1,696 results match your criteria RNA biology[Journal]


Boosting AgoshRNA activity by optimized 5'-terminal nucleotide selection.

RNA Biol 2019 Apr 16:1-9. Epub 2019 Apr 16.

a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands.

RNA interference (RNAi) can be triggered by synthetic small interfering RNAs (siRNAs) or transgene-expressed short hairpin RNAs (shRNAs). Recent evidence indicates that shRNA molecules, with a relatively short stem and small loop, are processed by Argonaute 2 protein (Ago2). We named these molecules AgoshRNA as Ago2 is involved in both the processing and the subsequent mRNA-silencing reaction. Read More

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http://dx.doi.org/10.1080/15476286.2019.1599259DOI Listing
April 2019
1 Read

How sequence variants of a plastid-replicating viroid with one single nucleotide change initiate disease in its natural host.

RNA Biol 2019 Apr 16:1-12. Epub 2019 Apr 16.

a Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV) , Valencia , Spain.

Understanding how viruses and subviral agents initiate disease is central to plant pathology. Whether RNA silencing mediates the primary lesion triggered by viroids (small non-protein-coding RNAs), or just intermediate-late steps of a signaling cascade, remains unsolved. While most variants of the plastid-replicating peach latent mosaic viroid (PLMVd) are asymptomatic, some incite peach mosaics or albinism (peach calico, PC). Read More

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http://dx.doi.org/10.1080/15476286.2019.1600396DOI Listing
April 2019
1 Read

Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts.

RNA Biol 2019 Apr 14:1-10. Epub 2019 Apr 14.

a Beijing Institutes of Life Science , Chinese Academy of Sciences , Beijing , China.

The large genome of the migratory locust (Locusta migratoria) genome accumulates massive amount of accumulated transposable elements (TEs), which show intrinsic transcriptional activities. Hampering the ability to precisely determine full-length RNA transcript sequences are exonized TEs, which produce numerous highly similar fragments that are difficult to resolve using short-read sequencing technology. Here, we applied a 5'-Cap capturing method using Nanopore long-read direct RNA sequencing to characterize full-length transcripts in their native RNA form and to analyze the TE exonization pattern in the locust transcriptome. Read More

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http://dx.doi.org/10.1080/15476286.2019.1602437DOI Listing

The RGG/RG motif of AUF1 isoform p45 is a key modulator of the protein's RNA chaperone and RNA annealing activities.

RNA Biol 2019 Apr 5:1-12. Epub 2019 Apr 5.

a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany.

The RNA-binding protein AUF1 regulates post-transcriptional gene expression by affecting the steady state and translation levels of numerous target RNAs. Remodeling of RNA structures by the largest isoform AUF1 p45 was recently demonstrated in the context of replicating RNA viruses, and involves two RNA remodeling activities, i.e. Read More

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http://dx.doi.org/10.1080/15476286.2019.1602438DOI Listing
April 2019
1 Read
4.974 Impact Factor

Structural features of an Xrn1-resistant plant virus RNA.

RNA Biol 2019 Apr 5:1-8. Epub 2019 Apr 5.

a Leiden Institute of Chemistry , Leiden University , Leiden , The Netherlands.

Xrn1 is a major 5'-3' exoribonuclease involved in the RNA metabolism of many eukaryotic species. RNA viruses have evolved ways to thwart Xrn1 in order to produce subgenomic non-coding RNA that affects the hosts RNA metabolism. The 3' untranslated region of several beny- and cucumovirus RNAs harbors a so-called 'coremin' motif that is required for Xrn1 stalling. Read More

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A novel human lncRNA SANT1 cis-regulates the expression of SLC47A2 by altering SFPQ/E2F1/HDAC1 binding to the promoter region in renal cell carcinoma.

RNA Biol 2019 Apr 5. Epub 2019 Apr 5.

a Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou 310006 , China.

