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Long-Read Sequencing - A Powerful Toll in Viral Transcriptome Research

TRENDS IN MICROBIOLOGY 2019年第7期27卷 578-592页

作者： Boldogkoi, Zsolt Moldovan, Norbert Balazs, Zsolt Snyder, Michael Tombacz, Ddra Univ Szeged Fac Med Dept Med Biol Szeged Hungary Stanford Univ Sch Med Dept Genet 300 Pasteur Dr Stanford CA 94305 USA

Long-read sequencing (LRS) has become increasingly popular due to its strengths in de novo assembly and in resolving complex DNA regions as well as in determining full-length rna molecules. Two important LRS technologies have been developed during the past few years, including single-molecule, real-time sequencing by Pacific Biosciences, and nanopore sequencing by Oxford Nanopore Technologies. Although current LRS methods produce lower coverage, and are more error prone than short-read sequencing, these methods continue to be superior in identifying transcript isoforms including multispliced rnas and transcript-length variants as well as overlapping transcripts and alternative polycistronic rna molecules. Viruses have small, compact genomes and therefore these organisms are ideal subjects for transcriptome analysis with the relatively low-throughput LRS techniques. Recent LRS studies have multiplied the number of previously known transcripts and have revealed complex networks of transcriptional overlaps in the examined viruses.

关键词： DNA replication replication origin nanopore sequencing Pacific Biosciences rna-Seq noncoding rna splicing

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The cardiac translational landscape reveals that micropeptides are new players involved in cardiomyocyte hypertrophy

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MOLECULAR THERAPY 2021年第7期29卷 2253-2267页

作者： Yan, Youchen Tang, Rong Li, Bin Cheng, Liangping Ye, Shangmei Yang, Tiqun Han, Yan-Chuang Liu, Chen Dong, Yugang Qu, Liang-Hu Lui, Kathy O. Yang, Jian-Hua Huang, Zhan-Peng Sun Yat Sen Univ Affiliated Hosp 1 Inst Precis Med Dept CardiolCtr Translat Med Guangzhou 510080 Peoples R China Sun Yat Sen Univ State Key Lab Biocontrol Minist Educ Key Lab Gene Engn Guangzhou 510275 Peoples R China Sun Yat Sen Univ NHC Key Lab Assisted Circulat Guangzhou 510080 Peoples R China Chinese Univ Hong Kong Prince Wales Hosp Li Ka Shing Inst Hlth Sci Dept Chem Pathol Hong Kong 999077 Peoples R China Natl Guangdong Joint Engn Lab Diag & Treatment Va Guangzhou 510080 Peoples R China

Hypertrophic growth of cardiomyocytes is one of the major compensatory responses in the heart after physiological or pathological stimulation. Protein synthesis enhancement, which is mediated by the translation of messenger rnas, is one of the main features of cardiomyocyte hypertrophy. Although the transcriptome shift caused by cardiac hypertrophy induced by different stimuli has been extensively investigated, translatome dynamics in this cellular process has been less studied. Here, we generated a nucleotide-resolution translatome as well as transcriptome data from isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORFs) were detected from the deep sequencing of ribosome-protected fragments (Ribo-seq), which orchestrated the shift of the translatome in hypertrophied cardiomyocytes. Our data suggest that rather than increase the translational rate of ribosomes, the increased efficiency of protein synthesis in cardiomyocyte hypertrophy was attributable to an increased quantity of ribosomes. In addition, more than 100 uncharacterized short ORFs (sORFs) were detected in long noncoding rna genes from Ribo-seq with potential of micropeptide coding. In a random test of 15 candidates, the coding potential of 11 sORFs was experimentally supported. Three micropeptides were identified to regulate cardiomyocyte hypertrophy by modulating the activities of oxidative phosphorylation, the calcium signaling pathway, and the mitogen-activated protein kinase (MAPK) pathway. Our study provides a genome-wide overview of the translational controls behind cardiomyocyte hypertrophy and demonstrates an unrecognized role of micropeptides in cardiomyocyte biology.

