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Hypoxia activated long non-coding RNA HABON regulates the growth and proliferation of hepatocarcinoma cells by binding to and antagonizing HIF-1 alpha RNA Biol. (IF 5.35) Pub Date : 2021-01-21 Cheng-Ning Ma; Lu-Lu Wo; Di-Fei Wang; Ci-Xiang Zhou; Jing-Chi Li; Xin Zhang; Xiu-Feng Gong; Chen-Long Wang; Ming He; Qian Zhao
ABSTRACT The adaptation of tumour cells to hypoxic microenvironment is one of the most significant characteristics of many malignant tumour diseases including hepatocarcinoma. Recently, long non-coding RNAs (lncRNAs) have been reported to play important roles in the various levels of gene regulation thus functioning in growth and survival of tumour cells. Here, new hypoxia-related lncRNAs in hepatocarcinoma
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Ribosome profiling analysis of human skeletal muscle identifies reduced translation of mitochondrial proteins with age RNA Biol. (IF 5.35) Pub Date : 2021-01-21 Ravi Tharakan; Ceereena Ubaida-Mohien; Yulan Piao; Myriam Gorospe; Luigi Ferrucci
ABSTRACT With advancing age, human muscle loses strength and function, but the molecular causes of these losses are unknown. Skeletal muscle shows an age-dependent decline in the levels of different proteins, but whether such decline is associated with reduced translation has not been studied. To address this gap of knowledge, we used the technique of ribosome profiling to study translation in muscle
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Molecular correction of Duchenne muscular dystrophy by splice modulation and gene editing RNA Biol. (IF 5.35) Pub Date : 2021-01-20 Britt Hanson; Matthew J.A. Wood; Thomas C. Roberts
ABSTRACT Duchenne muscular dystrophy (DMD) is a currently incurable X-linked neuromuscular disorder, characterized by progressive muscle wasting and premature death, typically as a consequence of cardiac failure. DMD-causing mutations in the dystrophin gene are highly diverse, meaning that the development of a universally-applicable therapy to treat all patients is very challenging. The leading therapeutic
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Intron-assisted, viroid-based production of insecticidal circular double-stranded RNA in Escherichia coli RNA Biol. (IF 5.35) Pub Date : 2021-01-20 Beltrán Ortolá; Teresa Cordero; Xu Hu; José-Antonio Daròs
ABSTRACT RNA interference (RNAi) is a natural mechanism for protecting against harmful genetic elements and regulating gene expression, which can be artificially triggered by the delivery of homologous double-stranded RNA (dsRNA). This mechanism can be exploited as a highly specific and environmentally friendly pest control strategy. To this aim, systems for producing large amounts of recombinant dsRNA
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Target-capture full-length double-strand cDNA sequencing for alternative splicing analysis RNA Biol. (IF 5.35) Pub Date : 2021-01-20 Hiroki Ura; Sumihito Togi; Yo Niida
ABSTRACT Alternative splicing is a regulated process by which eukaryotic genes may produce diverse biological products. Defects in the process typically affect cellular function and can lead to disease. Next-generation sequencing (NGS) technologies have been developed to detect alternative splicing events; however, the alternative splicing events detected by standard RNA-Seq may or may not be derived
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Identification of host-factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome RNA Biol. (IF 5.35) Pub Date : 2021-01-18 Sander Jansen; Enisa Smlatic; Daniëlle Copmans; Sarah Debaveye; Frédéric Tangy; Pierre-Olivier Vidalain; Johan Neyts; Kai Dallmeier
ABSTRACT Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions
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Differential transcription profiling of the phage LUZ19 infection process in different growth media RNA Biol. (IF 5.35) Pub Date : 2021-01-15 Ana Brandão; Diana P. Pires; Lucas Coppens; Marleen Voet; Rob Lavigne; Joana Azeredo
ABSTRACT RNA sequencing of phage-infected bacterial cultures offers a snapshot of transcriptional events occurring during the infection process, providing insights into the phage transcriptional organization as well as the bacterial response. To better mimic real environmental contexts, we performed RNA-seq of Pseudomonas aeruginosa PAO1 cultures infected with phage LUZ19 in a mammalian cell culture
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HSM6AP: A high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching RNA Biol. (IF 5.35) Pub Date : 2021-01-14 Jing Li; Shida He; Fei Guo; Quan Zou