SLC47A2 encodes MATE 2-K in the kidney, which mediates the secretion of certain endogenous and exogenous compounds. SLC47A2 was dramatically repressed in patients with renal cell carcinoma (RCC), and a lower level of SLC47A2 might act as a negative prognostic marker, although the mechanism is not well understood. In this study, we aimed to investigate the mechanism via which SLC47A2 is downregulated in RCC. Read More

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http://dx.doi.org/10.1080/15476286.2019.1602436DOI Listing
April 2019
3 Reads

DNA cleavage and reverse splicing of ribonucleoprotein particles reconstituted in vitro with linear RmInt1 RNA.

RNA Biol 2019 Apr 4:1-10. Epub 2019 Apr 4.

a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain.

The RmInt1 group II intron is an efficient self-splicing mobile retroelement that catalyzes its own excision as lariat, linear and circular molecules. In vivo, the RmInt1 lariat and the reverse transcriptase (IEP) it encodes form a ribonucleoprotein particle (RNP) that recognizes the DNA target for site-specific full intron insertion via a two-step reverse splicing reaction. RNPs containing linear group II intron RNA are generally thought to be unable to complete the reverse splicing reaction. Read More

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http://dx.doi.org/10.1080/15476286.2019.1601379DOI Listing
April 2019
1 Read

MiR-195 regulates mitochondrial function by targeting mitofusin-2 in breast cancer cells.

RNA Biol 2019 Apr 1. Epub 2019 Apr 1.

a Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology , Mall Road, Delhi - 110007 , India.

Mitochondrial dynamics is a highly dysregulated process in cancer. Apoptosis and mitochondrial fission are two concurrent events wherein increased mitochondrial fragmentation serves as a hallmark of apoptosis. We have shown earlier that miR-195 exerts pro-apoptotic effects in breast cancer cells. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1600999DOI Listing
April 2019
9 Reads

Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA.

RNA Biol 2019 Mar 30:1-14. Epub 2019 Mar 30.

a Institute of Clinical Physiology , CNR , Pisa , Italy.

Here we present miR-CATCHv2.0, an implemented experimental method that allows the identification of the microRNA species directly bound to an RNA of interest. After cross-linking of microRNA::RNA::Ago2 complexes using formaldehyde, the RNA is fragmented using sonication and then subjected to affinity purification using two sets of biotinylated tiling probes (ODD and EVEN). Read More

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http://dx.doi.org/10.1080/15476286.2019.1600934DOI Listing
March 2019
1 Read

Small molecules with big roles in microRNA chemical biology and microRNA-targeted therapeutics.

RNA Biol 2019 Mar 22:1-12. Epub 2019 Mar 22.

g Department of Geraeology, Yancheng City No.1 People's Hospital , Yancheng , China.

MicroRNAs (miRNAs) are small, non-coding RNAs that post-transcriptionally regulate gene expression. Aberrant miRNA expression or function have close links with various human diseases. Therefore, therapeutic treatments with disease-associated miRNAs as targets are emerging. Read More

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http://dx.doi.org/10.1080/15476286.2019.1593094DOI Listing
March 2019
4.974 Impact Factor

Bisubstrate analogues as structural tools to investigate mA methyltransferase active sites.

RNA Biol 2019 Mar 17:1-11. Epub 2019 Mar 17.

a Laboratoire d'Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS , Université Paris Diderot , Paris , France.

RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. Read More

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http://dx.doi.org/10.1080/15476286.2019.1589360DOI Listing
March 2019
2 Reads

Strategic labeling approaches for RNA single molecule spectroscopy.

RNA Biol 2019 Mar 15. Epub 2019 Mar 15.

a Goethe-University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7, 60438 Frankfurt , Germany.

Most single molecule techniques observing RNA in vitro or in vivo require fluorescent labels that have to be connected to the RNA of interest. In recent years, a plethora of methods has been developed to achieve site-specific labeling, in many cases under near-native conditions. Here, we review chemical as well as enzymatic labeling methods that are compatible with single molecule fluorescence spectroscopy or microscopy, and show how these can be combined to offer a large variety of options to site-specifically place one or more labels in an RNA of interest. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1593093DOI Listing
March 2019
4 Reads

MALAT1 long non-coding RNA and breast cancer.

RNA Biol 2019 Mar 15:1-4. Epub 2019 Mar 15.

a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA.

