DOCSLIB.ORG

Structural and Functional Characterization of Noncoding Rnas in Mammalian Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Structural and Functional Characterization of Noncoding Rnas in Mammalian Cells STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF NONCODING RNAS IN MAMMALIAN CELLS by Sungyul Lee A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland December, 2015 © 2015 Sungyul Lee All Rights Reserved Abstract Francis Crick proposed the central dogma of molecular biology more than a half century ago focusing on the role of RNA as a messenger which delivers genetic information from DNA to protein. However, it is now clear that RNA constitute a major player in every aspects of biological processes as much as protein does, through their noncoding functions. While early studies of RNA biology were mostly centered around abundant and constitutive noncoding RNAs in ribosome, spliceosome, transcriptional machinery and telomere, recent studies are now shifting their heads toward less abundant and dynamically regulated tissue or developmental time specific noncoding RNAs such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). With advent of new analytic tools and massive amount of sequencing data, there have been continued unexpected discoveries revealing how our genome is written and read inside the cell. MicroRNAs are ~22 nt small RNAs that guide RISC proteins to their target genes through their base complementary thereby achieve posttranscriptional gene repression. The mechanism of repression is almost universal in animals but the regulation of their expression is one of big questions in the field. In order to facilitate investigations of expression control of miRNAs in mammals, we annotated genome-wide primary miRNA transcripts of mouse and human. We undertook this endeavor to provide most comprehensive transcriptional pictures across human and mouse genomes, which is a major bottleneck in the elucidation of mechanisms that controls miRNA abundance. To do this, we had to overcome 3 obstacles. First, we expressed dominant-negative DROSHA mutant to suppress efficient hairpin cropping of microprocessor thefore enriched un-processed primary transcripts for sequencing. Second, we used panel of ii human and mouse cell lines of diverse origin to increase coverage of miRNAs that are expressed tissue specifically. Lastly, we collaborated with Steven Salzberg’s lab to employ recently developed assembly algorithm, StringTie, which outperforms other existing assembly tools for this application. Together these, we uncovered unanticipated features and new potential regulatory mechanisms, including link between pri-miRNAs and distant mRNAs, and alternative splicing and alternative promoter usage that can produce transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results provide a valuable resource for the study of mammalian miRNA regulation. Another class of emerging regulatory noncoding RNA is long noncoding RNA (lncRNA). Although current human genome annotation predicts almost similar number of genes encoding lncRNA as protein coding genes, the question remains how many of them are indeed plays integral part of diverse biological functions. Unlike miRNA, mechanisms of lncRNAs are quite unique in each case, making it difficult to predict their function based on primary sequence. One of very limited number of ways to find their functions is to investigate their phenotype in cellular or organismal level after introducing genetic ablation. Through the screening of lncRNA that are induced after DNA damage, we identified NORAD which suggested its functionality given their high conservation in mammals, high abundance, and association with an interesting biological cue (i.e. induction after DNA damage). Surprisingly, cells inactivated NORAD expression showed increased level of numerical and structural chromosomal instability. We found this transcript harbors unusually high number of PUMILIO binding motifs allowing it to sequester this RNA binding protein (RBP), thereby suppressing its repressive activity on its targets. PUMILIO targets includes factors important for DNA damage response, DNA iii repair, and mitosis. Overexpression of PUMILIO also showed suppression of these target genes and phenocopied NORAD knockout cells. I also generated knockout mouse of clear NORAD ortholog Norad, using CRISPR/Cas9 technology. It might be very interesting to see the same phenotype in this animal, and possibly other phenotypes that we couldn’t observe due to simplicity of cultured cells. Altogether this study shows novel mechanism of genomic stability maintenance through sequestrating PUMILIO by a lncRNA, NORAD. Advisor: Joshua T. Mendell, M.D., Ph.D. Reader: Ben Ho Park, M.D., Ph.D. and Haig H. Kazazian, M.D., Ph.D. iv Preface My dissertation work written in this book only partially reflects what I was given and supported from wonderful people and institutions around me. Without helps and influences from them, this work could never been materialized. First and foremost, I’m immensely grateful to my mentor Joshua Mendell, and I’m truly indebted for his scientific acumen and critical thinking. His enthusiasm for unknowns and pursuit of perfection always inspired me and motivated my scientific creativity. I believe his influence and legacy will continue to be remained on my future career. My thesis committee members, Haig Kazazian and Ben Ho Park provided me valuable guidance throughout my thesis work. I could only continue to be professionally nurtured through our annual meetings, with their constructive criticisms and solutions for problems each time I had. I also thank my colleagues in Mendell lab. In particular, Tsung-Cheng Chang taught me so