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The coding and noncoding transcriptome of Neurospora crassa

BMC GENOMICS 2017年第1期18卷 1-11页

作者： Cemel, Ibrahim Avi Ha, Nati Schermann, Geza Yonekawa, Shusuke Brunner, Michael Heidelberg Univ Biochem Ctr D-69120 Heidelberg Germany Cellzome GmbH D-69117 Heidelberg Germany Yoshida & Co Ltd Tokyo 1518580 Japan

Background: Long non protein coding rnas (lncrnas) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these rna species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncrnas is incomplete. Results: We have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, rna-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding rnas (lincrnas) and 1056 natural antisense transcripts, indicating that 20% of the rna Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncrnas accumulate at lower levels than protein-coding mrnas and they are considerably shorter. Our analysis showed that the vast majority of lincrnas and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincrna genes. We show furthermore most lincrna sequences evolve rapidly, even between phylogenetically close species. Conclusions: Our transcriptome analyses revealed distinct features of Neurospora lincrnas and antisense transcripts in comparison to mrnas and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncrnas.

关键词： Neurospora Transcriptome noncoding rna Antisense Splicing

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Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

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MOLECULAR CELL 2017年第2期65卷 220-230页

作者： Nelson, James W. Atilho, Ruben M. Sherlock, Madeline E. Stockbridge, Randy B. Breaker, Ronald R. Yale Univ Dept Mol Cellular & Dev Biol New Haven CT 06520 USA Yale Univ Dept Mol Biophys & Biochem New Haven CT 06520 USA Univ Michigan Dept Biophys Ann Arbor MI 48109 USA Univ Michigan Dept Mol Cellular & Dev Biol Ann Arbor MI 48109 USA Yale Univ Howard Hughes Med Inst New Haven CT 06520 USA

The guanidyl moiety is a component of fundamental metabolites, including the amino acid arginine, the energy carrier creatine, and the nucleobase guanine. Curiously, reports regarding the importance of free guanidine in biology are sparse, and no biological receptors that specifically recognize this compound have been previously identified. We report that many members of the ykkC motif rna, the longest unresolved riboswitch candidate, naturally sense and respond to guanidine. This rna is found throughout much of the bacterial domain of life, where it commonly controls the expression of proteins annotated as urea carboxylases and multidrug efflux pumps. Our analyses reveal that these proteins likely function as guanidine carboxylases and guanidine transporters, respectively. Furthermore, we demonstrate that bacteria are capable of endogenously producing guanidine. These and related findings demonstrate that free guanidine is a biologically relevant compound, and several gene families that can alleviate guanidine toxicity exist.

关键词： EmrE SugE aptamer multidrug efflux noncoding rna orphan riboswitch urea carboxylase ykkC

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Long noncoding rnas: Lessons from genomic imprinting

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BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016年第1期1859卷 102-111页

作者： Kanduri, Chandrasekhar Univ Gothenburg Sahlgrenska Acad Inst Biomed Dept Med Genet S-40530 Gothenburg Sweden

Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding rnas (lncrnas). In this article, I overview the functional role of intergenic lncrnas (H19, IPW, and MEG3), antisense lncrnas (Kcnq1ot1, Airn, Nespas, Ube3a-ATS), and enhancer lncrnas (IG-DMR ernas) to understand the diverse mechanisms being employed by them in cis and/or trans to regulate the parent-of-origin specific expression of target genes. Recent evidence suggests that some of the Incrnas regulate imprinting by promoting intra-chromosomal higher-order chromatin compartmentalization, affecting replication timing and subnuclear positioning. Whereas others act via transcriptional occlusion or transcriptional collision-based mechanisms. By establishing genomic imprinting of target genes, the lncrnas play a critical role in important biological functions, such as placental and embryonic growth, pluripotency maintenance, cell differentiation, and neural-related functions such as synaptic development and plasticity. An emerging consensus from the recent evidence is that the imprinted lncrnas fine-tune gene expression of the protein-coding genes to maintain their dosage in cell. Hence, lncrnas from imprinted clusters offer insights into their mode of action, and these mechanisms have been the basis for uncovering the mode of action of lncrnas in several other biological contexts. This article is part of a Special Issue entitled: Clues to long noncoding rna taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. (C) 2015 Elsevier B.V. All rights reserved.

关键词： Long noncoding rna Genomic imprinting Chromatin Epigenetics noncoding rna lncrna

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Genome-wide identification of potato long intergenic noncoding rnas responsive to Pectobacterium carotovorum subspecies brasiliense infection

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BMC GENOMICS 2016年第1期17卷 1-14页

作者： Kwenda, Stanford Birch, Paul R. J. Moleleki, Lucy N. Univ Pretoria Dept Microbiol & Plant Pathol FABI GRI ZA-0028 Pretoria South Africa Univ Dundee Div Plant Sci Coll Life Sci James Hutton Inst Dundee DD2 5DA Scotland

Background: Long noncoding rnas (lncrnas) represent a class of rna molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncrnas in mammals, the functional roles of lncrnas in plants are still poorly understood. Specifically, the roles of long intergenic nocoding rnas (lincrnas) in plant defence responses are yet to be fully explored. Results: In this study, we used strand-specific rna sequencing to identify 1113 lincrnas in potato (Solanum tuberosum) from stem tissues. The lincrnas are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincrnas possess single exons. A time-course rna-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincrnas are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincrnas are highly associated with 12 potato defence-related genes. Conclusions: Together, these results suggest that lincrnas have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincrnas and a set of novel lincrnas implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.