Non-coding RNAs are becoming major players in disease pathogenesis such as cancer. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is a nuclear enriched long non-coding RNA that is generally overexpressed in patient tumors and metastases. Overexpression of MALAT1 has been shown to be positively correlated with tumor progression and metastasis in a large number of tumor types including breast tumors. Read More

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http://dx.doi.org/10.1080/15476286.2019.1592072DOI Listing

Circular RNAs in human and vertebrate neural retinas.

RNA Biol 2019 Mar 15:1-9. Epub 2019 Mar 15.

a Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics , The Eye Hospital, Wenzhou Medical University , Wenzhou , China.

Circular RNAs (circRNAs) belong to an endogenous class of RNA molecules with both ends covalently linked in a circle. Although their expression pattern in the mammalian brain has been well studied, the characteristics and functions of circRNAs in retinas remain unknown. To reveal the whole expression profiles of circRNAs in the neural retina, we investigated retinal RNAs of human, monkey, mouse, pig, zebrafish and tree shrew and detected thousands of circRNAs showing conservation and variation in the retinas across different vertebrate species. Read More

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http://dx.doi.org/10.1080/15476286.2019.1591034DOI Listing

Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region.

RNA Biol 2019 Mar 14:1-8. Epub 2019 Mar 14.

a College of Life Sciences , Nankai University , Tianjin , P.R.China.

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. The high-resolution annotations cover both entire strands of the mitochondrial genome without any gaps or overlaps. Most of the new annotations were consistent with the previous annotations which had been obtained using PacBio full-length transcripts. Read More

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http://dx.doi.org/10.1080/15476286.2019.1591035DOI Listing
March 2019
2 Reads

Identification of Hfq-binding RNAs in Caulobacter crescentus.

RNA Biol 2019 Mar 14:1-8. Epub 2019 Mar 14.

a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil.

Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium Caulobacter crescentus, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). Read More

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http://dx.doi.org/10.1080/15476286.2019.1593091DOI Listing

De novo origination of MIRNAs through generation of short inverted repeats in target genes.

Authors:
Shanfa Lu

RNA Biol 2019 Mar 14:1-14. Epub 2019 Mar 14.

a Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , China.

MIRNA (MIR) gene origin and early evolutionary processes, such as hairpin precursor sequence origination, promoter activity acquirement and the sequence of these two processes, are fundamental and fascinating subjects. Three models, including inverted gene duplication, spontaneous evolution and transposon transposition, have been proposed for de novo origination of hairpin precursor sequence. However, these models still open to discussion. Read More

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http://dx.doi.org/10.1080/15476286.2019.1593744DOI Listing

CRISPR-Cas in Streptococcus pyogenes.

RNA Biol 2019 Mar 11:1-10. Epub 2019 Mar 11.

a Max Planck Unit for the Science of Pathogens , Berlin , Germany.

The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. Read More

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http://dx.doi.org/10.1080/15476286.2019.1582974DOI Listing
March 2019
3 Reads
4.974 Impact Factor

Alternative splicing regulation of doublesex gene by RNA-binding proteins in the silkworm Bombyx mori.

RNA Biol 2019 Mar 5:1-12. Epub 2019 Mar 5.

c College of Life Science , Wuhan University , Wuhan , China.

Doublesex is highly conserved and sex-specifically spliced in insect sex-determination pathways, and its alternative splicing (AS) is regulated by Transformer, an exonic splicing activator, in the model system of Drosophila melanogaster. However, due to the lack of a transformer gene, AS regulation of doublesex remains unclear in Lepidoptera, which contain the economically important silkworm Bombyx mori and thousands of agricultural pests. Here, we use yeast three-hybrid system to screen for RNA-binding proteins that recognize sex-specific exons 3 and 4 of silkworm doublesex (Bm-dsx); this approach identified BxRBP1/Lark binding to the exon 3, and BxRBP2/TBPH and BxRBP3/Aret binding to the exon 4. Read More

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http://dx.doi.org/10.1080/15476286.2019.1590177DOI Listing
March 2019
1 Read
4.974 Impact Factor

Extracellular microRNAs exhibit sequence-dependent stability and cellular release kinetics.