关键词： cardiac hypertrophy translational landscape Ribo-seq micropeptide short open reading frame noncoding rna

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Viruses join the circular rna world

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FEBS JOUrnaL 2021年第15期288卷 4488-4502页

作者： Tan, Ke-En Lim, Yat-Yuen Univ Malaya Inst Biol Sci Fac Sci Kuala Lumpur 50603 Malaysia

Circular rnas (circrnas) are a recently discovered class of noncoding rnas found in many species across the eukaryotic kingdom. These intriguing rna species are formed through a unique mechanism that is known as back splicing in which the 5 ' and 3 ' termini are covalently joined. Recent research has revealed that viruses also encode a repertoire of circrnas. Some of these viral circrnas are abundantly expressed and are reported to play a role in disease pathogenesis. A growing number of studies also indicate that host circrnas are involved in immune responses against virus infections with either an antiviral or proviral role. In this review, we briefly introduce circrna, its biogenesis, and mechanism of action. We go on to summarize the latest research on the expression, regulation, and functions of viral and host-encoded circrnas during the host-virus interaction, with the aim of highlighting the potential of viral and host circrnas as a suitable target for diagnostic biomarker development and therapeutic treatment of viral-associated diseases. We conclude by discussing the current limitations in knowledge and significance of elucidating the roles of circrnas in host-virus interactions, as well as future directions for this emerging field.

关键词： circrna circular rna mirna sponge noncoding rna virus

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Epigenetically regulated micrornas and their prospect in cancer diagnosis

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EXPERT REVIEW OF MOLECULAR DIAGNOSTICS 2014年第6期14卷 673-683页

作者： Kita, Yoshiaki Vincent, Kimberly Natsugoe, Shoji Berindan-Neagoe, Ioana Calin, George A. Univ Texas MD Anderson Canc Ctr Dept Expt Therapeut Houston TX 77030 USA Kagoshima Univ Grad Sch Med Dept Digest Surg Breast & Thyroid Surg Kagoshima 8908520 Japan Iuliu Hatieganu Univ Med & Pharm Dept Immunol Cluj Napoca Romania Ion Chiricuta Oncol Inst Dept Funct Genom & Expt Pathol Cluj Napoca Romania Univ Texas MD Anderson Canc Ctr Ctr RNA Interference & Noncoding RNAs Houston TX 77030 USA

Epigenetic alterations have been reported to deregulate the expression of many transcripts, including noncoding rnas that have no apparent protein-coding capacity. Recently, as the result of numerous studies focused on mirnas, novel sequencing technologies have made available the transcription profile of the entire human genome. mirnas as drivers of tumor-suppressive and oncogenic functions have been found to be dysregulated in numerous cancer types. However, the functions of epigenetically regulated genetic elements other than protein-coding genes are still a matter of debate. In this review, the authors focus mainly on describing the epigenetic regulation of mirnas in cancer. They also discuss the role of mirnas as potential diagnostic and/or prognostic biomarkers.

关键词： biomarker cancer epigenetics mirna noncoding rna prognosis

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Different phosphoisoforms of rna polymerase II engage the Rtt103 termination factor in a structurally analogous manner

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2017年第20期114卷 E3944-E3953页

作者： Nemec, Corey M. Yang, Fan Gilmore, Joshua M. Hintermair, Corinna Ho, Yi-Hsuan Tseng, Sandra C. Heidemann, Martin Zhang, Ying Florens, Laurence Gasch, Audrey P. Eick, Dirk Washburn, Michael P. Varani, Gabriele Ansari, Aseem Z. Univ Wisconsin Madison Dept Biochem Madison WI 53706 USA Univ Washington Dept Chem Seattle WA 98195 USA Stowers Inst Med Res Kansas City MO 64110 USA Helmholtz Ctr Munich Ctr Integrated Prot Sci Dept Mol Epigenet D-81377 Munich Germany Univ Wisconsin Madison Lab Genet Madison WI 53706 USA Univ Wisconsin Madison Genome Ctr Wisconsin Madison WI 53706 USA Univ Kansas Med Ctr Dept Pathol & Lab Med Kansas City KS 66150 USA Univ Calif San Diego Cell & Dev Biol La Jolla CA 92093 USA