Abstract Motivation: Recent studies have shown that RNA methylation modification can affect RNA transcription, metabolism, splicing and stability. In addition, RNA methylation modification has been associated with cancer, obesity and other diseases. Based on information about human genome and machine learning, this paper discusses the effect of the fusion sequence and gene level feature extraction
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Long non-coding RNA NEAT1_1 ameliorates TDP-43 toxicity in in vivo models of TDP-43 proteinopathy RNA Biol. (IF 5.35) Pub Date : 2021-01-11 Koji Matsukawa; Michail S. Kukharsky; Sei-Kyoung Park; Sangeun Park; Naruaki Watanabe; Takeshi Iwatsubo; Tadafumi Hashimoto; Susan W. Liebman; Tatyana A. Shelkovnikova
ABSTRACT Pathological changes involving TDP-43 protein (‘TDP-43 proteinopathy’) are typical for several neurodegenerative diseases, including frontotemporal lobar degeneration (FTLD). FTLD-TDP cases are characterized by increased binding of TDP-43 to an abundant lncRNA, NEAT1, in the cortex. However it is unclear whether enhanced TDP-43-NEAT1 interaction represents a protective mechanism. We show that
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Characterization of synthetic riboswitch in cell-free protein expression systems RNA Biol. (IF 5.35) Pub Date : 2021-01-11 Yaroslav Chushak; Svetlana Harbaugh; Kathryn Zimlich; Bryan Alfred; Jorge Chávez; Nancy Kelley-Loughnane
ABSTRACT Riboswitches are RNA-based regulatory elements that utilize ligand-induced structural changes in the 5ʹ-untranslated region of mRNA to regulate the expression of associated genes. The majority of synthetic riboswitches have been selected and tested in cell-based systems. Cell-free protein expression systems (CFPS) have several advantages for the development and testing of synthetic riboswitches
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U1 snRNP telescripting: molecular mechanisms and beyond RNA Biol. (IF 5.35) Pub Date : 2021-01-08 Yi Ran; Yanhui Deng; Chengguo Yao
Abstracts U1 snRNP is one of the most abundant ribonucleoprotein (RNP) complexes in eukaryotic cells, and is estimated to be approximately 1 million copies per cell. Apart from its canonical role in mRNA splicing, this complex has emerged as a key regulator of eukaryotic mRNA length via inhibition of mRNA 3ʹ-end processing at numerous intronic polyadenylation sites (PASs), in a process that is also
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Dengue virus strain 2 capsid protein switches the annealing pathway and reduces intrinsic dynamics of the conserved 5’ untranslated region RNA Biol. (IF 5.35) Pub Date : 2021-01-07 Xin Ee Yong; Palur Venkata Raghuvamsi; Ganesh S. Anand; Thorsten Wohland; Kamal K. Sharma
ABSTRACT The capsid protein of dengue virus strain 2 (DENV2C) promotes nucleic acid structural rearrangements using chaperone activity. However, the role of DENV2C during the interaction of RNA elements in the conserved 5’ untranslated region (5’UTR) to the 3’ untranslated region (3’UTR) is still unclear. Thus, we investigated the effect of DENV2C on the annealing mechanism of two RNA hairpin elements
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Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay RNA Biol. (IF 5.35) Pub Date : 2021-01-07 Sebastian Grosse; Yen-Yun Lu; Ivo Coban; Bettina Neumann; Heike Krebber
ABSTRACT One important task of eukaryotic cells is to translate only mRNAs that were correctly processed to prevent the production of truncated proteins, found in neurodegenerative diseases and cancer. Nuclear quality control of splicing requires the SR-like proteins Gbp2 and Hrb1 in S. cerevisiae, where they promote the degradation of faulty pre-mRNAs. Here we show that Gbp2 and Hrb1 also function
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Molecular determinants and heterogeneity underlying host response to EV-A71 infection at single-cell resolution RNA Biol. (IF 5.35) Pub Date : 2021-01-07 Rei-Lin Kuo; Yi-Tung Chen; Huai-An Li; Chih-Ching Wu; Hsiao-Chu Chiang; Jhao-Yin Lin; Hsing-I Huang; Shin-Ru Shih; Bertrand Chin-Ming Tan
ABSTRACT The pathogenic human enterovirus EV-A71 has raised serious public health concerns. A hallmark of EV-A71 infection is the distortion of host transcriptomes in favor of viral replication. While high-throughput approaches have been exploited to dissect these gene dysregulations, they do not fully capture molecular perturbations at single-cell level and in a physiologically relevant context. In
