1,668 results match your criteria RNA biology[Journal]


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

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. Epub 2019 Feb 13.

a Institute of Pathology, Otto von Guericke University Magdeburg , Leipziger Str. 44, D39120 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

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

RNA Biol 2019 Feb 13. Epub 2019 Feb 13.

a Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085 , F-35000 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

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

RNA Biol 2019 Mar 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
March 2019
4 Reads

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

RNA Biol 2019 Feb 5. Epub 2019 Feb 5.

a ESI, Biosciences , University of Exeter , Cornwall Campus, Penryn TR10 9EZ , 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
2 Reads

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

RNA Biol 2019 Mar 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

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

RNA Biol 2019 Mar 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
March 2019
2 Reads

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

RNA Biol 2019 Jan 28. Epub 2019 Jan 28.

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

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

RNA Biol 2019 Mar 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
March 2019
5 Reads

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

RNA Biol 2019 Mar 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
March 2019
2 Reads
4.974 Impact Factor

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

RNA Biol 2019 Jan 24. Epub 2019 Jan 24.

d Department of Oncology , Huai'an Hongze District People's Hospital , Huai'an 223100 , 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 Feb 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
February 2019
2 Reads

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

RNA Biol 2019 Mar 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
March 2019
2 Reads

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

RNA Biol 2019 Mar 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
March 2019
5 Reads

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

RNA Biol 2019 Mar 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
March 2019
2 Reads

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

RNA Biol 2019 Mar 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
March 2019
2 Reads

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

RNA Biol 2019 Mar 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
March 2019
1 Read

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

RNA Biol 2019 Mar 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
March 2019
1 Read

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

RNA Biol 2019 Feb 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
February 2019
2 Reads

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

RNA Biol 2019 Feb 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
February 2019
2 Reads

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

RNA Biol 2019 Feb 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
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http://dx.doi.org/10.1080/15476286.2019.1565665DOI Listing
February 2019
7 Reads
4.974 Impact Factor

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

RNA Biol 2019 Feb 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
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http://dx.doi.org/10.1080/15476286.2019.1565284DOI Listing
February 2019
6 Reads
4.974 Impact Factor

Novel classes of replication-associated transcripts discovered in viruses.

RNA Biol 2019 Feb 15;16(2):166-175. Epub 2019 Jan 15.

a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary.

The role of RNA molecules in the priming of DNA replication and in providing a template for telomerase extension has been known for decades. Since then, several transcripts have been discovered, which play diverse roles in governing replication, including regulation of RNA primer formation, the recruitment of replication origin (Ori) recognition complex, and the assembly of replication fork. Recent studies on viral transcriptomes have revealed novel classes of replication-associated (ra)RNAs, which are expressed from the genomic locations in close vicinity to the Ori. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564468DOI Listing
February 2019
2 Reads

Towards understanding of PRC2 binding to RNA.

RNA Biol 2019 Feb 8;16(2):176-184. Epub 2019 Jan 8.

a Cancer Science Institute of Singapore , National University of Singapore , Singapore , Singapore.

Polycomb repressive complex 2 (PRC2) and its methylation of histone 3 at lysine 27 (H3K27me3) play a crucial role in epigenetic regulation of normal development and malignancy. Several factors regulate the recruitment of PRC2 and affects its chromatin modification function. Over the past years, emerging discoveries have portrayed the association of RNA (protein-coding and non-coding) with PRC2 as a critical factor in understanding PRC2 function. Read More

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http://dx.doi.org/10.1080/15476286.2019.1565283DOI Listing
February 2019
1 Read

Pneumococcal RNase R globally impacts protein synthesis by regulating the amount of actively translating ribosomes.

RNA Biol 2019 Feb 13;16(2):211-219. Epub 2019 Jan 13.

a Instituto de Tecnologia Química e Biológica , Universidade Nova de Lisboa , Oeiras , Portugal.

Ribosomes are macromolecular machines that carry out protein synthesis. After each round of translation, ribosome recycling is essential for reinitiating protein synthesis. Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyse the transient split of the 70S ribosome into subunits. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564616DOI Listing
February 2019
3 Reads

Circular RNA Vav3 sponges gga-miR-375 to promote epithelial-mesenchymal transition.

RNA Biol 2019 Jan 4. Epub 2019 Jan 4.

a College of Animal Science , South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , Guangzhou , 510642 , P. R. China.