The carboxyl-terminal domain (CTD) of the largest subunit of rna polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar rna (snorna) genes. Quantitative proteomics reveals an interactome of known readers as well as protein complexes that were not known to rely on Thr4 for association with Pol II. The data indicate a key role for Thr4 in engaging the machinery used for transcription elongation and termination. We focus on Rtt103, a protein that binds phospho-Ser2 and phospho-Thr4 marks and facilitates transcription termination at protein-coding genes. To elucidate how Rtt103 engages two distinct CTD modifications that are differentially enriched at noncoding genes, we relied on NMR analysis of Rtt103 in complex with phospho-Thr4- or phospho-Ser2-bearing CTD peptides. The structural data reveal that Rtt103 interacts with phospho-Thr4 in a manner analogous to its interaction with phospho-Ser2-modified CTD. The same set of hydrogen bonds involving either the oxygen on phospho-Thr4 and the hydroxyl on Ser2, or the phosphate on Ser2 and the Thr4 hydroxyl, can be formed by rotation of an arginine side chain, leaving the intermolecular interface otherwise unperturbed. This economy of design enables Rtt103 to engage Pol II at distinct sets of genes with differentially enriched CTD marks.

关键词： CTD code CTD interactome noncoding rna NMR phosphothreonine

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Arthropod 7SK rna

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MOLECULAR BIOLOGY AND EVOLUTION 2008年第9期25卷 1923-1930页

作者： Gruber, Andreas R. Kilgus, Carsten Mosig, Axel Hofacker, Ivo L. Hennig, Wolfgang Stadler, Peter F. Univ Vienna Inst Theoret Chem Vienna Austria Shanghai Inst Biol Sci PICB Dept Combinator & Geometry CAS MPG Shanghai Peoples R China Max Planck Inst Math Sci Leipzig Germany Univ Leipzig Bioinformat Grp Dept Comp Sci Leipzig Germany Univ Leipzig Interdisciplinary Ctr Bioinformat Leipzig Germany Fraunhofer Inst Zelltherapie & Immunol Leipzig Germany Johannes Gutenberg Univ Mainz Inst Genet Mainz Germany Johannes Gutenberg Univ Mainz Santa Fe Inst Mainz Germany

The 7SK small nuclear rna (snrna) is a key player in the regulation of polymerase (pol) II transcription. The 7SK rna was long believed to be specific to vertebrates where it is highly conserved. Homologs in basal deuterostomes and a few lophotrochozoan species were only recently reported. On longer timescales, 7SK evolves rapidly with only few conserved sequence and structure motifs. Previous attempts to identify the Drosophila homolog thus have remained unsuccessful despite considerable efforts. Here we report on the discovery of arthropod 7SK rnas using a novel search strategy based on pol III promoters, as well as the subsequent verification of its expression. Our results demonstrate that a 7SK snrna featuring 2 highly structured conserved domains was present already in the bilaterian ancestor.

