1
|
Palos K, Yu L, Railey CE, Nelson Dittrich AC, Nelson ADL. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. THE PLANT CELL 2023; 35:1762-1786. [PMID: 36738093 PMCID: PMC10226578 DOI: 10.1093/plcell/koad027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
Collapse
Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Li’ang Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Caylyn E Railey
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA
| | | | | |
Collapse
|
2
|
Meena SK, Heidecker M, Engelmann S, Jaber A, de Vries T, Triller S, Baumann-Kaschig K, Abel S, Behrens SE, Gago-Zachert S. Altered expression levels of long non-coding natural antisense transcripts overlapping the UGT73C6 gene affect rosette size in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:460-477. [PMID: 36495314 DOI: 10.1111/tpj.16058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Natural antisense long non-coding RNAs (lncNATs) are involved in the regulation of gene expression in plants, modulating different relevant developmental processes and responses to various stimuli. We have identified and characterized two lncNATs (NAT1UGT73C6 and NAT2UGT73C6 , collectively NATsUGT73C6 ) from Arabidopsis thaliana that are transcribed from a gene fully overlapping UGT73C6, a member of the UGT73C subfamily of genes encoding UDP-glycosyltransferases (UGTs). Expression of both NATsUGT73C6 is developmentally controlled and occurs independently of the transcription of UGT73C6 in cis. Downregulation of NATsUGT73C6 levels through artificial microRNAs results in a reduction of the rosette area, while constitutive overexpression of NAT1UGT73C6 or NAT2UGT73C6 leads to the opposite phenotype, an increase in rosette size. This activity of NATsUGT73C6 relies on its RNA sequence and, although modulation of UGT73C6 in cis cannot be excluded, the observed phenotypes are not a consequence of the regulation of UGT73C6 in trans. The NATsUGT73C6 levels were shown to affect cell proliferation and thus individual leaf size. Consistent with this concept, our data suggest that the NATsUGT73C6 influence the expression levels of key transcription factors involved in regulating leaf growth by modulating cell proliferation. These findings thus reveal an additional regulatory layer on the process of leaf growth. In this work, we characterized at the molecular level two long non-coding RNAs (NATsUGT73C6 ) that are transcribed in the opposite direction to UGT73C6, a gene encoding a glucosyltransferase involved in brassinosteroid homeostasis in A. thaliana. Our results indicate that NATsUGT73C6 expression influences leaf growth by acting in trans and by modulating the levels of transcription factors that are involved in the regulation of cell proliferation.
Collapse
Affiliation(s)
- Shiv Kumar Meena
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Michel Heidecker
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Susanne Engelmann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Ammar Jaber
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Tebbe de Vries
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Saskia Triller
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Katja Baumann-Kaschig
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
| | - Sven-Erik Behrens
- Section Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, D-06120, Germany
| | - Selma Gago-Zachert
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, D-06120, Germany
- Section Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, D-06120, Germany
| |
Collapse
|
3
|
Širvinskas D, Steponaitis G, Stakaitis R, Tamašauskas A, Vaitkienė P, Skiriutė D. Antisense lncRNA CHROMR is linked to glioma patient survival. Front Mol Biosci 2023; 10:1101953. [PMID: 36950523 PMCID: PMC10025505 DOI: 10.3389/fmolb.2023.1101953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
Background: Natural non-coding antisense transcripts (ncNATs) are long non-coding RNAs (lncRNA) transcribed from the opposite strand of a separate protein coding or non-coding gene. As such, ncNATs can increase overlapping mRNA (and the coded protein) levels by stabilizing mRNA, absorbing inhibitory miRNAs and protecting the mRNA from degradation, or conversely decrease mRNA (or protein) levels by directing the mRNA towards degradation or inhibiting protein translation. Recently, growing numbers of ncNATs were shown to be dysregulated in cancerous cells, however, actual impact of ncNATs on cancer progression remains largely unknown. We therefore investigated gene expression levels of natural antisense lncRNA CHROMR (Cholesterol Induced Regulator of Metabolism RNA) and its sense protein coding gene PRKRA (Protein Activator of Interferon Induced Protein Kinase EIF2AK2) in gliomas. Next, we checked CHROMR effect on the survival of glioma patients. Methods: We performed RNA-seq on post-surgical tumor samples from 26 glioma patients, and normal brain tissue. Gene expression in TPM values were extracted for CHROMR and PRKRA genes. These data were validated using the TCGA and GTEx gene expression databases. Results: The gene expression level of ncNAT lncRNA CHROMR in glioma tissue was significantly higher compared to healthy brain tissue, while the expression of its sense counterpart protein coding PRKRA mRNA did not differ between glioma and healthy samples. Survival analysis showed lower survival rates in patients with low mRNA PRKRA/lncRNA CHROMR gene expression ratio compared to high ratio showing a link between lncRNA CHROMR and glioma patient survival prognosis. Conclusion: Here we show that elevated levels of lncRNA CHROMR (i.e., low ratio of mRNA PRKRA/lncRNA CHROMR) is associated with poor prognosis for glioma patients.
