 30% of them were unknown non-coding RNAs. These poly(A) RNAs contained piRNA-encoding RNAs transcribed from piRNA cluster regions and piRNA-encoding mRNA, such as Aym1 mRNA. Mature piRNAs specifically encoded in these piRNA-encoding RNAs were generated in pachytene spermatocytes and not detected in Miwi-deficient (Miwi-/-) testes. Moreover, MIWI associated with a large number of known mRNAs whose expression levels were increased in pachytene spermatocytes, and the expression of these mRNAs was decreased in Miwi-/- testes at 20 days postpartum when pachytene spermatocytes were most abundant. These results strongly suggest that MIWI is involved in pachytene piRNA biogenesis and the positive regulation of target mRNA metabolism in pachytene spermatocytes via association with pachytene piRNA precursors and target mRNAs.

Antisense transcription is coupled to nucleosome occupancy in sense promoters

Genome-wide pervasive transcription is widespread in eukaryotes, revealing an extensive array of antisense transcription that involves hundreds of previously unknown non-coding RNAs. Individual cases have shown that antisense transcription influences sense transcription, however, genome-wide mechanisms of how antisense transcription regulates sense transcription remain to be elucidated. Here, we performed a systematic analysis of sense-antisense transcription and nucleosome occupancy in yeast. We found that antisense transcription is associated with nucleosome occupancy in sense promoters. Using RNA polymerase II inactivation data as a reasonable approximation to antisense transcription inactivation data, we further showed that antisense transcripts increase nucleosome occupancy in sense promoter regions they overlap, and reduce nucleosome occupancy in sense promoter regions around their transcription termination sites. These results reveal the previously unappreciated roles of antisense transcription in directing nucleosome occupancy in sense promoters. Our findings will have implications in understanding regulatory functions of antisense transcription.