关键词： 7SK snrna homology search noncoding rna

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Epigenetic regulation of immune function in asthma

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JOUrnaL OF ALLERGY AND CLINICAL IMMUNOLOGY 2022年第2期150卷 259-265页

作者： Sharma, Sunita Yang, Ivana, V Schwartz, David A. Univ Colorado Dept Med Div Pulm Sci & Crit Care Med Aurora South Africa Univ Colorado Dept Med Div Biomed Informat & Personalized Med Anschutz Med Campus Aurora South Africa 12700 E 19th Ave C-272 Aurora CO 80045 USA

Asthma is a common complex respiratory disease characterized by chronic airway inflammation and partially reversible airflow obstruction resulting from genetic and environmental determinants. Because epigenetic marks influence gene expression and can be modified by both environmental exposures and genetic variation, they are increasingly recognized as relevant to the pathogenesis of asthma and may be a key link between environmental exposures and asthma susceptibility. Unlike changes to DNA sequence, epigenetic signatures are dynamic and reversible, creating an opportunity for not only therapeutic targets but may serve as biomarkers to follow disease course and identify molecular subtypes in heterogeneous diseases such as asthma. In this review, we will examine the relationship between asthma and 3 key epigenetic processes that modify gene expression: DNA methylation, modification of histone tails, and noncoding rnas. In addition to presenting a comprehensive assessment of the existing epigenetic studies focusing on immune regulation in asthma, we will discuss future directions for epigenetic investigation in allergic airway disease. (J Allergy Clin Immunol 2022;150:259-65.)

关键词： Asthma epigenetics DNA methylation histone modifi-cations noncoding rna microrna

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The roles of non-coding rnas in Parkinson's disease

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MOLECULAR BIOLOGY REPORTS 2016年第11期43卷 1193-1204页

作者： Majidinia, Maryam Mihanfar, Aynaz Rahbarghazi, Reza Nourazarian, Alireza Bagca, BakiyeGoker Avci, Cigir Biray Tabriz Univ Med Sci Dept Biochem & Clin Labs Fac Med Tabriz Iran Tabriz Univ Med Sci Stem Cell Res Ctr Tabriz Iran Tabriz Univ Med Sci Res Ctr Pharmaceut Nanotechnol Tabriz Iran Ege Univ Dept Med Biol Fac Med Izmir Turkey

Parkinson's disease (PD) is considered as a high prevalence neurodegenerative disorders worldwide. Pathologically, the demise of dopamine-producing cells, in large part due to an abnormal accumulation of the alpha-synuclein in the substantia nigra, is one of the main causes of the disease. Up until now, many de novo investigations have been conducted to disclose the mechanisms underlying in PD. Among them, impacts of non-coding rnas (ncrnas) on the pathogenesis and/or progression of PD need to be highlighted. micrornas (mirnas) and long ncrnas (lncrnas) are more noteworthy in this context. mirnas are small ncrnas (with 18-25 nucleotide in length) that control the expression of multiple genes at post-transcriptional level, while lncrnas have longer size (over 200 nucleotides) and are involved in some key biological processes through various mechanisms. Involvement of mirnas has been well documented in the development of PD, particularly gene expression. Hence, in this current review, we will discuss the impacts of mirnas in regulation of the expression of PD-related genes and the role of lncrnas in the pathogenesis of PD.

关键词： noncoding rna Parkinson' disease Microrna Long non-coding rna

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Biology of rna Surveillance in Development and Disease

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TRENDS IN CELL BIOLOGY 2019年第5期29卷 428-445页

作者： Laffleur, Brice Basu, Uttiya Columbia Univ Dept Microbiol & Immunol Vagelos Coll Phys & Surg New York NY 10032 USA

The 'rna world', in which rna molecules stored information and acquired enzymatic properties, has been proposed to have preceded organism life. rna is now recognized for its central role in biology, with accumulating evidence implicating coding and noncoding (nc)rnas in myriad mechanisms regulating cellular physiology and disequilibrium in transcriptomes resulting in pathological conditions. Nascently synthesized rnas are subjected to stringent regulation by sophisticated rna surveillance pathways. In this review, we integrate these pathways from a developmental viewpoint, proposing rna surveillance as the convergence of mechanisms that ensure the exact titration of rna molecules in a spatiotemporally controlled manner, leading to development without the onset of pathological conditions, including cancer.

关键词： rna surveillance rna processing noncoding rna differentiation development developmental disease

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The coding and noncoding transcriptome of Neurospora crassa

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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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