RNA Biol 2019 Mar 5:1-11. Epub 2019 Mar 5.

a Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK.

Multiple studies have described extracellular microRNAs (ex-miRNAs) as being remarkably stable despite the hostile extracellular environment, when stored at 4ºC or lower. Here we show that many ex-miRNAs are rapidly degraded when incubated at 37ºC in the presence of serum (thereby simulating physiologically relevant conditions). Stability varied widely between miRNAs, with half-lives ranging from ~1. Read More

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http://dx.doi.org/10.1080/15476286.2019.1582956DOI Listing
March 2019
2 Reads

Early splicing functions of fission yeast Prp16 and its unexpected requirement for gene Silencing is governed by intronic features.

RNA Biol 2019 Feb 27:1-16. Epub 2019 Feb 27.

a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India.

Prp16 is a DEAH box pre-mRNA splicing factor that triggers a key spliceosome conformational switch to facilitate second step splicing in Saccharomyces cerevisiae. However, Prp16 functions are largely unexplored in Schizosaccharomyces pombe, an attractive model with exon-intron architecture more relevant to several other eukaryotes. Here, we generated mis-sense alleles in SpPrp16 whose consequences on genome-wide splicing uncover its nearly global splicing role with only a small subset of unaffected introns. Read More

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http://dx.doi.org/10.1080/15476286.2019.1585737DOI Listing
February 2019
7 Reads
4.974 Impact Factor

Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution.

RNA Biol 2019 Feb 27:1-13. Epub 2019 Feb 27.

a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China.

Alternative polyadenylation (APA) has been discovered to play regulatory roles in the development of many cancer cells through preferential addition of a poly(A) tail at specific sites of pre-mRNA. A recent study found that APA was involved in the mediation of acute myeloid leukaemia (AML). However, unlike gene expression heterogeneity, little attention has been directed toward variations in single-cell APA for different cell types during AML development. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1586139DOI Listing
February 2019
1 Read

The origin of exosomal miR-1246 in human cancer cells.

RNA Biol 2019 Mar 23:1-15. Epub 2019 Mar 23.

a Department of Pathology , University of Oklahoma Health Sciences Center , Oklahoma City , OK , USA.

miR-1246 is considered an oncomiR in various cancer types. However, the origin and biogenesis of miR-1246 remain controversial which often leads to misinterpretation of its detection and biological function, and inevitably masking its mechanisms of action. Using next generation small RNA sequencing, CRISPR-Cas9 knockout, siRNA knockdown and the poly-A tailing SYBR qRT-PCR, we examined the biogenesis of exosomal miR-1246 in human cancer cell model systems. Read More

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http://dx.doi.org/10.1080/15476286.2019.1585738DOI Listing

An RNA aptamer to HP1/Swi6 facilitates heterochromatin formation at an ectopic locus in S.pombe.

RNA Biol 2019 Feb 22:1-12. Epub 2019 Feb 22.

a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India.

In the fission yeast Schizosaccharomyces pombe (S.pombe), heterochromatin domains are established and maintained by protein complexes that contain numerous RNA binding domains among their components. The fission yeast HP1 protein Swi6 is one such component and contains an unstructured RNA-binding hinge, which is important for the integrity and silencing of heterochromatin. Read More

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http://dx.doi.org/10.1080/15476286.2019.1584026DOI Listing
February 2019
2 Reads

HuR controls apoptosis and activation response without effects on cytokine 3' UTRs.

Authors:
Fedor V Karginov

RNA Biol 2019 Feb 19:1-10. Epub 2019 Feb 19.

a Department of Molecular, Cell, and Systems Biology , Institute for Integrative Genome Biology, University of California , Riverside , CA , USA.

RNA binding proteins regulate gene expression through several post-transcriptional mechanisms. The broadly expressed HuR/ELAVL1 is important for proper function of multiple immune cell types, and has been proposed to regulate cytokine and other mRNA 3' UTRs upon activation. However, this mechanism has not been previously dissected in stable cellular settings. Read More

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http://dx.doi.org/10.1080/15476286.2019.1582954DOI Listing
February 2019
7 Reads

Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus.