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Exploring the expression and functionality of the rsm sRNAs in Pseudomonas syringae pv. tomato DC3000 RNA Biol. (IF 5.35) Pub Date : 2021-01-07 María-Dolores Ferreiro; Lara Vanessa Behrmann; Ana Corral; Joaquina Nogales; María-Trinidad Gallegos
ABSTRACT The Gac-rsm pathway is a global regulatory network that governs mayor lifestyle and metabolic changes in gamma-proteobacteria. In a previous study, we uncovered the role of CsrA proteins promoting growth and repressing motility, alginate production and virulence in the model phytopathogen Pseudomonas syringae pv. tomato (Pto) DC3000. Here, we focus on the expression and regulation of the rsm
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A chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene RNA Biol. (IF 5.35) Pub Date : 2021-01-06 Elżbieta Wanowska; Magdalena Kubiak; Izabela Makałowska; Michał Wojciech Szcześniak
Abstract A large portion of the human genome is transcribed into long noncoding RNAs that can range from 200 nucleotides to several kilobases in length. The number of identified lncRNAs is still growing, but only a handful of them have been functionally characterized. However, it is known that the functions of lncRNAs are closely related to their subcellular localization. Cytoplasmic lncRNAs can regulate
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Interplay between host non-coding RNAs and influenza viruses RNA Biol. (IF 5.35) Pub Date : 2021-01-06 Gayan Bamunuarachchi; Samuel Pushparaj; Lin Liu
Abstract Influenza virus infection through seasonal epidemics and occasional pandemics has been a major public health concern for decades. Incomplete protection from vaccination and increased antiviral resistance due to frequent mutations of influenza viruses have led to a continuous need for new therapeutic options. The functional significance of host protein and influenza virus interactions has been
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Identification and initial characterization of POLIII-driven transcripts by msRNA-sequencing. RNA Biol. (IF 5.35) Pub Date : 2021-01-06 Peter Zorn; Danny Misiak; Michael Gekle; Marcel Köhn
Abstract Non-coding RNAs (ncRNAs) are powerful regulators of gene expression but medium-sized (50-300 nts in length) ncRNAs (msRNAs) are barely picked-up precisely by RNA-sequencing. Here we describe msRNA-sequencing (msRNAseq), a modified protocol that associated with a computational analyses pipeline identified about ~1800 msRNA loci, including over 300 putatively novel msRNAs, in human and murine
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Off-target effects of RNAi correlate with the mismatch rate between dsRNA and non-target mRNA RNA Biol. (IF 5.35) Pub Date : 2021-01-04 Jiasheng Chen; Yingchuan Peng; Hainan Zhang; Kangxu Wang; Chunqing Zhao; Guanheng Zhu; Subba Reddy Palli; Zhaojun Han
ABSTRACT RNAi is a potent technique for the knockdown of target genes. However, its potential off-target effects limit the widespread applications in both reverse genetic analysis and genetic manipulation. Previous efforts have uncovered rules underlying specificity of siRNA-based silencing, which has broad applications in humans, but the basis for specificity of dsRNAs, which are better suited for
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On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain RNA Biol. (IF 5.35) Pub Date : 2021-01-04 Wei-Siang Liau; Sarbani Samaddar; Sourav Banerjee; Timothy W. Bredy
ABSTRACT The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic
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Adenosine-to-inosine RNA editing in neurological development and disease RNA Biol. (IF 5.35) Pub Date : 2021-01-04 Yuxi Yang; Shunpei Okada; Masayuki Sakurai
Abstract Adenosine-to-inosine (A-to-I) editing is one of the most prevalent post-transcriptional RNA modifications in metazoan. This reaction is catalyzed by enzymes called adenosine deaminases acting on RNA (ADARs). RNA editing is involved in the regulation of protein function and gene expression. The numerous A-to-I editing sites have been identified in both coding and non-coding RNA transcripts
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Bulges control pri-miRNA processing in a position and strand-dependent manner RNA Biol. (IF 5.35) Pub Date : 2020-12-31 Shaohua Li; Thi Nhu-Y Le; Trung Duc Nguyen; Tam Anh Trinh; Tuan Anh Nguyen