Circular RNAs (circRNAs) are evolutionarily conserved and widely present, but their functions remain largely unknown. Recent development has highlighted the importance of circRNAs as the sponge of microRNA (miRNA) in cancer. We previously reported that gga-miR-375 was downregulated in the liver tumors of chickens infected with avian leukosis virus subgroup J (ALV-J) by microRNA microarray assay. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564462DOI Listing
January 2019
2 Reads

Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum.

RNA Biol 2019 Jan 3. Epub 2019 Jan 3.

b Cincinnati Cancer Center , Cincinnati , OH , United States of America.

Ultracentrifugation remains the gold standard for isolation of small extracellular vesicles (sEV), particularly for cancer applications. The objective of this study was to determine if a widely used ultracentrifugation protocol for isolation of serum sEV could be modified to reduce the number of ultracentrifugation cycles and increase efficiency, while maintaining equal or better sample purity and yield. Serum was obtained from two healthy subjects. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1
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http://dx.doi.org/10.1080/15476286.2018.1564465DOI Listing
January 2019
3 Reads

Transcriptome protection by the expanded family of hnRNPs.

RNA Biol 2019 Feb 6;16(2):155-159. Epub 2019 Jan 6.

a Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences , University of Manitoba , Winnipeg , Canada.

The family of heterogeneous ribonucleoproteins (hnRNPs) have multiple functions in RNA metabolism. In recent years, several hnRNPs have also been shown to be essential for the maintenance of transcriptome integrity, by preventing intronic cryptic splicing signals from mis-splicing of many endogeneous pre-mRNA transcripts. Here we discuss the possibility for a general role of this family of proteins and their expansion in transcriptome protection. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564617DOI Listing
February 2019
1 Read

PAX3-FOXO1 escapes miR-495 regulation during muscle differentiation.

RNA Biol 2018 Dec 28. Epub 2018 Dec 28.

a Department of Pathology , University of Virginia , Charlottesville , VA 22908.

Pax3 plays an essential role in myogenesis. Previously, we found a tumor-signature chimeric fusion RNA, PAX3-FOXO1 also present during muscle differentiation, raising the possibility of its physiological role. Here we demonstrated that the fusion is needed transiently for muscle lineage commitment. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564464DOI Listing
December 2018
1 Read

Trypanosoma brucei RRP44 is involved in an early stage of large ribosomal subunit RNA maturation.

RNA Biol 2018 Dec 28. Epub 2018 Dec 28.

a Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR , R. Prof. Algacyr Munhoz Mader 3775, 81350-010 , Curitiba - PR , Brazil .

Ribosomal RNA precursors undergo a series of structural and chemical modifications to generate matured RNA molecules that will comprise ribosomes. This maturation process involves a large set of accessory proteins as well as ribonucleases, responsible for removal of the external and internal transcribed spacers from the pre-rRNA. Early-diverging eukaryotes belonging to the Kinetoplastida class display several unique characteristics, in particular in terms of RNA synthesis and maturation. Read More

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http://dx.doi.org/10.1080/15476286.2018.1564463DOI Listing
December 2018
2 Reads

Major Contribution of Transcription Initiation to 5'-end Formation of Mitochondrial Steady-state Transcripts in Maize.

RNA Biol 2018 Dec 26. Epub 2018 Dec 26.

a State key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources , South China Agricultural University , Guangzhou , China.

In plant mitochondria, some steady-state transcripts contain primary 5' ends derived from transcription initiation, while the others have processed 5' termini generated by post-transcriptional processing. Differentiation and mapping of the primary and processed transcripts are important for unraveling the molecular mechanism(s) underlying transcription and transcript end maturation. However, previous efforts to systematically differentiate these two types of transcripts in plant mitochondria failed. Read More

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http://dx.doi.org/10.1080/15476286.2018.1561604DOI Listing
December 2018
1 Read

Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.

RNA Biol 2019 Jan 20:1-13. Epub 2019 Jan 20.

a Berlin Institute for Molecular and Systems Biology , Max Delbrück Center for Molecular Medicine , Berlin , Germany.

During Drosophila melanogaster embryogenesis, tight regulation of gene expression in time and space is required for the orderly emergence of specific cell types. While the general importance of microRNAs in regulating eukaryotic gene expression has been well-established, their role in early neurogenesis remains to be addressed. In this survey, we investigate the transcriptional dynamics of microRNAs and their target transcripts during neurogenesis of Drosophila melanogaster. Read More

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http://dx.doi.org/10.1080/15476286.2018.1558907DOI Listing
January 2019
1 Read

The human RNA helicase DHX37 is required for release of the U3 snoRNP from pre-ribosomal particles.