many useful experimental technics and Florian Kopp was always there with me to discuss and perform exciting works together. I thank my graduate program Pathobiology at Johns Hopkins for giving me administrative and financial support. Lab manager Ana Doughty was the most helpful people I ever met and Molecular biology department in UT Southwestern enabled me to continue my work in Dallas. I thank our excellent collaboration groups including Stephen Salzberg lab, Yang Xie lab, and Hongtao Yu lab. Finally, I can’t finish my acknowledgements without saying thank you to my family. My parents Se-il and Young-sook inherited in me their appreciation of hard-work and thankfulness for everything happening around me. My proud son, Shihoo is the energy that always drives me go and the best motivation of my life. This dissertation is dedicated to Jung Hee, mother of my son and wife of mine, who shares every sorrows and joys of my life with me. v Table of Contents Abstract ........................................................................................................................... ii Preface ............................................................................................................................ v Table of Contents ........................................................................................................... vi List of Tables ................................................................................................................. vii List of Figures ............................................................................................................... viii Chapter 1: Introduction ................................................................................................... 1 Chapter 2: Genome-wide annotation of microRNA primary transcript structures ...........10 Introduction ................................................................................................................10 Results .......................................................................................................................14 Discussion .................................................................................................................61 Materials and methods ...............................................................................................64 Chapter 3: Characterization and loss of function study of a human long noncoding RNA induced by DNA damage, NORAD ................................................................................74 Introduction ................................................................................................................74 Results .......................................................................................................................77 Discussion ............................................................................................................... 107 Materials and Methods ............................................................................................. 109 Chapter 4: Mechanism of chromosome instability in NORAD depleted cells ................ 120 Introduction .............................................................................................................. 120 Results ..................................................................................................................... 123 Discussion ............................................................................................................... 156 Materials and Methods ............................................................................................. 161 Chapter 5: Generation of Norad knockout mouse using CRISPR/Cas9 genome editing system ......................................................................................................................... 175 Introduction .............................................................................................................
Load more

Recommended publications
  • Requirement of the Fusogenic Micropeptide Myomixer for Muscle Formation in Zebrafish
    Requirement of the fusogenic micropeptide myomixer for muscle formation in zebrafish Jun Shia,b,1, Pengpeng Bia,b,c,1, Jimin Peid, Hui Lia,b,c, Nick V. Grishind,e, Rhonda Bassel-Dubya,b,c, Elizabeth H. Chena,b,2, and Eric N. Olsona,b,c,2 aDepartment of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390; bHamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390; cSenator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390; dHoward Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390; and eDepartment of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390 Contributed by Eric N. Olson, September 28, 2017 (sent for review August 29, 2017; reviewed by Chen-Ming Fan and Thomas A. Rando) Skeletal muscle formation requires fusion of mononucleated myo- CRISPR/Cas9, we show that myomixer is required for zebrafish blasts to form multinucleated myofibers. The muscle-specific mem- myoblast fusion. We also identify additional distantly related brane proteins myomaker and myomixer cooperate to drive myomixer orthologs from genomes of turtle and elephant shark, mammalian myoblast fusion. Whereas myomaker is highly conserved which like zebrafish myomixer can substitute for mouse myomixer across diverse vertebrate species, myomixer is a micropeptide that to promote cell fusion together with myomaker in cultured cells. shows relatively weak cross-species conservation. To explore the By comparison of amino acid sequences across these diverse functional conservation of myomixer, we investigated the expres- species, we identify a unique protein motif required for the sion and function of the zebrafish myomixer ortholog.