ABSTRACT MicroRNAs (miRNAs) play critical roles in gene expression and numerous human diseases. The success of miRNA biogenesis is largely determined by the primary miRNA (pri-miRNA) processing by the DROSHA-DGCR8 complex, called Microprocessor. Here, we analysed the high-throughput pri-miRNA processing assays and secondary structures of pri-miRNAs to investigate the roles of bulges in the pri-miRNA
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5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA RNA Biol. (IF 5.35) Pub Date : 2020-12-31 Unn Kugelberg; Daniel Nätt; Signe Skog; Claudia Kutter; Anita Öst
ABSTRACT Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture
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Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS RNA Biol. (IF 5.35) Pub Date : 2020-12-23 Pavlina Gregorova; Nina H. Sipari; L. Peter Sarin
ABSTRACT Post-transcriptional RNA modifications play an important role in cellular metabolism with homoeostatic disturbances manifesting as a wide repertoire of phenotypes, reduced stress tolerance and translational perturbation, developmental defects, and diseases, such as type II diabetes, leukaemia, and carcinomas. Hence, there has been an intense effort to develop various methods for investigating
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An epigenetic “extreme makeover”: the methylation of flaviviral RNA (and beyond) RNA Biol. (IF 5.35) Pub Date : 2020-12-23 Alessia Ruggieri; Mark Helm; Laurent Chatel-Chaix
ABSTRACT Beyond their high clinical relevance worldwide, flaviviruses (comprising dengue and Zika viruses) are of particular interest to understand the spatiotemporal control of RNA metabolism. Indeed, their positive single-stranded viral RNA genome (vRNA) undergoes in the cytoplasm replication, translation and encapsidation, three steps of the flavivirus life cycle that are coordinated through a fine-tuned
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Discovery and Functional Understanding of MiRNAs in Mollusks: A Genome-wide Profiling Approach RNA Biol. (IF 5.35) Pub Date : 2020-12-23 Songqian Huang; Kazutoshi Yoshitake; Md Asaduzzaman; Shigeharu Kinoshita; Shugo Watabe; Shuichi Asakawa
Abstract Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction
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The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation RNA Biol. (IF 5.35) Pub Date : 2020-12-21 Jin-Der Wen; Syue-Ting Kuo; Hsin-Hung David Chou
ABSTRACT Shine-Dalgarno (SD) sequences, the core element of prokaryotic ribosome-binding sites, facilitate mRNA translation by base-pair interaction with the anti-SD (aSD) sequence of 16S rRNA. In contrast to this paradigm, an inspection of thousands of prokaryotic species unravels tremendous SD sequence diversity both within and between genomes, whereas aSD sequences remain largely static. The pattern
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3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists RNA Biol. (IF 5.35) Pub Date : 2020-12-19 Wenbin Guo; Nikoleta A Tzioutziou; Gordon Stephen; Iain Milne; Cristiane PG Calixto; Robbie Waugh; John W. S. Brown; Runxuan Zhang
ABSTRACT RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the ‘3D RNA-seq’ App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism
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Polynucleotide phosphorylase and RNA helicase CshA cooperate in Bacillus subtilis mRNA decay RNA Biol. (IF 5.35) Pub Date : 2020-12-16 Shakti Ingle; Shivani Chhabra; Denise Laspina; Elizabeth Salvo; Bo Liu; David H. Bechhofer
ABSTRACT Polynucleotide phosphorylase (PNPase), a 3ʹ exoribonuclease that degrades RNA in the 3ʹ-to-5ʹ direction, is the major mRNA decay activity in Bacillus subtilis. PNPase is known to be inhibited in vitro by strong RNA secondary structure, and rapid mRNA turnover in vivo is thought to require an RNA helicase activity working in conjunction with PNPase. The most abundant RNA helicase in B. subtilis
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Determination of the vRNA and cRNA promoter activity by M segment-specific non-coding nucleotides of influenza A virus RNA Biol. (IF 5.35) Pub Date : 2020-12-15 Heegwon Shin; Yejin Jang; Sangmi Jun; Younghoon Lee; Meehyein Kim
Abstract Eight-segmented, negative-sense, single-stranded genomic RNAs of influenza A virus are terminated with 5′ and 3′ untranslated regions (UTRs). All segments have highly conserved extremities of 13 and 12 nucleotides at the 5′ and 3′ UTRs, respectively, constructing the viral RNA (vRNA) promoter. Adjacent to the duplex stem of 3 base pairs (bps) between the two conserved strands, additional 1-4
