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Functional Domains of NEAT1 Architectural lncrna Induce Paraspeckle Assembly through Phase Separation

MOLECULAR CELL 2018年第6期70卷 1038-+页

作者： Yamazaki, Tomohiro Souquere, Sylvie Chujo, Takeshi Kobelke, Simon Chong, Yee Seng Fox, Archa H. Bond, Charles S. Nakagawa, Shinichi Pierron, Gerard Hirose, Tetsuro Hokkaido Univ Inst Genet Med Sapporo Hokkaido 0600815 Japan Inst Gustave Roussy UMR 8122 CNRS F-94805 Villejuif France Univ Western Australia Sch Human Sci Crawley WA 6009 Australia Univ Western Australia Sch Mol Sci Crawley WA 6009 Australia Hokkaido Univ Fac Pharmaceut Sci Sapporo Hokkaido 0600812 Japan

A class of long noncoding rnas (lncrnas) has architectural functions in nuclear body construction;however, specific rna domains dictating their architectural functions remain uninvestigated. Here, we identified the domains of the architectural NEAT1 lncrna that construct paraspeckles. Systematic deletion of NEAT1 portions using CRISPR/Cas9 in haploid cells revealed modular domains of NEAT1 important for rna stability, isoform switching, and paraspeckle assembly. The middle domain, containing functionally redundant subdomains, was responsible for paraspeckle assembly. Artificial tethering of the NONO protein to a NEAT1_2 mutant lacking the functional subdomains rescued paraspeckle assembly, and this required the NOPS dimerization domain of NONO. Paraspeckles exhibit phase-separated properties including susceptibility to 1,6-hexanediol treatment. rna fragments of the NEAT1_2 subdomains preferentially bound NONO/SFPQ, leading to phase-separated aggregates in vitro. Thus, we demonstrate that the enrichment of NONO dimers on the redundant NEAT1_2 subdomains initiates construction of phase-separated paraspeckles, providing mechanistic insights into lncrna-based nuclear body formation.

关键词： noncoding rna architectural rna nuclear bodies paraspeckle rna-binding proteins prion-like domain phase separation 1 6-hexanediol CRISPR/Cas9 haploid cell

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Markers associated with neuron-specific Ube3a imprinting during neuronal differentiation of mouse embryonic stem cells

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CYTOTECHNOLOGY 2018年第1期70卷 45-53页

作者： Eitoku, Masamitsu Kato, Hidemasa Suganuma, Narufumi Kiyosawa, Hidenori Kochi Univ Kochi Med Sch Dept Environm Med Oko Cho Kohasu Nanko Ku Kochi 7838505 Japan Ehime Univ Grad Sch Med Div Funct Histol Dept Funct Biomed Toon Ehime 7910295 Japan Chiba Inst Technol Dept Life Sci Narashino Chiba 2750016 Japan

Understanding gene expression in the brain requires allele-specific transcriptome analysis because of the presence of neuron-specific imprinted genes, which are expressed in a neuron-specific and parent-of-origin-specific manner. Ube3a is a neuron-specific imprinted gene with an expression pattern that changes from biallelic to maternal only (Ube3a imprinting) during differentiation. Because Ube3a imprinting occurs only in neurons, it has the potential to be a marker to assess the quality of neurons produced by in vitro neuronal differentiation of embryonic stem cells (ESCs). For the analysis of Ube3a imprinting, genetic polymorphisms between the two alleles are necessary to identify the parental origin of each. However, ESCs derived from commonly used inbred mouse strains have no genetic polymorphisms. To overcome this problem, we examined 10 markers of neurogenesis to determine whether they were associated with Ube3a imprinting. We measured the relative expression levels of these 10 gene markers and assessed the Ube3a imprinting status of 54 neuron samples differentiated under various in vitro conditions. Then we divided the samples into two groups depending on their Ube3a imprinting status and selected markers statistically associated with Ube3a imprinting. The identified markers included the antisense noncoding transcript of Ube3a and a mature neuron marker Mtap2, consistent with the markers we used empirically in our previous study to assess the quality of differentiated neurons. These findings provide new quality control criteria for differentiated neurons, and could also be applied to human ESCs and induced pluripotent stem cells.