RNA Biol 2018 Dec 24. Epub 2018 Dec 24.

a Department of Molecular Biology , University Medical Centre Göttingen , Göttingen , Germany.

Ribosome synthesis is an essential cellular process, and perturbation of human ribosome production is linked to cancer and genetic diseases termed ribosomopathies. During their assembly, pre-ribosomal particles undergo numerous structural rearrangements, which establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome biogenesis. RNA helicases are essential mediators of such remodelling events and here, we demonstrate that the DEAH-box RNA helicase DHX37 is required for maturation of the small ribosomal subunit in human cells. Read More

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http://dx.doi.org/10.1080/15476286.2018.1556149DOI Listing
December 2018
1 Read

Identification and epigenetic analysis of divergent long non-coding RNAs in multilineage differentiation of human Neural Progenitor Cells.

RNA Biol 2018 Dec 21. Epub 2018 Dec 21.

a National Brain Research Centre , Gurgaon , India.

Long non-coding RNAs have emerged as an important regulatory layer in biological systems. Of the various types of lncRNAs, one class (designated as divergent RNAs/XH), which is in head-to-head overlap with the coding genes, has emerged as a critical biotype that regulates development and cellular differentiation. This work aimed to analyze previously published data on differential expression, epigenetic and network analysis in order to demonstrate the association of divergent lncRNAs, a specific biotype with the differentiation of human neural progenitor cells (hNPCs). Read More

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http://dx.doi.org/10.1080/15476286.2018.1553482DOI Listing
December 2018
1 Read

Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity.

RNA Biol 2018 12 26. Epub 2018 Dec 26.

a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.

The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e. Read More

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http://dx.doi.org/10.1080/15476286.2018.1559689DOI Listing
December 2018
1 Read

Molecular network of miR-1343 regulates the pluripotency of porcine pluripotent stem cells via repressing OTX2 expression.

RNA Biol 2018 Dec 20. Epub 2018 Dec 20.

a Department of Animal Biotechnology , College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China.

Porcine OTX2 was found to be highly activated in porcine iPS cells (piPSCs) that were reported by different laboratories worldwide. To reveal the regulatory function of OTX2 in porcine reprogrammed cells, we screened porcine miRNA-seq databases and found two miRNAs, miR-1343 and miR-545, that could specifically bind to 3'UTR of OTX2 and suppress endogenous OTX2 expression in piPSCs. Knockdown of OTX2 by miR-1343 and miR-545 could significantly increase the expression of SOX2 and ESRRB, but did not alter the expressions of OCT4 and KLF4, and improve the pluripotency of piPSCs. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1
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http://dx.doi.org/10.1080/15476286.2018.1559688DOI Listing
December 2018
7 Reads

The nuclear export of circular RNAs is primarily defined by their length.

RNA Biol 2018 Dec 11. Epub 2018 Dec 11.

a School of Life Sciences , Chongqing University , Chongqing , China.

Although it was long assumed that eukaryotic pre-mRNAs are almost always spliced to generate linear mRNAs, it is now clear that thousands of protein-coding genes can be non-canonically spliced using backsplicing to produce circular RNAs (circRNAs). Most mature circRNAs accumulate in the cytoplasm; however, little is known about how circRNAs are exported from the nucleus to the cytoplasm as they lack many of the common signals used for mRNA export. In this point-of-view article, we will discuss our recently identified circRNA nuclear export pathway and address important open questions in the field. Read More

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http://dx.doi.org/10.1080/15476286.2018.1557498DOI Listing
December 2018
2 Reads

Long noncoding RNA SMRG regulates Drosophila macrochaetes by antagonizing scute through E(spl)mβ.

RNA Biol 2018 Dec 11:1-12. Epub 2018 Dec 11.

a State Key Laboratory of Brain and Cognitive Science , Institute of Biophysics, Chinese Academy of Sciences , Beijing , China.