RNA Biol 2019 Feb 19:1-11. Epub 2019 Feb 19.

d Department of Life and Environmental Sciences , Polytechnic University of Marche , Ancona , Italy.

Translation factor a/eIF5A is highly conserved in Eukarya and Archaea. The eukaryal eIF5A protein is required for transit of ribosomes across consecutive proline codons, whereas the function of the archaeal orthologue remains unknown. Here, we provide a first hint for an involvement of Sulfolobus solfataricus (Sso) aIF5A in translation. Read More

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http://dx.doi.org/10.1080/15476286.2019.1582953DOI Listing
February 2019
2 Reads

La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates.

RNA Biol 2019 Feb 19:1-10. Epub 2019 Feb 19.

a Department of Biology , York University , Toronto , Ontario , Canada.

La shuttles between the nucleus and cytoplasm where it binds nascent RNA polymerase III (pol III) transcripts and mRNAs, respectively. La protects the 3' end of pol III transcribed RNA precursors, such as pre-tRNAs, through the use of a well-characterized UUU-3'OH binding mode. La proteins are also RNA chaperones, and La-dependent RNA chaperone activity is hypothesized to promote pre-tRNA maturation and translation at cellular and viral internal ribosome entry sites via binding sites distinct from those used for UUU-3'OH recognition. Read More

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http://dx.doi.org/10.1080/15476286.2019.1582955DOI Listing
February 2019
1 Read

Stabilizing role of structural elements within the 5´ Untranslated Region (UTR) and gag sequences in Mason-Pfizer monkey virus (MPMV) genomic RNA packaging.

RNA Biol 2019 Feb 17:1-14. Epub 2019 Feb 17.

a Department of Microbiology & Immunology College of Medicine and Health Sciences , United Arab Emirates University , Al Ain , United Arab Emirates (UAE).

The Mason-Pfizer monkey virus (MPMV) genomic RNA (gRNA) packaging signal is a highly-structured element with several stem-loops held together by two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences. These LRIs play a critical role in maintaining the structure of the 5´ end of the MPMV gRNA. Thus, one could hypothesize that the overall RNA secondary structure of this region is further architecturally held together by three other stem loops (SL3, Gag SL1, and Gag SL2) comprising of sequences from the distal parts of the 5´untranslated region (5' UTR) to ~ 120 nucleotides into gag, excluding gag sequences involved in forming the U5-Gag LRIs. Read More

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http://dx.doi.org/10.1080/15476286.2019.1572424DOI Listing
February 2019

Identification of a novel antisense RNA that regulates growth hormone receptor expression in chickens.

RNA Biol 2019 Feb 14:1-13. Epub 2019 Feb 14.

a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China.

Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identified a novel antisense transcript in the chicken, designated GHR-AS-EST, transcribed from the growth hormone receptor (GHR) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. Read More

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http://dx.doi.org/10.1080/15476286.2019.1572440DOI Listing
February 2019
4 Reads
4.974 Impact Factor

Time resolved gene expression analysis during tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic impact.

RNA Biol 2019 Feb 13:1-14. Epub 2019 Feb 13.

d Institute of Pathology, Otto von Guericke University Magdeburg , Magdeburg , Germany.

Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Read More

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http://dx.doi.org/10.1080/15476286.2019.1581597DOI Listing
February 2019
1 Read

The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast.

RNA Biol 2019 Feb 13:1-15. Epub 2019 Feb 13.

a Univ Rennes , Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085 , Rennes , France.

5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU's cytotoxicity has been focused on mRNAs and non-coding transcripts such as rRNAs, tRNAs and snoRNAs. Read More

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http://dx.doi.org/10.1080/15476286.2019.1581596DOI Listing
February 2019
3 Reads

Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy.

RNA Biol 2019 03 8;16(3):295-308. Epub 2019 Feb 8.

a Department of Molecular Evolution , Centro de Astrobiología (CSIC-INTA) , Torrejón de Ardoz , Madrid , Spain.

Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1572436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380281PMC
March 2019
5 Reads

CRISPR evolution and bacteriophage persistence in the context of population bottlenecks.