关键词： Ube3a imprinting Embryonic stem cell In vitro neuronal differentiation Mus musculus molossinus Mtap2 noncoding rna SNP ratio quantification

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Small and Low but Potent: the Complex Regulatory Role of the Small rna SolB in Solventogenesis in Clostridium acetobutylicum

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APPLIED AND ENVIRONMENTAL MICROBIOLOGY 2018年第14期84卷 e00597-18页

作者： Jones, Alexander J. Fast, Alan G. Clupper, Michael Papoutsakis, Eleftherios T. Univ Delaware Dept Biol Sci Newark DE 19716 USA Univ Delaware Dept Chem & Biomol Engn Newark DE 19716 USA Univ Delaware Delaware Biotechnol Inst Mol Biotechnol Lab Newark DE 19716 USA BD Biosci Sparks MD USA

The recently revived Clostridium acetobutylicum-based acetone-butanolethanol (ABE) fermentation is widely celebrated and studied for its impact on industrial biotechnology. C. acetobutylicum has been studied and engineered extensively, yet critical areas of the molecular basis for how solvent formation is regulated remain unresolved. The core solventogenic genes (adhEl/aad, ctfA, ctfB, and adc) are carried on the sol locus of the pSOL1 megaplasmid, whose loss leads to asporogenous, "degenerate" cells. The sol locus includes a noncoding small rna (srna), SolB, whose role is presumed to be critical for solventogenesis but has eluded resolution. In the present study, SolB overexpression downregulated the sol-locus genes at the transcript level, resulting in attenuated protein expression and a solvent-deficient phenotype, thus suggesting that SolB affects expression of all sol-locus transcripts and seemingly validating its hypothesized role as a repressor. However, deletion of solB resulted in a total loss of acetone production and severe attenuation of butanol formation, with complex effects on sol-locus genes and proteins: it had a small impact on adc mrna or its corresponding protein (acetoacetate decarboxylase) expression level, somewhat reduced adhE1 and ctfA-ctfB mrna levels, and abolished the ctfA-ctfB-encoded coenzyme A transferase (CoAT) activity. Computational predictions support a model whereby SolB expressed at low levels enables the stabilization and translation of sol-locus transcripts to facilitate tuning of the production of various solvents depending on the prevailing culture conditions. A key predicted SolB target is the ribosome binding site (RBS) of the ctfA transcript, and this was verified by expressing variants of the ctfA-ctfB genes to demonstrate the importance of SolB for acetone formation. IMPORTANCE Small noncoding rnas regulate many important metabolic and developmental programs in prokaryotes, but their role in anaerobes has been explored m

关键词： SolB small rna noncoding rna Clostridium acetobutylicum acetone butanol ABE sol locus metabolic engineering mrna stability solvent formation RBS translational regulation

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MOXI Is a Mitochondrial Micropeptide That Enhances Fatty Acid β-Oxidation

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CELL REPORTS 2018年第13期23卷 3701-3709页

作者： Makarewich, Catherine A. Baskin, Kedryn K. Munir, Amir Z. Bezprozvannaya, Svetlana Sharma, Gaurav Khemtong, Chalermchai Shah, Akansha M. McAnally, John R. Malloy, Craig R. Szweda, Luke I. Bassel-Duby, Rhonda Olson, Eric N. Univ Texas Southwestern Med Ctr Dallas Dept Mol Biol Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Hamon Ctr Regenerat Sci & Med Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Adv Imaging Res Ctr Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Dept Radiol Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Dept Internal Med Dallas TX 75390 USA

Micropeptide regulator of beta-oxidation (MOXI) is a conserved muscle-enriched protein encoded by an rna transcript misannotated as non-coding. MOXI localizes to the inner mitochondria! membrane where it associates with the mitochondria! trifunctional protein, an enzyme complex that plays a critical role in fatty acid 13-oxidation. Isolated heart and skeletal muscle mitochondria from MOXI knockout mice exhibit a diminished ability to metabolize fatty acids, while transgenic MOXI overexpression leads to enhanced 13-oxidation. Additionally, hearts from MOXI knockout mice preferentially oxidize carbohydrates over fatty acids in an isolated perfused heart system compared to wild-type (WT) animals. MOXI knockout mice also exhibit a profound reduction in exercise capacity, highlighting the role of MOXI in metabolic control. The functional characterization of MOXI provides insight into the regulation of mitochondria! metabolism and energy homeostasis and underscores the regulatory potential of additional micropeptides that have yet to be identified.

关键词： micropeptide fatty acid oxidation metabolism mitochondria trifunctional protein noncoding rna

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Dysregulation of microrna biogenesis machinery and microrna/rna ratio in skeletal muscle of amyotrophic lateral sclerosis mice

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MUSCLE & NERVE 2018年第5期57卷 838-847页

作者： Russell, Aaron P. Ghobrial, Lobna Ngo, Shyuan Yerbury, Justin Zacharewicz, Evelyn Chung, Roger Lamon, Severine Deakin Univ IPAN Geelong Vic Australia Univ Queensland Australian Inst Bioengn & Nanotechnol Australia Queensland Brain Inst Brisbane Qld Australia Univ Wollongong Illawarra Hlth & Med Res Inst Wollongong NSW Australia Macquarie Univ Dept Biomed Sci Sydney NSW Australia