It is obvious that the majority of cellular transcripts are long noncoding RNAs (lncRNAs). Although studies suggested that lncRNAs participate in many biological processes through diverse mechanisms, however, little is known about their effects on epidermal mechanoreceptors. Here, we identified one novel Drosophila lncRNA, Scutellar Macrochaetes Regulatory Gene (SMRG), which regulates scutellar macrochaetes that act as mechanoreceptors by antagonizing the proneural gene scute (sc), through the repressor Enhancer-of-split mβ (E(spl)mβ). Read More

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http://dx.doi.org/10.1080/15476286.2018.1556148DOI Listing
December 2018
1 Read

Length and secondary structure of the 5' non-coding regions of mouse p53 mRNA transcripts - mouse as a model organism for p53 gene expression studies.

RNA Biol 2018 Dec 6. Epub 2018 Dec 6.

a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland.

Transcription initiation sites of Trp53 gene in mice were determined using the 5'RACE method. Based on sequence alignment of the 5'-terminal regions of p53 mRNA in mammals, the site for the most abundant transcript turned out to be essentially identical with that determined for human TP53 gene and slightly differed for the longest transcripts, in mice and humans. Secondary structures of the 5' -terminal regions of the shorter, most abundant and the longest mouse transcripts were determined in vitro and the shorter transcript was also mapped in transfected mouse cells. Read More

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http://dx.doi.org/10.1080/15476286.2018.1556084DOI Listing
December 2018
2 Reads

Bovine leukemia virus pre-miRNA genes' polymorphism.

RNA Biol 2018 Dec 4. Epub 2018 Dec 4.

a Federal State Budget Scientific Institution Center of Experimental Embryology and Reproductive Biotechnologies , Ul.Kostyakova, Build.12/4, Moscow 127422 , Russian Federation.

MicroRNAs (miRNAs) are small non-coding RNAs with a wide distribution in nature among the living things. They play a key role both in normal signaling pathways and in pathological ones. Bovine leukemia virus (BLV) is an oncogenic retrovirus of Deltaretrovirus genus causing persistent infection in its natural hosts - cattle, zebu and water buffalo with diverse clinical manifestations through the defeat of B-lymphocytes (B-cells). Read More

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http://dx.doi.org/10.1080/15476286.2018.1555406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333434PMC
December 2018
16 Reads

Restoring LINC00673 expression triggers cellular senescence in lung cancer.

RNA Biol 2018 Nov 30. Epub 2018 Nov 30.

a Division of RNA Biology & Cancer (B150) , German Cancer Research Center (DKFZ) , Heidelberg , Germany.

Aberrant expression of noncoding RNAs plays a critical role during tumorigenesis. To uncover novel functions of long non-coding RNA (lncRNA) in lung adenocarcinoma, we used a microarray-based screen identifying LINC00673 with elevated expression in matched tumor versus normal tissue. We report that loss of LINC00673 is sufficient to trigger cellular senescence, a tumor suppressive mechanism associated with permanent cell cycle arrest, both in lung cancer and normal cells in a p53-dependent manner. Read More

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http://dx.doi.org/10.1080/15476286.2018.1553481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333431PMC
November 2018
1 Read
4.974 Impact Factor

Different Effects of Long Noncoding RNA NDRG1-OT1 Fragments on NDRG1 Transcription in Breast Cancer Cells Under Hypoxia.

RNA Biol 2018 Nov 30. Epub 2018 Nov 30.

a Graduate Institute of Physiology, College of Medicine , National Taiwan University , Taipei , Taiwan.

Hypoxia plays a crucial role in the aggressiveness of solid tumors by driving multiple signaling pathways. Recently, long non-coding RNA (lncRNA) has been reported to promote or inhibit tumor aggressiveness by regulating gene expression. Previous studies in our laboratory found that the lncRNA NDRG1-OT1 is significantly up-regulated under hypoxia and inhibits its target gene NDRG1 at both the mRNA and protein levels. Read More

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http://dx.doi.org/10.1080/15476286.2018.1553480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333435PMC
November 2018
1 Read

Deep learning identifies genome-wide DNA binding sites of long noncoding RNAs.

RNA Biol 2018 Nov 28:1-9. Epub 2018 Nov 28.

c Computer Science and Engineering Technology , University of Houston-Downtown , Houston , TX , USA.

Long noncoding RNAs (lncRNAs) can exert their function by interacting with the DNA via triplex structure formation. Even though this has been validated with a handful of experiments, a genome-wide analysis of lncRNA-DNA binding is needed. In this paper, we develop and interpret deep learning models that predict the genome-wide binding sites deciphered by ChIRP-Seq experiments of 12 different lncRNAs. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1
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http://dx.doi.org/10.1080/15476286.2018.1551704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333433PMC
November 2018
7 Reads

Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation.