RNA Biol 2019 Feb 5:1-7. Epub 2019 Feb 5.

a ESI, Biosciences , University of Exeter , Penryn , UK.

Population bottlenecks often cause strong reductions in genetic diversity and alter population structure. In the context of host-parasite interactions, bottlenecks could in theory benefit either the host or the pathogen. We predicted that bottlenecking of bacterial populations that evolve CRISPR immunity against bacteriophages (phage) would benefit the pathogen, because CRISPR spacer diversity can rapidly drive phages extinct. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1578608DOI Listing
February 2019
10 Reads

The LhrC sRNAs control expression of T cell-stimulating antigen TcsA in Listeria monocytogenes by decreasing tcsA mRNA stability.

RNA Biol 2019 03 1;16(3):270-281. Epub 2019 Feb 1.

a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark.

The bacterial pathogen Listeria monocytogenes encodes seven homologous small regulatory RNAs, named the LhrC family of sRNAs. The LhrCs are highly induced under infection-relevant conditions and are known to inhibit the expression of multiple target mRNAs encoding virulence-associated surface proteins. In all cases studied so far, the LhrCs use their CU-rich regions for base pairing to complementary AG-rich sequences of the ribosomal binding site (RBS) of specific target mRNAs. Read More

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http://dx.doi.org/10.1080/15476286.2019.1572423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380316PMC
March 2019
2 Reads

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis.

RNA Biol 2019 03 31;16(3):320-329. Epub 2019 Jan 31.

a Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona , Spain.

Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four Caenorhabditis species. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1572438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380332PMC
March 2019
7 Reads

Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages.

RNA Biol 2019 Jan 28:1-22. Epub 2019 Jan 28.

a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil.

Leishmaniasis is a worldwide public health problem caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the most important species responsible for tegumentary leishmaniases in Brazil. An understanding of the molecular mechanisms underlying the success of this parasite is urgently needed. Read More

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http://dx.doi.org/10.1080/15476286.2019.1574161DOI Listing
January 2019
1 Read

Identification and characterization of circular RNAs during the sea buckthorn fruit development.

RNA Biol 2019 03 29;16(3):354-361. Epub 2019 Jan 29.

a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China.

As a rising star of noncoding RNA, circular RNAs (circRNAs) have a covalently closed loop structure, which formed by 3'-5' ligation during splicing. A few circRNAs were identified and thought to be transcriptional noise due to cognitive defect over the past 40 years. Recently, with the development of high-throughput RNA sequencing techniques and specific algorithms for circRNA detection and quantification, plenty of potential circRNAs were identified in many species which play important roles in various biological processes. Read More

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http://dx.doi.org/10.1080/15476286.2019.1574162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380330PMC
March 2019
10 Reads

MicroRNA414c affects salt tolerance of cotton by regulating reactive oxygen species metabolism under salinity stress.

RNA Biol 2019 03 29;16(3):362-375. Epub 2019 Jan 29.

a State Key Laboratory of Crop Biology, College of Agronomy , Shandong Agricultural University , Tai'an , Shandong , People's Republic of China.

Salinity stress is a major abiotic stress affecting the productivity and fiber quality of cotton. Although reactive oxygen species (ROS) play critical roles in plant stress responses, their complex molecular regulatory mechanism under salinity stress is largely unknown in cotton, especially microRNA (miRNA)-mediated regulation of superoxide dismutase gene expression. Here, we report that a cotton iron superoxide dismutase gene GhFSD1 and the cotton miRNA ghr-miR414c work together in response to salinity stress. Read More

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http://dx.doi.org/10.1080/15476286.2019.1574163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380294PMC
March 2019
3 Reads
4.974 Impact Factor

Dual Laplacian regularized matrix completion for microRNA-disease associations prediction.

RNA Biol 2019 Jan 24:1-11. Epub 2019 Jan 24.

d Department of Oncology , Huai'an Hongze District People's Hospital , Huai'an , China.