Collapse
Affiliation(s)
- Dovydas Širvinskas
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Giedrius Steponaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rytis Stakaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Arimantas Tamašauskas
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Paulina Vaitkienė
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
- *Correspondence: Paulina Vaitkienė,
| | - Daina Skiriutė
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| |
Collapse
|
4
|
Santos F, Capela AM, Mateus F, Nóbrega-Pereira S, Bernardes de Jesus B. Non-coding antisense transcripts: fine regulation of gene expression in cancer. Comput Struct Biotechnol J 2022; 20:5652-5660. [PMID: 36284703 PMCID: PMC9579725 DOI: 10.1016/j.csbj.2022.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/14/2022] Open
Abstract
Natural antisense transcripts (NATs) are coding or non-coding RNA sequences transcribed on the opposite direction from the same genomic locus. NATs are widely distributed throughout the human genome and seem to play crucial roles in physiological and pathological processes, through newly described and targeted mechanisms. NATs represent the intricate complexity of the genome organization and constitute another layer of potential targets in disease. Here, we focus on the interesting and unique role of non-coding NATs in cancer, paying particular attention to those acting as miRNA sponges.
Collapse
Affiliation(s)
| | | | | | | | - Bruno Bernardes de Jesus
- Corresponding author at: Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| |
Collapse
|
5
|
Yang K, Niu Y, Cui Z, Jin L, Peng S, Dong Z. Long noncoding RNA TFAP2A-AS1 promotes oral squamous cell carcinoma cell growth and movement via competitively binding miR-1297 and regulating TFAP2A expression. Mol Carcinog 2022; 61:865-875. [PMID: 35730908 DOI: 10.1002/mc.23438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/23/2022] [Accepted: 06/02/2022] [Indexed: 01/17/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is an aggressive and common malignancy in the head and neck, characterized by poor prognosis and high incidence. This study aimed to investigate the role of long noncoding RNA TFAP2A-AS1 in OSCC. The competing endogenous RNA network of TFAP2A-AS1 was constructed by bioinformatics analysis. The expressions of miR-1297, TFAP2A-AS1, and TFAP2A were measured by quantitative reverse transcription-polymerase chain reaction. The correlations of TFAP2A-AS1, miR-1297, and TFAP2A with clinicopathological characteristics of OSCC were assessed. RNA immunoprecipitation and dual-luciferase reporter assay were used to identify the target of miR-1297. Cell proliferation was measured by colony formation assay and [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay. Transwell assay and wound healing assay were performed to assess cell movement. TFAP2A-AS1 and TFAP2A were upregulated in OSCC and their expression levels were positively correlated. The levels of TFAP2A-AS1, miR-1297, and TFAP2A were also associated with lymphatic metastasis and the tumor-node-metastasis (TNM) stage of OSCC patients. TFAP2A-AS1 acted as a miR-1297 sponge. OSCC cell growth and movement were inhibited by miR-1297. Changes in the miR-1297 expression abolished the effects of TFAP2A-AS1 on OSCC cells. Additionally, TFAP2A was a target of miR-1297. TFAP2A promoted OSCC cell growth and migration/invasion, indicating that TFAP2A mediated the effects of TFAP2A-AS1 and miR-1297. TFAP2A-AS1 exerts an oncogenic effect in OSCC via the TFAP2A-AS1/miR-1297/TFAP2A axis, which may provide new targets and strategies for OSCC treatments.