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Hormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito Aedes aegypti RNA Biol. (IF 5.35) Pub Date : 2020-12-15 Xiufeng Zhang; Alexander S. Raikhel
Abstract The yellow fever mosquito Aedes aegypti is an obligatory blood feeder and a major arboviral disease vector, evoking severe public health concerns worldwide. In adult female mosquitoes, the gut is critical for blood digestion and pathogen entry. We aimed for a systematic exploration of microRNA expression dynamics in the gut during the gonadotrophic cycle. Small RNA libraries were constructed
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The uniqueness of AlaRS and its human disease connections RNA Biol. (IF 5.35) Pub Date : 2020-12-15 Han Zhang; Xiang-lei Yang; Litao Sun
Abstract Among the 20 cytoplasmic aminoacyl-tRNA synthetases (aaRSs), alanyl-tRNA synthetase (AlaRS) has unique features. AlaRS is the only aaRS that exclusively recognizes a single G3:U70 wobble base pair in the acceptor stem of tRNA, which serves as the identity element for both the synthetic and the proofreading activities of the synthetase. The recognition is relaxed during evolution and eukaryotic
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Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson’s disease RNA Biol. (IF 5.35) Pub Date : 2020-12-11 Marc-Antoine Turcotte; Jean-Michel Garant; Hélène Cossette-Roberge; Jean-Pierre Perreault
ABSTRACT RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous
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Regulation of mRNA stability by RBPs and noncoding RNAs contributing to the pathogenicity of Th17 cells RNA Biol. (IF 5.35) Pub Date : 2020-12-10 Yiwei Zhang; Zhiyuan Wei; Hui Dong; Jian Zhou; Jizhao Yuan; Bing Ni; Yuzhang Wu; Chao Han; Yi Tian
Abstract Th17 cells remain one of the most important subsets of T cells in numerous autoimmune and chronic inflammatory diseases. Posttranscriptional regulation (PTR), especially mRNA stability, has recently emerged as an important mechanism that controls the fate of Th17 cells. This review summarizes the current knowledge on RNA-binding proteins (RBPs), microRNAs (miRNAs) and long non-coding RNAs
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DISSECTING PROTEIN DOMAIN VARIABILITY IN THE CORE RNA INTERFERENCE MACHINERY OF FIVE INSECT ORDERS RNA Biol. (IF 5.35) Pub Date : 2020-12-10 Fabricio Barbosa Monteiro Arraes; Diogo Martins de-Sa; Daniel D. Noriega Vasquez; Bruno Paes Melo; Muhammad Faheem; Leonardo Lima Pepino de Macedo; Carolina Vianna Morgante; João Alexandre R. G Barbosa; Roberto Coiti Togawa; Valdeir Junio Vaz Moreira; Etienne G. J. Danchin; Maria Fatima Grossi-de-Sa
ABSTRACT RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate
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Differential roles of YTHDF1 and YTHDF3 in embryonic stem cell-derived cardiomyocyte differentiation RNA Biol. (IF 5.35) Pub Date : 2020-12-09 Shen Wang; Jun Zhang; Xiang Wu; Xianrong Lin; Xiao-Min Liu; Jun Zhou
ABSTRACT N6-methyladenosine (m6A) has emerged as a crucial epitranscriptomic mark which regulates a broad spectrum of physiological processes including stem cell differentiation. m6A-binding YTHDF proteins have recently been proposed to mediate differentiation of leukemia cell in a redundant manner. However, whether these proteins play semblable roles in pluripotent stem cell remain largely unknown
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The isolated La-module of LARP1 mediates 3’ poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1 RNA Biol. (IF 5.35) Pub Date : 2020-12-08 Sandy Mattijssen; Guennadi Kozlov; Sergei Gaidamakov; Amitabh Ranjan; Bruno D. Fonseca; Kalle Gehring; Richard J. Maraia
ABSTRACT The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activity in a specific aspect of RNA metabolism. The La-modules vary among the
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Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation RNA Biol. (IF 5.35) Pub Date : 2020-12-06 Huiming Zhang; Zhaolian Lu; Yu Zhan; Judith Rodriguez; Chen Lu; Yong Xue; Zhenguo Lin
Abstract Regulation of gene expression starts from the transcription initiation. Regulated transcription initiation is critical for generating correct transcripts with proper abundance. The impact of epigenetic control, such as histone modifications and chromatin remodeling, on gene regulation has been extensively investigated, but their specific role in regulating transcription initiation is far from