Introduction: The pathology of amyotrophic lateral sclerosis (ALS) is associated with impaired rna processing and microrna (mirna) dysregulation. Here we investigate the regulation of the members of the mirna biogenesis pathways and total mirna levels at different stages of the disease. Methods: Muscle, brain, and spinal cord tissue were obtained from presymptomatic, symptomatic, and end-stage superoxide dismutase 1 (SOD1)(G93A) mice. mirna and transcript levels were measured by quantitative polymerase chain reaction. Results: As the diseases progresses, several genes involved in mirna biogenesis as well as the mirna/total rna (totrna) ratio increased in the tibialis anterior (TA) muscle but not in the soleus or in neural tissue. Discussion: We propose that a dysregulation in the mirna/totrna ratio in the TA muscle from SOD1(G93A) mice reflects a pathological increase in mirna biogenesis machinery. Alterations in the mirna/totrna ratio influence the levels of reference noncoding rnas and may therefore potentially compromise the accuracy of commonly used mirna normalization strategies. Muscle Nerve57: 838-847, 2018

关键词： ALS biogenesis microrna noncoding rna normalization skeletal muscle

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Novel circular rna expression profile of uveal melanoma revealed by microarray

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Chinese Journal of Cancer Research 2018年第6期30卷 656-668页

作者： Xuan Yang Yang Li Yueming Liu Xiaolin Xu Yingzhi Wang Yanni Yan Wenjia Zhou Jingyan Yang Wenbin Wei Beijing Tongren Eye Center Beijing Key Laboratory of Intraocular Tumor Diagnosis and TreatmentBeijing Ophthalmology & Visual Sciences Key LabBeijing Tongren HospitalCapital Medical University Beijing Institute of Ophthalmology Beijing Key Laboratory of Intraocular Tumor Diagnosis and TreatmentBeijing Tongren Eye CenterBeijing Tongren HospitalCapital Medical UniversityBeijing Ophthalmology & Visual Sciences Key Laboratory

Objective: The present study aimed to investigate circular rna(circrna) expression in uveal melanoma(UM).Methods: First,we used microarray to compare the expression profiles of circrna in five UM samples and five normal uvea ***,bioinformatics analyses,including gene ontology(GO) analysis and pathway analysis,were applied to study these differentially expressed circrnas to predict pathogenic pathways that may be *** real-time polymerase chain reaction(qRT-PCR) in 20 UM samples and 20 normal uvea samples was used to confirm the circrna expression profiles obtained from the microarray ***,we analyzed the interaction between validated circrnas and their potential cancer-associated mirna ***: In total,50,579 circrnas [fold change(FC) ≥2.0; P<0.05],including 20,654 up-regulated and 29,925 down-regulated circrnas,were identified as differentially expressed between UM tissues and normal uvea *** used qRT-PCR to verify seven dysregulated circrnas indicated by the microarray data,including hsacirc0119873,hsacirc0128533,hsacirc0047924,hsacirc0103232,hsa-circrna10628-6,hsacirc0032148 and hsacirc0133460,which may be promising candidates to study future molecular ***: This study explored,for the first time,the abnormal expression of circrnas in UM and described the expression profile of circrnas,providing a new potential target for the mechanism of UM and future treatment of UM.

关键词： Uveal melanoma circular rna microarray noncoding rna

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Nuclear noncoding rna surveillance: is the end in sight?

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TRENDS IN GENETICS 2012年第7期28卷 306-313页

作者： Wolin, Sandra L. Sim, Soyeong Chen, Xinguo Yale Univ Sch Med Dept Cell Biol New Haven CT 06536 USA Yale Univ Sch Med Dept Mol Biophys & Biochem New Haven CT 06536 USA

Nuclear noncoding rna (ncrna) surveillance pathways play key roles in shaping the steady-state transcriptomes of eukaryotic cells. Defective and unneeded ncrnas are primarily degraded by exoribonucleases that rely on protein cofactors to identify these rnas. Recent studies have begun to elucidate both the mechanisms by which these cofactors recognize aberrant rnas and the features that mark rnas for degradation. One crucial rna determinant is the presence of an accessible end;in addition, the failure of aberrant rnas to fold into compact structures and assemble with specific binding proteins probably also contributes to their recognition and subsequent degradation. To date, ncrna surveillance has been most extensively studied in budding yeast. However, mammalian cells possess nucleases and cofactors that have no known yeast counterparts, indicating that rna surveillance pathways may be more complex in metazoans. Importantly, there is evidence that the failure of ncrna surveillance pathways contributes to human disease.