    [Show full text]
  • Computational Analysis Predicts Hundreds of Coding Lncrnas in Zebrafish
    biology Communication Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish Shital Kumar Mishra 1,2 and Han Wang 1,2,* 1 Center for Circadian Clocks, Soochow University, Suzhou 215123, China; [email protected] 2 School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China * Correspondence: [email protected] or [email protected]; Tel.: +86-512-6588-2115 Simple Summary: Noncoding RNAs (ncRNAs) regulate a variety of fundamental life processes such as development, physiology, metabolism and circadian rhythmicity. RNA-sequencing (RNA- seq) technology has facilitated the sequencing of the whole transcriptome, thereby capturing and quantifying the dynamism of transcriptome-wide RNA expression profiles. However, much remains unrevealed in the huge noncoding RNA datasets that require further bioinformatic analysis. In this study, we applied six bioinformatic tools to investigate coding potentials of approximately 21,000 lncRNAs. A total of 313 lncRNAs are predicted to be coded by all the six tools. Our findings provide insights into the regulatory roles of lncRNAs and set the stage for the functional investigation of these lncRNAs and their encoded micropeptides. Abstract: Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Citation: Mishra, S.K.; Wang, H. Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool Computational Analysis Predicts (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify Hundreds of Coding lncRNAs in 2730–6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted Zebrafish.
    [Show full text]
  • Stem Cell Metabolic and Epigenetic Reprogramming
    RESEARCH HIGHLIGHTS Cell 16, 39–50, 2015). They discovered that inactivating Rb facilitates Enhancer evolution in mammals reprogramming of fibroblasts to a pluripotent state. Surprisingly, their Widespread changes in regulatory genomic regions have data indicate that this does not involve interference with the cell cycle but underpinned mammalian evolution, but our knowledge about instead that Rb directly binds to and represses pluripotency-associated these regions is still incomplete. Paul Flicek, Duncan Odom and loci such as Oct4 (Pou5f1) and Sox2. Loss of Rb seems to compensate colleagues have now contributed to a better understanding of for the omission of Sox2 from the cocktail of reprogramming factors. how the noncoding portions of mammalian genomes have been Furthermore, genetic disruption of Sox2 precludes tumor formation in reshaped over the last 180 million years (Cell 160, 554–566, mice lacking functional Rb protein. This study positions Rb as a repres- 2015). They characterized active promoters and enhancers in sor of the pluripotency gene regulatory network and suggests that loss of liver samples from 20 mammalian species—from Tasmanian Rb might clear the path for Sox2, or other master regulators of stem cell devil to human—by examining the genome-wide enrichment identity, to induce cancer. It will be interesting to analyze the potential profiles of H3K4me3 and H3K27ac, two histone modifications role of Rb in other types of in vitro reprogramming. TF associated with transcriptional activity. Their analyses suggest that rapid enhancer evolution and high promoter conservation are fundamental traits of mammalian genomes. Intriguingly, they Micropeptide regulates muscle performance find that the majority of newly evolved enhancers originated via It is becoming increasingly recognized that some transcripts anno- functional exaptation of ancestral DNA and not through clade- tated as long noncoding RNAs (lncRNAs) contain short ORFs that specific expansions of repeat elements.
    [Show full text]
  • The Lncrna Toolkit: Databases and in Silico Tools for Lncrna Analysis
    non-coding RNA Review The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis Holly R. Pinkney † , Brandon M. Wright † and Sarah D. Diermeier * Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand; [email protected] (H.R.P.); [email protected] (B.M.W.) * Correspondence: [email protected] † These authors contributed equally to this work. Received: 29 November 2020; Accepted: 15 December 2020; Published: 16 December 2020 Abstract: Long non-coding RNAs (lncRNAs) are a rapidly expanding field of research, with many new transcripts identified each year. However, only a small subset of lncRNAs has been characterized functionally thus far. To aid investigating the mechanisms of action by which new lncRNAs act, bioinformatic tools and databases are invaluable. Here, we review a selection of computational tools and databases for the in silico analysis of lncRNAs, including tissue-specific expression, protein coding potential, subcellular localization, structural conformation, and interaction partners. The assembled lncRNA toolkit is aimed primarily at experimental researchers as a useful starting point to guide wet-lab experiments, mainly containing multi-functional, user-friendly interfaces. With more and more new lncRNA analysis tools available, it will be essential to provide continuous updates and maintain the availability of key software in the future. Keywords: non-coding RNAs; long non-coding RNAs; databases; computational analysis; bioinformatic prediction software; RNA interactions; coding potential; RNA structure; RNA function 1. Introduction For decades, the human genome was thought to be a desert of ‘junk DNA’ with sporadic oases of transcriptionally active genes, most of them coding for proteins.