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MHC Class III RNA Binding Proteins and Immunity RNA Biol. (IF 5.35) Pub Date : 2020-12-06 Geraldine Schott; Mariano A. Garcia-Blanco
Abstract Here we review data suggestive of a role for RBPs in vertebrate immunity. We focus on the products of genes found in the class III region of the Major Histocompatibility Complex. Six of these genes, DDX39B (aka BAT1), DXO, LSM2, NELFE, PRRC2A (aka BAT2), and SKIV2L, encode RNA binding proteins with clear roles in post-transcriptional gene regulation and RNA surveillance. These genes are likely
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Towards the mechanism(s) of YB-3 synthesis regulation by YB-1 RNA Biol. (IF 5.35) Pub Date : 2020-12-06 D.N. Lyabin; E.A. Smolin; K.S. Budkina; I.A. Eliseeva; L.P. Ovchinnikov
ABSTRACT Y-box binding proteins are members of the family of proteins containing the evolutionarily conserved cold shock domain. Their cellular functions are quite diverse, including transcription and translation regulation, participation in pre-mRNA splicing, mRNA stabilization and packaging into mRNPs, involvement in DNA repair, and some others. To date, we know little about the plausible functional
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Recruitment of Xrn1 to stress-induced genes allows efficient transcription by controlling RNA polymerase II backtracking RNA Biol. (IF 5.35) Pub Date : 2020-12-01 José García-Martínez; María E. Pérez-Martínez; José E. Pérez-Ortín; Paula Alepuz
ABSTRACT A new paradigm has emerged proposing that the crosstalk between nuclear transcription and cytoplasmic mRNA stability keeps robust mRNA levels in cells under steady-state conditions. A key piece in this crosstalk is the highly conserved 5′–3′ RNA exonuclease Xrn1, which degrades most cytoplasmic mRNAs but also associates with nuclear chromatin to activate transcription by not well-understood
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Identification of nucleotide sequences and some proteins involved in polyadenylation of RNA transcribed by Pol III from SINEs RNA Biol. (IF 5.35) Pub Date : 2020-12-01 Ilia G. Ustyantsev; Olga R. Borodulina; Dmitri A. Kramerov
ABSTRACT We have previously reported that not only transcripts of RNA polymerase II (pol II), but also one type of RNA transcribed by RNA polymerase III (pol III), undergo AAUAAA-dependent polyadenylation. Such an unusual feature is inherent in Short Interspersed Elements (SINEs) from genomes of certain mammals. For polyadenylation of its transcript, SINE should contain, besides an AATAAA hexamer and
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Antisense RNA asPcrL regulates expression of photosynthesis genes in Rhodobacter sphaeroides by promoting RNase III-dependent turn-over of puf mRNA RNA Biol. (IF 5.35) Pub Date : 2020-12-01 Carina M. Reuscher; Gabriele Klug
Abstract Anoxygenic photosynthesis is an important pathway for Rhodobacter sphaeroides to produce ATP under oxygen-limiting conditions. The expression of its photosynthesis genes is tightly regulated at transcriptional and post-transcriptional levels in response to light and oxygen signals, to avoid photooxidative stress by the simultaneous presence of pigments, light and oxygen. The puf operon encodes
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Silencing Long Non-Coding RNA NEAT1 Attenuates Rheumatoid Arthritis via the MAPK/ERK Signaling Pathway by Downregulating microRNA-129 and microRNA-204 RNA Biol. (IF 5.35) Pub Date : 2020-12-01 Jie Chen; Xiao Luo; Mao Liu; Lihui Peng; Zixia Zhao; Chengsong He; Yue He
ABSTRACT The participation of long noncoding RNAs (lncRNAs) and microRNAs (miRs) in the progression of rheumatoid arthritis (RA) is a key area of investigation. The current study aimed to investigate the action of lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in fibroblast-like synoviocyte (FLS) proliferation and synovitis in RA. A rat model of RA was established. LncRNA NEAT1 expression
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Natural variation of the cardiac transcriptome in humans RNA Biol. (IF 5.35) Pub Date : 2020-12-01 Tatiana Domitrovic; Mariana H. Moreira; Rodolfo L. Carneiro; Marcelo Ribeiro-Alves; Fernando L. Palhano
ABSTRACT We investigated the gene-expression variation among humans by analyzing previously published mRNA-seq and ribosome footprint profiling of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features compared to the rest of the genome, such as lower mRNA levels and shorter