关键词： noncoding rna Potato Pectobacterium lincrna Plant defence Soft rot bacteria Solanum tuberosum Entereobacteria

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Long noncoding rnas: Central to nervous system development

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INTErnaTIONAL JOUrnaL OF DEVELOPMENTAL NEUROSCIENCE 2016年第1期55卷 109-116页

作者： Hart, Ronald P. Goff, Loyal A. Rutgers State Univ Dept Cell Biol & Neurosci Piscataway NJ 08854 USA Rutgers State Univ Human Genet Inst New Jersey Piscataway NJ 08854 USA Johns Hopkins Univ Sch Med McKusick Nathans Inst Genet Med Baltimore MD 21025 USA Johns Hopkins Univ Sch Med Dept Neurosci Baltimore MD 21025 USA

The development of the central nervous system (CNS) is a complex orchestration of stem cells, transcription factors, growth/differentiation factors, and epigenetic control. noncoding rnas have been identified, classified, and studied for their functional roles in many systems including the CNS. In particular, the class of long noncoding rnas (Incrnas) has generated both enthusiasm and skepticism due to the unexpected discovery, the diversity of mechanisms, and the lower level of expression than found in protein-coding rnas. Here we describe evidence supporting the role of Incrnas in driving CNS-specific differentiation. It is clear that Incrnas exhibit a functional diversity that makes their study and compartmentalization more challenging than other classes of noncoding rnas. We predict, however, that Incrnas will be essential for the characterization of discrete neuronal cell types in the age of single-cell transcriptomics and that these regulatory rnas contribute to the multitude of functional mechanisms during CNS differentiation that will rival the diversities of protein-based mechanisms. (C) 2016 ISDN. Published by Elsevier Ltd. All rights reserved.

关键词： noncoding rna Transcription Differentiation Neurogenesis Transcriptome Micropeptides

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A second rna-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2018年第27期115卷 E6319-E6328页

作者： Harris, Kimberly A. Zhou, Zhiyuan Peters, Michelle L. Wilkins, Sarah G. Breaker, Ronald R. Yale Univ Howard Hughes Med Inst New Haven CT 06520 USA Yale Univ Dept Mol Cellular & Dev Biol New Haven CT 06520 USA Yale Univ Dept Mol Biophys & Biochem New Haven CT 06520 USA

OLE (ornate, large, extremophilic) rnas comprise a class of structured noncoding rnas (ncrnas) found in many extremophilic bacteria species. OLE rnas constitute one of the longest and most widespread bacterial ncrna classes whose major biochemical function remains unknown. In the Gram-positive alkaliphile Bacillus halodurans, OLE rna is abundant, and localizes to the cell membrane by association with the transmembrane OLE-associated protein called OapA (formerly OAP). These characteristics, along with the well-conserved sequence and structural features of OLE rnas, suggest that the OLE ribonucleoprotein (RNP) complex performs important biological functions. B. halodurans strains lacking OLE rna (Delta ole) or OapA (Delta oapA) are less tolerant of cold (20 degrees C) and shortchain alcohols (e.g., ethanol). Here, we describe the effects of a mutant OapA (called PM1) that more strongly inhibits growth under cold or ethanol stress compared with strains lacking the oapA gene, even when wild-type OapA is present. This dominant-negative effect of PM1 is reversed by mutations that render OLE rna nonfunctional. This finding demonstrates that the deleterious PM1 phenotype requires an intact RNP complex, and suggests that the complex has one or more additional undiscovered components. A genetic screen uncovered PM1 phenotype suppressor mutations in the ybzG gene, which codes for a putative rna-binding protein of unknown biological function. We observe that YbzG protein (also called OapB) selectively binds OLE rna in vitro, whereas a mutant version of the protein is not observed to bind OLE rna. Thus, YbzG/OapB is an important component of the functional OLE RNP complex in B. halodurans.