    [Show full text]
  • Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods
    fgene-12-651485 May 6, 2021 Time: 11:28 # 1 MINI REVIEW published: 06 May 2021 doi: 10.3389/fgene.2021.651485 Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods Ravi Tharakan1* and Akira Sawa2,3 1 National Institute on Aging, National Institutes of Health, Baltimore, MD, United States, 2 Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States, 3 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and Edited by: conceptual challenges facing future micropeptide endeavors. Liangliang Sun, Keywords: micropeptides, miniproteins, proteogenomics, sORF, ribosome profiling, proteomics, genomics, RNA Michigan State University, sequencing United States Reviewed by: Yanbao Yu, INTRODUCTION J. Craig Venter Institute (Rockville), United States The sequencing and publication of complete genomic sequences of many organisms have aided Hongqiang Qin, the medical sciences greatly, allowing advances in both human genetics and the biology of human Dalian Institute of Chemical Physics, Chinese Academy of Sciences, China disease, as well as a greater understanding of the biology of human pathogens (Firth and Lipkin, 2013).
    [Show full text]
  • Micropeptide Regulates Muscle Performance
    RESEARCH HIGHLIGHTS Cell 16, 39–50, 2015). They discovered that inactivating Rb facilitates Enhancer evolution in mammals reprogramming of fibroblasts to a pluripotent state. Surprisingly, their Widespread changes in regulatory genomic regions have data indicate that this does not involve interference with the cell cycle but underpinned mammalian evolution, but our knowledge about instead that Rb directly binds to and represses pluripotency-associated these regions is still incomplete. Paul Flicek, Duncan Odom and loci such as Oct4 (Pou5f1) and Sox2. Loss of Rb seems to compensate colleagues have now contributed to a better understanding of for the omission of Sox2 from the cocktail of reprogramming factors. how the noncoding portions of mammalian genomes have been Furthermore, genetic disruption of Sox2 precludes tumor formation in reshaped over the last 180 million years (Cell 160, 554–566, mice lacking functional Rb protein. This study positions Rb as a repres- 2015). They characterized active promoters and enhancers in sor of the pluripotency gene regulatory network and suggests that loss of liver samples from 20 mammalian species—from Tasmanian Rb might clear the path for Sox2, or other master regulators of stem cell devil to human—by examining the genome-wide enrichment identity, to induce cancer. It will be interesting to analyze the potential profiles of H3K4me3 and H3K27ac, two histone modifications role of Rb in other types of in vitro reprogramming. TF associated with transcriptional activity. Their analyses suggest that rapid enhancer evolution and high promoter conservation are fundamental traits of mammalian genomes. Intriguingly, they Micropeptide regulates muscle performance find that the majority of newly evolved enhancers originated via It is becoming increasingly recognized that some transcripts anno- functional exaptation of ancestral DNA and not through clade- tated as long noncoding RNAs (lncRNAs) contain short ORFs that specific expansions of repeat elements.
    [Show full text]
  • 2790.Full.Pdf
    Published OnlineFirst March 13, 2020; DOI: 10.1158/0008-5472.CAN-19-3440 CANCER RESEARCH | MOLECULAR CELL BIOLOGY A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma Siqi Wu1, Liyuan Zhang2, Jieqiong Deng1, Binbin Guo1, Fang Li1, Yirong Wang1, Rui Wu1, Shenghua Zhang1, Jiachun Lu3, and Yifeng Zhou1 ABSTRACT ◥ Long noncoding RNAs (lncRNA) have been shown to play critical Graphical Abstract: http://cancerres.aacrjournals.org/content/ roles in many diseases, including esophageal squamous cell carcino- canres/80/13/2790/F1.large.jpg. ma (ESCC). Recent studies have reported that some lncRNA encode See related commentary by Banday et al., p. 2718 functional micropeptides. However, the association between ESCC and micropeptides encoded by lncRNA remains largely unknown. In this study, we characterized a Y-linked lncRNA, LINC00278,which was downregulated in male ESCC. LINC00278 encoded a Yin Yang 1 Chr.Y (YY1)-binding micropeptide, designated YY1BM. YY1BM was LINC0027 involved in the ESCC progression and inhibited the interaction 8 sORF A A METTL3 A between YY1 and androgen receptor (AR), which in turn decreased METTL14 eEF2K ALKBH5 eEF2K eEF2K expression of through the AR signaling pathway. Down- AR YY1 regulation of YY1BM significantly upregulated eEF2K expression WTAP m6A Smoking and inhibited apoptosis, thus conferring ESCC cells more adaptive to LINC00278 sORF A A nutrient deprivation. Cigarette smoking decreased m6A modification A eEF2 of LINC00278 and YY1BM translation. In conclusion, these results YTHDF1 provide a novel mechanistic link between cigarette smoking and AR YY1BM Translation Caspase-3 signaling in male ESCC progression.