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Long noncoding RNA HOTAIR regulates myeloid differentiation through the upregulation of p21 via miR-17-5p in acute myeloid leukemia RNA Biol. (IF 5.35) Pub Date : 2020-11-26 Linhui Hu; Jun Liu; Ye Meng; Huimin Zheng; Chen Ding; Huiping Wang; Alice Charwudzi; Manman Li; Jingrong Li; Zhimin Zhai; Shudao Xiong
Abstract Long non-coding RNA HOTAIR has been reported to play a key role in regulating various biological processes in various cancers. However, the roles and mechanisms of HOTAIR in acute myeloid leukemia (AML) are still unclear and need to be investigated. In this study, we induced differentiation of four AML cell lines by all-trans retinoic acid (ATRA) and found HOTAIR was significantly upregulated
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New progresses of circular RNA biology: from nuclear export to degradation RNA Biol. (IF 5.35) Pub Date : 2020-11-26 Min Zhou; Mei-Sheng Xiao; Zhengguo Li; Chuan Huang
Abstract Circular RNA, typically generated from backsplicing reaction, is a class of single stranded and covalently linked RNA. Although most circular RNAs are lowly expressed, some of them are able to accumulate to high levels and even exceed their cognate mRNAs due to their longer half-lives. Once produced in the nucleus, the majority of circular RNAs are exported to the cytoplasm for their proper
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Selective Packaged Circular RNAs in Milk Extracellular Vesicles during Staphylococcus aureus Infection May Have Potential against Bacterial Infection RNA Biol. (IF 5.35) Pub Date : 2020-11-26 Shaoyang Ma; Mingze Niu; Zehua Hao; Miaomiao Liu; Chao Tong; Xin Zhao
Abstract Extracellular vesicles (EVs) provide a novel intercellular communication mechanism to transfer biologically important molecules to target cells. Although several pieces of evidence have shown that EVs have potential to respond to bacterial infections, our knowledge about the role of circular RNA (circRNA), an important cargo of EV, behind this process remains poor. In particular, the mechanism
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A new fungus-mediated RNAi method established and used to study the fatty acid and retinol binding protein function of the plant-parasitic nematode Aphelenchoides besseyi RNA Biol. (IF 5.35) Pub Date : 2020-11-20 Shanwen Ding; Dongwei Wang; Chunling Xu; Sihua Yang; Xi Cheng; Xiaofang Peng; Chun Chen; Hui Xie
Abstract RNA interference (RNAi) is a powerful tool for gene functional analysis of plant-parasitic nematodes (PPNs). RNAi involving soaking in a dsRNA solution and in planta methods is commonly applied in the study of gene function in PPNs. However, certain problems restrict the application of these methods. Therefore, more convenient and effective RNAi methods need to be established for different
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Substrate recognition mechanism of tRNA-targeting ribonuclease, colicin D, and an insight into tRNA cleavage-mediated translation impairment RNA Biol. (IF 5.35) Pub Date : 2020-11-19 Tetsuhiro Ogawa; Kazutoshi Takahashi; Wataru Ishida; Toshihiro Aono; Makoto Hidaka; Tohru Terada; Haruhiko Masaki
ABSTRACT Colicin D is a plasmid-encoded bacteriocin that specifically cleaves tRNAArg of sensitive Escherichia coli cells. E. coli has four isoaccepting tRNAArgs; the cleavage occurs at the 3′ end of anticodon-loop, leading to translation impairment in the sensitive cells. tRNAs form a common L-shaped structure and have many conserved nucleotides that limit tRNA identity elements. How colicin D selects
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Human umbilical cord mesenchymal stem cells-derived exosomal microRNA-451a represses epithelial-mesenchymal transition of hepatocellular carcinoma cells by inhibiting ADAM10 RNA Biol. (IF 5.35) Pub Date : 2020-11-18 Yunxiuxiu Xu; Linhui Cao; Guangcheng Chen; Liang Chen; Yanshan Li; Yu Lai; Hanqin Weng; Tao Chen; Linyun Wang; Yibiao Ye
Abstract Objective: Exosomes derived from human umbilical cord mesenchymal stem cells (hucMSCs) expressing microRNAs (miRNAs) have been highlighted in human cancers. However, the detailed molecular mechanism of hucMSCs-derived exosomal miR-451a on hepatocellular carcinoma (HCC) remains further investigation. Our study aims to explore the impact of exosomal miR-451a on the progression of HCC. Methods:
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Targeting IRES-dependent Translation as a Novel Approach for Treating Duchenne Muscular Dystrophy RNA Biol. (IF 5.35) Pub Date : 2020-11-08 Christine Péladeau; Bernard J. Jasmin