RNA Biol 2018 10;15(12):1433-1439. Epub 2018 Dec 10.

a Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute , Lucknow, Uttar Pradesh , India.

Cross-kingdom gene regulation by microRNAs (miRNAs) initiated a hot debate on the effective role of orally acquired plant miRNAs on human gene expression. It resulted in the expansion of gene regulation theories and role of plant miRNAs in cross-kingdom regulation of gene expression. This opened up the discussion that 'Whether we really get what we eat?' and 'Whether the orally acquired miRNAs really have a biologically important consequences after entering our digestive and circulatory system?' The reports of orally acquired plant miRNAs inside human alimentary canal have been a topic of discussion in the scientific community. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1
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http://dx.doi.org/10.1080/15476286.2018.1551693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333437PMC
December 2018
10 Reads

Long noncoding RNA Malat1 is not essential for T cell development and response to LCMV infection.

RNA Biol 2018 Nov 26. Epub 2018 Nov 26.

a Beijing Advanced Innovation Center for Food Nutrition and Human Health , China Agricultural University , Beijing , China.

Long noncoding RNAs (lncRNAs) are emerging as critical mediators of various biological processes in the immune system. The current data showed that the lncRNA Malat1 is highly expressed in T cell subsets, but the function of Malat1 in T cell remains unclear. In this study, we detected the T cell development and both CD8 and CD4 T cell response to LCMV infection using Malat1 mice model. Read More

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http://dx.doi.org/10.1080/15476286.2018.1551705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333432PMC
November 2018
15 Reads

Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA.

RNA Biol 2018 29;15(12):1458-1467. Epub 2018 Nov 29.

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

The recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 system expands the genome editing toolbox. This system exhibits several distinct features compared to the widely used CRISPR-Cas9 system, but has reduced gene editing efficiency. To optimize the CRISPR-Cpf1 (Cas12a) system, we report the inclusion of self-cleaving ribozymes that facilitate processing of the crRNA transcript to produce the precise guide molecule. Read More

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http://dx.doi.org/10.1080/15476286.2018.1551703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333430PMC
November 2018
22 Reads

Regulation of Mcl-1 alternative splicing by hnRNP F, H1 and K in breast cancer cells.

RNA Biol 2018 Nov 23. Epub 2018 Nov 23.

a Institute of Cellular Medicine, Faculty of Medical Sciences , Newcastle University , Newcastle upon Tyne , NE2 4HH , UK .

Myeloid cell leukemia-1 (Mcl -1) is one of the most frequently amplified genes in cancer, and its overexpression is associated with poor prognosis and drug resistance. As a member of the Bcl-2 family it is involved in the control of the mitochondrial (intrinsic) cell death pathway. Alternative splicing of the (Mcl-1) gene results in the expression of two functionally distinct proteins, the anti-apoptotic Mcl-1 (exon 2 included) and the pro-apoptotic Mcl-1 (exon 2 skipped). Read More

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http://dx.doi.org/10.1080/15476286.2018.1551692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333436PMC
November 2018
11 Reads

Correction.

Authors:

RNA Biol 2018 Nov 22. Epub 2018 Nov 22.

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http://dx.doi.org/10.1080/15476286.2018.1551481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333429PMC
November 2018
9 Reads

Transformation of nad7 into the nuclear genome rescues the slow growth3 mutant in Arabidopsis.

RNA Biol 2018 18;15(11):1385-1391. Epub 2018 Nov 18.

a Institute of Plant and Microbial Biology , Academia Sinica , Taipei , Taiwan.

Plant pentatricopeptide repeat (PPR) proteins are mostly involved in chloroplast or mitochondrial RNA metabolism. However, direct evidence that correction of the molecular defects in the organelles can restore the plant phenotypes has yet to be demonstrated in a ppr mutant. Arabidopsis slow growth3 (slo3), a ppr mutant, is impaired in the splicing of mitochondrial nad7 intron 2. Read More

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https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1
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http://dx.doi.org/10.1080/15476286.2018.1546528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284581PMC
January 2019
10 Reads

Correction.

Authors:

RNA Biol 2018 Nov 1. Epub 2018 Nov 1.

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http://dx.doi.org/10.1080/15476286.2018.1541386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351021PMC
November 2018
3 Reads