Since lots of miRNA-disease associations have been verified, it is meaningful to discover more miRNA-disease associations for serving disease diagnosis and prevention of human complex diseases. However, it is not practical to identify potential associations using traditional biological experimental methods since the process is expensive and time consuming. Therefore, it is necessary to develop efficient computational methods to accomplish this task. Read More

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http://dx.doi.org/10.1080/15476286.2019.1570811DOI Listing
January 2019
1 Read

Mutagenesis of Snu114 domain IV identifies a developmental role in meiotic splicing.

RNA Biol 2019 02 23;16(2):185-195. Epub 2019 Jan 23.

a Wellcome Centre for Cell Biology , University of Edinburgh , Edinburgh , UK.

Snu114, a component of the U5 snRNP, plays a key role in activation of the spliceosome. It controls the action of Brr2, an RNA-stimulated ATPase/RNA helicase that disrupts U4/U6 snRNA base-pairing prior to formation of the spliceosome's catalytic centre. Snu114 has a highly conserved domain structure that resembles that of the GTPase EF-2/EF-G in the ribosome. Read More

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http://dx.doi.org/10.1080/15476286.2018.1561145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380292PMC
February 2019
3 Reads

Long non-coding RNA PSMB8-AS1 regulates influenza virus replication.

RNA Biol 2019 03 28;16(3):340-353. Epub 2019 Jan 28.

a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.

Long non-coding RNAs (lncRNAs) are a new arm of gene regulatory mechanism as discovered by sequencing techniques and follow-up functional studies. There are only few studies on lncRNAs as related to gene expression regulation and anti-viral activity during influenza virus infection. We sought to identify and characterize lncRNAs involved in influenza virus replication. Read More

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http://dx.doi.org/10.1080/15476286.2019.1572448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380333PMC
March 2019
2 Reads

Identification and characterization of stem-bulge RNAs in Drosophila melanogaster.

RNA Biol 2019 03 2;16(3):330-339. Epub 2019 Feb 2.

a Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Paraná , Brazil.

Non-coding Y RNAs and stem-bulge RNAs are homologous small RNAs in vertebrates and nematodes, respectively. They share a conserved function in the replication of chromosomal DNA in these two groups of organisms. However, functional homologues have not been found in insects, despite their common early evolutionary history. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
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http://dx.doi.org/10.1080/15476286.2019.1572439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380336PMC
March 2019
14 Reads

Bi-phased regulation of the post-transcriptional inflammatory response by Tristetraprolin levels.

RNA Biol 2019 03 28;16(3):309-319. Epub 2019 Jan 28.

a Molecular BioMedicine Program , King Faisal Specialist Hospital & Research Centre , Riyadh , Saudi Arabia.

AU-rich elements (AREs) are cis-acting instability and translation inhibition elements that are present in the 3'UTR of most inducible inflammatory mRNAs such as TNF and Cxcl2. mRNAs that contain AREs are, by default, repressed and only transiently expressed in response to stimuli. They are targeted by the inducible RNA-binding protein Tristetraprolin (TTP) which blocks their translation and facilitates their decay, thereby contributing to the quick termination of their expression. Read More

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http://dx.doi.org/10.1080/15476286.2019.1572437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380337PMC
March 2019
2 Reads

miR-151-5p modulates APH1a expression to participate in contextual fear memory formation.

RNA Biol 2019 03 29;16(3):282-294. Epub 2019 Jan 29.

e Department of Breast Surgery , Qilu hospital, Shandong University , Jinan , Shandong , People's Republic of China.

Long-term memory formation requires gene expression and new protein synthesis. MicroRNAs (miRNAs), a family of small non-coding RNAs that inhibit target gene mRNA expression, are involved in new memory formation. In this study, elevated miR-151-5p (miR-151) levels were found to be responsible for hippocampal contextual fear memory formation. Read More

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http://dx.doi.org/10.1080/15476286.2019.1572435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380341PMC
March 2019
3 Reads

Division of labour: tRNA methylation by the NSun2 tRNA methyltransferases Trm4a and Trm4b in fission yeast.

RNA Biol 2019 03 1;16(3):249-256. Epub 2019 Feb 1.

a Institut für Biologie, Molekulare Zellbiologie , Humboldt-Universität zu Berlin , Berlin , Germany.