Abstract Internal-ribosomal entry sites (IRES) are translational elements that allow the initiation machinery to start protein synthesis via internal initiation. IRESs promote tissue-specific translation in stress conditions when conventional cap-dependent translation is inhibited. Since many IRES-containing mRNAs are relevant to diseases, this cellular mechanism is emerging as an attractive therapeutic
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Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator gene dnaA by the attenuator sRNA rnTrpL in Escherichia coli RNA Biol. (IF 5.35) Pub Date : 2020-11-08 Siqi Li; Daniel Edelmann; Bork A. Berghoff; Jens Georg; Elena Evguenieva-Hackenberg
ABSTRACT DnaA is the initiator protein of chromosome replication, but the regulation of its homeostasis in enterobacteria is not well understood. The DnaA level remains stable at different growth rates, suggesting a link between metabolism and dnaA expression. In a bioinformatic prediction, which we made to unravel targets of the sRNA rnTrpL in Enterobacteriaceae, the dnaA mRNA was the most conserved
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Gastrodin promotes CNS myelination via a lncRNA Gm7237/miR-142a/MRF pathway RNA Biol. (IF 5.35) Pub Date : 2020-11-05 Yue Shu; Tianyuan Luo; Mingda Wang; Yu Zhang; Lin Zhang; Zhi Xiao; Qianxing Wang; Qiang Zhang; Jia Zou; Changyin Yu; Shangfu Xu; Tian Yu; Liang Zhou; Shouyang Yu
ABSTRACT Treatment of central nervous system (CNS) demyelination is greatly hindered by lack of the knowledge regarding to underlying molecular mechanisms as well as therapeutic agents. Here, we report a novel small molecule agent, gastrodin (GAS), which can significantly promote CNS myelination in in vivo mice models. By using high-throughput sequencing analysis, we discover a key long non-coding
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The role of lncRNAs in innate immunity and inflammation RNA Biol. (IF 5.35) Pub Date : 2020-11-02 Katharina Walther; Leon N Schulte
Abstract The innate immune system relies on a germ-line encoded repertoire of pattern recognition receptors (PRRs), activated by deeply conserved pathogen signatures, such as bacterial cell wall components or foreign nucleic acids. To enable effective defence against invading pathogens and prevent from deleterious inflammation, PRR-driven immune responses are tightly controlled by a dense network of
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Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration RNA Biol. (IF 5.35) Pub Date : 2020-11-02 Victoria Begley; Antonio Jordán-Pla; Xenia Peñate; Ana I. Garrido-Godino; Drice Challal; Abel Cuevas-Bermúdez; Adrià Mitjavila; Mara Barucco; Gabriel Gutiérrez; Abhyudai Singh; Paula Alepuz; Francisco Navarro; Domenico Libri; José E. Pérez-Ortín; Sebastián Chávez
Abstract mRNA homeostasis is favored by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed
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Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins RNA Biol. (IF 5.35) Pub Date : 2020-11-01 Ritwika Basu; Catherine D. Eichhorn; Ryan Cheng; Robert D. Peterson; Juli Feigon
ABSTRACT La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3′ ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate Tetrahymena the LARP7 protein p65 is a component of telomerase, an essential ribonucleoprotein
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Identification and characterization of key long non-coding RNAs in the mouse cochlea RNA Biol. (IF 5.35) Pub Date : 2020-11-01 Tal Koffler-Brill; Shahar Taiber; Alejandro Anaya; Mor Bordeynik-Cohen; Einat Rosen; Likhitha Kolla; Naama Messika-Gold; Ran Elkon; Matthew W. Kelley; Igor Ulitsky; Karen B. Avraham
ABSTRACT The auditory system is a complex sensory network with an orchestrated multilayer regulatory programme governing its development and maintenance. Accumulating evidence has implicated long non-coding RNAs (lncRNAs) as important regulators in numerous systems, as well as in pathological pathways. However, their function in the auditory system has yet to be explored. Using a set of specific criteria
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LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients RNA Biol. (IF 5.35) Pub Date : 2020-10-28 Troyee Das; Aritra Deb; Sibun Parida; Sudip Mondal; Sunirmal Khatua; Zhumur Ghosh
ABSTRACT The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding
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Structural dynamics govern substrate recruitment and catalytic turnover in H/ACA RNP pseudouridylation RNA Biol. (IF 5.35) Pub Date : 2020-10-28