    [Show full text]
  • Fusogenic Micropeptide Myomixer Is Essential for Satellite Cell Fusion and Muscle Regeneration
    Fusogenic micropeptide Myomixer is essential for satellite cell fusion and muscle regeneration Pengpeng Bia,b,c, John R. McAnallya,b,c, John M. Sheltond, Efrain Sánchez-Ortiza,b,c, Rhonda Bassel-Dubya,b,c, and Eric N. Olsona,b,c,1 aDepartment of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390; bHamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390; cSenator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390; and dDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 Contributed by Eric N. Olson, March 1, 2018 (sent for review January 3, 2018; reviewed by Bradley B. Olwin and Nadia A. Rosenthal) Regeneration of skeletal muscle in response to injury occurs through fusion and muscle formation during embryogenesis in mice and fusion of a population of stem cells, known as satellite cells, with zebrafish (14, 16–20). Myomaker is also required for fusion of injured myofibers. Myomixer, a muscle-specific membrane micro- SCs during adult muscle regeneration (21). peptide, cooperates with the transmembrane protein Myomaker Myomaker and Myomixer are up-regulated in SCs during to regulate embryonic myoblast fusion and muscle formation. To muscle regeneration (14, 16, 17, 21). However, the perinatal investigate the role of Myomixer in muscle regeneration, we used lethality of Myomixer null mice has precluded an analysis of its CRISPR/Cas9-mediated genome editing to generate conditional potential involvement in myofiber regeneration in response to knockout Myomixer alleles in mice. We show that genetic deletion injury (14).
    [Show full text]
  • Identification of Rhythmically Expressed Lncrnas in the Zebrafish Pineal Gland and Testis
    International Journal of Molecular Sciences Article Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis Shital Kumar Mishra 1,2, Taole Liu 1,2 and Han Wang 1,2,* 1 Center for Circadian Clocks, Soochow University, Suzhou 215123, China; [email protected] (S.K.M.); [email protected] (T.L.) 2 School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China * Correspondence: [email protected] or [email protected]; Tel.: +86-51265882115 Abstract: Noncoding RNAs have been known to contribute to a variety of fundamental life processes, such as development, metabolism, and circadian rhythms. However, much remains unrevealed in the huge noncoding RNA datasets, which require further bioinformatic analysis and experimental investigation—and in particular, the coding potential of lncRNAs and the functions of lncRNA- encoded peptides have not been comprehensively studied to date. Through integrating the time- course experimentation with state-of-the-art computational techniques, we studied tens of thousands of zebrafish lncRNAs from our own experiments and from a published study including time-series transcriptome analyses of the testis and the pineal gland. Rhythmicity analysis of these data revealed approximately 700 rhythmically expressed lncRNAs from the pineal gland and the testis, and their GO, COG, and KEGG pathway functions were analyzed. Comparative and conservative analyses determined 14 rhythmically expressed lncRNAs shared between both the pineal gland and the testis, and 15 pineal gland lncRNAs as well as 3 testis lncRNAs conserved among zebrafish, mice, and humans. Further, we computationally analyzed the conserved lncRNA-encoded peptides, and revealed three pineal gland and one testis lncRNA-encoded peptides conserved among these three Citation: Mishra, S.K.; Liu, T.; Wang, species, which were further investigated for their three-dimensional (3D) structures and potential H.