关键词： alcohol toxicity Bacillus halodurans noncoding rna OLE rna YbzG

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Circ-104916 is downregulated in gastric cancer and suppresses migration and invasion of gastric cancer cells

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ONCOTARGETS AND THERAPY 2017年 10卷 3521-3529页

作者： Li, Jin Zhen, Li Zhang, Yan Zhao, Liying Liu, Hao Cai, Danxian Chen, Hao Yu, Jiang Qi, Xiaolong Li, Guoxin Southern Med Univ Nanfang Hosp Dept Gen Surg 1838 North Guangzhou Ave Guangzhou 510515 Guangdong Peoples R China

Circular rnas are a large class of noncoding rna that have shown huge capabilities as gene regulators. Recent evidence suggest that circular rnas are associated with many diseases, especially cancer. However, little attention has been focused on the expression and function of circular rna in gastric cancer (GC). In this study, we demonstrate that the expression of circ-104916 is downregulated in GC tissues and cell lines. A lower expression of circ-104916 appeared in deeper invasion depth, higher tumor stage and more frequent lymphatic metastasis patients. Overexpression of circ-104916 effectively inhibited the proliferation, migration and invasion abilities of GC cells in vitro. Western blot showed that circ-104916 overexpression upregulated E-cadherin and downregulated N-cadherin, Vimentin and Slug, indicating that circ-104916 was involved in the epithelial-mesenchymal transition process. Our results revealed that circ-104916 might be a novel potential tumor suppressor and biomarker of GC.

关键词： circular rna noncoding rna circ-104916 gastric cancer EMT

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In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines

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PROTEIN SCIENCE 2017年第7期26卷 1363-1379页

作者： Custer, Thomas C. Walter, Nils G. Univ Michigan Program Chem Biol Ann Arbor MI 48109 USA Univ Michigan Dept Chem Single Mol Anal Grp Ann Arbor MI 48109 USA Univ Michigan Dept Chem Ctr RNA Biomed Ann Arbor MI 48109 USA

rna plays a fundamental, ubiquitous role as either substrate or functional component of many large cellular complexesmolecular machinesused to maintain and control the readout of genetic information, a functional landscape that we are only beginning to understand. The cellular mechanisms for the spatiotemporal organization of the plethora of rnas involved in gene expression are particularly poorly understood. Intracellular single-molecule fluorescence microscopy provides a powerful emerging tool for probing the pertinent mechanistic parameters that govern cellular rna functions, including those of protein coding messenger rnas (mrnas). Progress has been hampered, however, by the scarcity of efficient high-yield methods to fluorescently label rna molecules without the need to drastically increase their molecular weight through artificial appendages that may result in altered behavior. Herein, we employ T7 rna polymerase to body label an rna with a cyanine dye, as well as yeast poly(A) polymerase to strategically place multiple 2-azido-modifications for subsequent fluorophore labeling either between the body and tail or randomly throughout the tail. Using a combination of biochemical and single-molecule fluorescence microscopy approaches, we demonstrate that both yeast poly(A) polymerase labeling strategies result in fully functional mrna, whereas protein coding is severely diminished in the case of body labeling.

关键词： single-molecule fluorescence imaging noncoding rna fluorophore labeling single particle tracking

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Epigenetic factors as drivers of fibrosis in systemic sclerosis

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EPIGENOMICS 2017年第4期9卷 463-477页

作者： Bergmann, Christina Distler, Joerg H. W. Friedrich Alexander Univ Nurnberg FAU Dept Internal Med 3 Erlangen Germany Univ Hosp Erlangen Erlangen Germany

Prolonged activation of fibroblasts is a central hallmark of fibrosing disorders such as systemic sclerosis (SSc). Fibroblasts are the key effector cells. They differentiate into an activated myofibroblast phenotype. In contrast to normal wound healing with transient activation, myofibroblasts persist in fibrosing disorders. Current hypothesis suggests that profibrotic cytokines might trigger epigenetic changes which contribute to the persistently activated fibroblast phenotype. In the last years, several epigenetic alterations have been described in SSc and have been linked to different pathogenic aspects of the disease, in particular to aberrant fibroblast activation and tissue fibrosis, but also to vascular manifestations and inflammation. The focus of this review is the current knowledge on epigenetic changes in fibroblast activation in SSc.

关键词： DNA-methylation epigenetics histone modification myofibroblast differentiation noncoding rna systemic sclerosis

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Small regulatory bacterial rnas regulating the envelope stress response

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BIOCHEMICAL SOCIETY TRANSACTIONS 2017年第2期45卷 417-425页

作者： Klein, Gracjana Raina, Satish Gdansk Univ Technol Unit Bacterial Genet Narutowicza 11-12 PL-80233 Gdansk Poland

Most bacteria encode a large repertoire of rna-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory rnas (srnas), regulatory rna-binding proteins and rna-degrading enzymes. Some of these rna-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve it by either direct posttranscriptional repression of several mrnas, including blocking access to ribosome and/or directing them to rna degradation when the synthesis of their cognate proteins is unwanted, or by enhanced translation of some key stress-regulated transcriptional factors. noncoding rnas that regulate the gene expression by binding to regulatory proteins/transcriptional factors often act negatively by sequestration, preventing target recognition. Expression of many srnas is positively regulated by stress-responsive sigma factors like RpoE and RpoS, and two-component systems like PhoP/Q, Cpx and Rcs. Some of these regulatory rnas act via a feedback mechanism on their own regulators, which is best reflected by recent discoveries, concerning the regulation of cell membrane composition by srnas in Escherichia coli and Salmonella, which are highlighted here.

关键词： RfaH RpoE sigma factor envelope stress noncoding rna stress response two-component system

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