关键词： noncoding rna quality control rna degradation oligoadenylation TRAMP complex exoribonucleases

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Alpha satellite DNA biology: finding function in the recesses of the genome

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CHROMOSOME RESEARCH 2018年第3期26卷 115-138页

作者： McNulty, Shannon M. Sullivan, Beth A. Duke Univ Med Ctr Dept Mol Genet & Microbiol Durham NC 27710 USA Duke Univ Med Ctr Div Human Genet Durham NC 27710 USA

Repetitive DNA, formerly referred to by the misnomer junk DNA, comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of thehighly repetitive nature ofalpha satellite, ithas been difficult to achieve genome assemblies at centromeres using traditional next-generation sequencing approaches, and thus, centromeres represent gaps in the current human genome assembly. Moreover, alpha satellite DNA is transcribed into repetitive noncoding rna and contributes to a large portion of the transcriptome. Recent efforts to characterize these transcripts and their function have uncovered pivotal roles for satellite rna in genome stability, including silencing selfish DNA elements and recruiting centromere and kinetochore proteins. This review will describe the genomic and epigenetic features of alpha satellite DNA, discuss recent findings of noncoding transcripts produced from distinct alpha satellite arrays, and address current progress in the functional understanding of this oft-neglected repetitive sequence. We will discuss unique challenges of studying human satellite DNAs and rnas and point toward new technologies that will continue to advance our understanding of this largely untapped portion of the genome.

关键词： satellite centromere kinetochore variation transcription noncoding rna repetitive DNA epiallele

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Molecules derived from trna and snorna: Entering the degradome pool

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BIOMEDICINE & PHARMACOTHERAPY 2018年 108卷 36-42页

作者： Swiatowy, Witold Jagodzinski, Pawel P. Poznan Univ Med Sci Dept Biochem & Mol Biol 6 Swiecickiego St PL-60781 Poznan Poland

Molecules built of rna have been the subjects of numerous studies, which have made known new functions and structures that these molecules can create. In recent years, thanks to next-generation sequencing, it is possible to observe very small rnas and the number of newly discovered rna molecules is rapidly increasing. Among other small oligonucleotides, structures derived from trna and snorna molecules have been observed, and these molecules were determined to not be precursors of known rna molecules. These structures have attracted the attention of researchers because the level of accumulation of trna or snorna fragments was relatively high. Additionally, other parts of the parent molecules were absent. Derivatives of well-known rna molecules also have functions that are different from their parent molecules. They are mainly involved in regulating the expression of genetic information in a similar way to mirna. In addition, some of the mirnas that have been described are derivatives of trna or snorna. Most of the research on these newly discovered molecules is based on their detection and on the study of the macro effects that they exert, in the absence of a description of the molecular mechanism by which they arise and work.

关键词： noncoding rna trna snorna rna processing sdrna tRF

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Yrna Expression Profiles are Altered in Clear Cell Renal Cell Carcinoma

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EUROPEAN UROLOGY FOCUS 2018年第2期4卷 260-266页

作者： Nientiedt, Malin Schmidt, Doris Kristiansen, Glen Mueller, Stefan C. Ellinger, Joerg Univ Hosp Bonn Dept Urol Bonn Germany Univ Hosp Bonn Inst Pathol Bonn Germany

Background: noncoding rnas play an important role in human carcinogenesis. Yrnas, a novel class of noncoding rnas, have been identified as biomarkers in breast cancer patients. Objective: To test the hypothesis that Yrna expression is dysregulated in clear cell renal cell carcinoma (ccRCC). Design, setting, and participants: We first measured the expression of all known Yrnas (hY1, hY3, hY4, and hY5) in a screening cohort (30 ccRCC and 15 normal renal tissues). Subsequently, hY3 and hY4 were validated in an independent cohort (88 ccRCC and 59 normal renal tissues). Finally, hY3 and hY4 levels in serum samples from 30 ccRCC and 15 control individuals were measured. Yrnas were detected using quantitative real-time polymerase chain reaction. Outcome measurements and statistical analysis: Relative expression values were analyzed using the Mann-Whitney-U test and Kaplan Meier estimates. Results and limitations: Expression of hY3 and hY4 was increased in ccRCC samples compared with normal renal tissue, whereas hY1 and hY5 levels were similar. Expression levels of hY4 correlated with ccRCC stage and the presence of lymph node metastases. Neither hY3 nor hY4 were circulating at different levels in ccRCC patients and control individuals. Conclusions: The expression of hY3 and hY4 is altered in ccRCC and associated with advanced disease. Patient summary: In this report we studied the expression of noncoding Yrna in clear cell renal cell carcinoma tissue. We observed increased hY3 and hY4 expression levels in cancer tissues. However, expression levels were not different in the serum of patients with cancer or benign disease. (C) 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

关键词： Renal cell carcinoma Yrna noncoding rna Gene expression

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