    [Show full text]
  • Prediction of Novel Bioactive Micropeptides in the Immune System
    Prediction of novel bioactive micropeptides in the immune system Fengyuan Hu The Babraham Institute St Edmund’s College, University of Cambridge June 2020 Submitted for the degree of Doctor of Philosophy at the University of Cambridge Declaration of Originality This thesis is the result of my own work and includes nothing which is the outcome of work done in collaboration except as declared in the Preface and specified in the text. It is not substantially the same as any that I have submitted, or, is being concurrently submitted for a degree or diploma or other qualification at the University of Cambridge or any other University or similar institution except as declared in the Preface and specified in the text. I further state that no substantial part of my dissertation has already been submitted, or, is being concurrently submitted for any such degree, diploma or other qualification at the University of Cambridge or any other University or similar institution except as declared in the Preface and specified in the text. It does not exceed the prescribed word limit for the relevant Degree Committee. Fengyuan Hu 1 Table of Contents Acknowledgements ……...……………………………………………………………………...06 Abstract……...…………………………………………………………………………………..08 Abbreviation……………………………………………………………………………………..09 1 Introduction……………………...…………..10 1.1 Roles of bioactive peptides and small proteins in the immune system ....................................... 111 1.2 Small open reading frames (smORFs) and micropeptides ............................................................
    [Show full text]
  • A Novel Micropeptide Encoded by Y-Linked LINC00278 Links
    Author Manuscript Published OnlineFirst on March 13, 2020; DOI: 10.1158/0008-5472.CAN-19-3440 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 1 A Novel Micropeptide Encoded by Y-Linked LINC00278 Links 2 Cigarette Smoking and AR Signaling in Male Esophageal Squamous 3 Cell Carcinoma 4 Running title: Role of micropeptide encoded by lncRNA in male ESCC. 5 6 Siqi Wu 1*, Liyuan Zhang2*, Jieqiong Deng1, Binbin Guo1, Fang Li1, Yirong Wang1, Rui Wu1, 7 Shenghua Zhang1, Jiachun Lu3, Yifeng Zhou1† 8 *Siqi Wu and Liyuan Zhang contributed equally to this work. 9 10 Author affiliations 11 1Department of Genetics, Medical College of Soochow University, Suzhou 215123, China; 12 2Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow 13 University, San Xiang Road No. 1055, Suzhou 215004, China 14 3The Institute for Chemical Carcinogenesis, The First Affiliated Hospital, The School of Public 15 Health, Guangzhou Medical University, Guangzhou 510182, China 16 17 Correspondence to: †Dr. Yifeng Zhou, Medical College of Soochow University, Suzhou 215123, 18 China. Tel: 86-512-65884720; Fax: 86-512-65884720; E-mail: [email protected] 19 20 Competing interests None. 21 Keywords: lncRNAs, micropeptide, m6A, male ESCC, cigarette smoking 1 Downloaded from cancerres.aacrjournals.org on September 24, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on March 13, 2020; DOI: 10.1158/0008-5472.CAN-19-3440 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 22 ABSTRACT 23 Long non-coding RNAs (lncRNA) have been shown to play critical roles in many diseases, 24 including esophageal squamous cell carcinoma (ESCC).
    [Show full text]
  • A Summary of Micropeptide Encoding Genes
    e u p a o p e n p r o t e o m i c s 3 ( 2 0 1 4 ) 128–137 Available online at www.sciencedirect.com ScienceDirect jou rnal homepage: http://www.elsevier.com/locate/euprot Little things make big things happen: A summary of micropeptide encoding genes ∗ ∗ Jeroen Crappé , Wim Van Criekinge, Gerben Menschaert Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium a r t i c l e i n f o a b s t r a c t Article history: Classical bioactive peptides are cleaved from larger precursor proteins and are targeted Received 31 October 2013 toward the secretory pathway by means of an N-terminal signaling sequence. In contrast, Received in revised form micropeptides encoded from small open reading frames, lack such signaling sequence and 6 December 2013 are immediately released in the cytoplasm after translation. Over the past few years many Accepted 14 February 2014 such non-canonical genes (including open reading frames, ORFs smaller than 100 AAs) have been discovered and functionally characterized in different eukaryotic organisms. Keywords: Furthermore, in silico approaches enabled the prediction of the existence of many more Micropeptide putatively coding small ORFs in the genomes of Sacharomyces cerevisiae, Arabidopsis thaliana, sORF Drosophila melanogaster and Mus musculus. However, questions remain as to what the func- Ribosome profiling tional role of this new class of eukaryotic genes might be, and how widespread they are. In Peptidomics the future, approaches integrating in silico, conservation-based prediction and a combina- (l)ncRNA tion of genomic, proteomic and functional validation methods will prove to be indispensable Bioactive peptide to answer these open questions.
    [Show full text]