Enzymes of the cytosine-5 RNA methyltransferase Trm4/NSun2 family methylate tRNAs at C48 and C49 in multiple tRNAs, as well as C34 and C40 in selected tRNAs. In contrast to most other organisms, fission yeast Schizosaccharomyces pombe carries two Trm4/NSun2 homologs, Trm4a (SPAC17D4.04) and Trm4b (SPAC23C4. Read More

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http://dx.doi.org/10.1080/15476286.2019.1568819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380293PMC
March 2019
2 Reads

An integrated framework for the identification of potential miRNA-disease association based on novel negative samples extraction strategy.

RNA Biol 2019 03 28;16(3):257-269. Epub 2019 Jan 28.

a School of Information and Control Engineering , China University of Mining and Technology , Xuzhou , China.

MicroRNAs (miRNAs) play an important role in prevention, diagnosis and treatment of human complex diseases. Predicting potential miRNA-disease associations could provide important prior information for medical researchers. Therefore, reliable computational models are expected to be an effective supplement for inferring associations between miRNAs and diseases. Read More

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http://dx.doi.org/10.1080/15476286.2019.1568820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380288PMC
March 2019
2 Reads

Regulation of RNA decay and cellular function by 3'-5' exoribonuclease DIS3L2.

RNA Biol 2019 02 13;16(2):160-165. Epub 2019 Jan 13.

a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China.

DIS3L2, in which mutations have been linked to Perlman syndrome, is an RNA-binding protein with 3'-5' exoribonuclease activity. It contains two CSD domains and one S1 domain, all of which are RNA-binding domains, and one RNB domain that is responsible for the exoribonuclease activity. The 3' polyuridine of RNA substrates can serve as a degradation signal for DIS3L2. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380269PMC
February 2019
2 Reads

Interactions and activities of factors involved in the late stages of human 18S rRNA maturation.

RNA Biol 2019 02 13;16(2):196-210. Epub 2019 Jan 13.

a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK.

Ribosome production is an essential cellular process involving a plethora of trans-acting factors, such as nucleases, methyltransferases, RNA helicases and kinases that catalyse key maturation steps. Precise temporal and spatial regulation of such enzymes is essential to ensure accurate and efficient subunit assembly. Here, we focus on the maturation of the 3' end of the 18S rRNA in human cells. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380343PMC
February 2019
3 Reads

Foxo3a-dependent miR-633 regulates chemotherapeutic sensitivity in gastric cancer by targeting Fas-associated death domain.

RNA Biol 2019 02 22;16(2):233-248. Epub 2019 Jan 22.

a Center for Regenerative Medicine, Institute for Translational Medicine , Qingdao University , Qingdao , Shandong Province , China.

The development of chemotherapeutic drugs resistance such as doxorubicin (DOX) and cisplatin (DDP) is the major barrier in gastric cancer therapy. Emerging evidences reveal that microRNAs (miRNAs) contribute to chemosensitivity. In this study, we investigated the role of miR-633, an oncogenic miRNA, in gastric cancer chemoresistance. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
Publisher Site
http://dx.doi.org/10.1080/15476286.2019.1565665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380283PMC
February 2019
12 Reads
4.974 Impact Factor

Circular RNA profiling provides insights into their subcellular distribution and molecular characteristics in HepG2 cells.

RNA Biol 2019 02 18;16(2):220-232. Epub 2019 Jan 18.

a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China.

Circular RNA (circRNA) is a novel RNA molecule that has become a research focus recently. Although some research indicated that the circRNAs in different subcellular compartments could execute different regulatory functions, a panoramic analysis of the subcellular distribution and the transport mechanism of circRNA is still required. In this study, we comprehensively analyzed the subcellular distribution/characteristics and the transport mechanism, through systemically investigating the circRNA profiles among the subcellular fractions of HepG2 cell (nucleus, cytoplasm, mitochondria, ribosome, cytosol and exosome). Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2019.1
Publisher Site
http://dx.doi.org/10.1080/15476286.2019.1565284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380345PMC
February 2019
11 Reads
4.974 Impact Factor