Collapse
Affiliation(s)
- Kaicheng Yang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Yunfeng Niu
- Department of Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Zifeng Cui
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Linyu Jin
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shixiong Peng
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Zhiming Dong
- Department of Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| |
Collapse
|
6
|
Matsushita M, Awazawa M, Kobayashi N, Ikushima YM, Soeda K, Tamura-Nakano M, Muratani M, Kobayashi K, Blüher M, Brüning JC, Ueki K. An antisense transcript transcribed from Irs2 locus contributes to the pathogenesis of hepatic steatosis in insulin resistance. Cell Chem Biol 2021; 29:680-689.e6. [PMID: 34986326 DOI: 10.1016/j.chembiol.2021.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022]
Abstract
During insulin resistance, lipid uptake by the liver is promoted by peroxisome proliferator-activated protein (PPAR) γ upregulation, leading to hepatic steatosis. Insulin, however, does not directly regulate adipogenic gene expression in liver, and the mechanisms for its upregulation in obesity remain unclear. Here, we show that the Irs2 locus, a critical regulator of insulin actions, encodes an antisense transcript, ASIrs2, whose expression increases in obesity or after refeeding in liver, reciprocal to that of Irs2. ASIrs2 regulates hepatic Pparg expression, and its suppression ameliorates steatosis in obese mice. The human ortholog AL162497.1, whose expression is correlated with that of hepatic PPARG and the severity of non-alcoholic steatohepatitis (NASH), shows genomic organization similar to that of ASIrs2. We also identified HARS2 as a potential binding protein for ASIrs2, functioning as a regulator of Pparg. Collectively, our data reveal a functional duality of the Irs2 gene locus, where reciprocal changes of Irs2 and ASIrs2 in obesity cause insulin resistance and steatosis.
Collapse
Affiliation(s)
- Maya Matsushita
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Motoharu Awazawa
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan.
| | - Naoki Kobayashi
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Yoshiko Matsumoto Ikushima
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Kotaro Soeda
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Miwa Tamura-Nakano
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Hojozaka 27, Myodaiji, Okazaki, Aichi 305-8575, Japan
| | - Matthias Blüher
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München, University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann Strasse 26, 50931 Cologne, Germany; National Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kohjiro Ueki
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan; Department of Molecular Diabetology, Graduate School of Medicine, The University of Tokyo, 3-7-1 Hongo, Bunkyo-Ku, Tokyo 113-8655, Japan.
| |
Collapse
|
7
|
Kakuk B, Tombácz D, Balázs Z, Moldován N, Csabai Z, Torma G, Megyeri K, Snyder M, Boldogkői Z. Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome. Sci Rep 2021; 11:14487. [PMID: 34262076 PMCID: PMC8280142 DOI: 10.1038/s41598-021-93593-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/28/2021] [Indexed: 02/08/2023] Open
Abstract
Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.
Collapse
Affiliation(s)
- Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
- MTA-SZTE Momentum GeMiNI Research Group, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, USA
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Klára Megyeri
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary.
| |
Collapse
|
8
|
Mosig RA, Kojima S. Timing without coding: How do long non-coding RNAs regulate circadian rhythms? Semin Cell Dev Biol 2021; 126:79-86. [PMID: 34116930 DOI: 10.1016/j.semcdb.2021.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and demonstrated that lncRNAs regulate core clock genes and the core clock machinery in mammals. In this review, we provide an overview of our current understanding of how lncRNAs regulate the circadian clock without coding a protein. We also offer additional insights into the challenges in understanding the functions of lncRNAs and other unresolved questions in the field. We do not cover other regulatory ncRNAs even though they also play important roles; readers are highly encouraged to refer to other excellent reviews on this topic.
Collapse
Affiliation(s)
- Rebecca A Mosig
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA.
| |
Collapse
|
9
|
Ghanbarian H, Aghamiri S, Eftekhary M, Wagner N, Wagner KD. Small Activating RNAs: Towards the Development of New Therapeutic Agents and Clinical Treatments. Cells 2021; 10:cells10030591. [PMID: 33800164 PMCID: PMC8001863 DOI: 10.3390/cells10030591] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
Small double-strand RNA (dsRNA) molecules can activate endogenous genes via an RNA-based promoter targeting mechanism. RNA activation (RNAa) is an evolutionarily conserved mechanism present in diverse eukaryotic organisms ranging from nematodes to humans. Small activating RNAs (saRNAs) involved in RNAa have been successfully used to activate gene expression in cultured cells, and thereby this emergent technique might allow us to develop various biotechnological applications, without the need to synthesize hazardous construct systems harboring exogenous DNA sequences. Accordingly, this thematic issue aims to provide insights into how RNAa cellular machinery can be harnessed to activate gene expression leading to a more effective clinical treatment of various diseases.
Collapse
MESH Headings
- Animals
- Brain/cytology
- Brain/growth & development
- Brain/metabolism
- Genetic Therapy/methods
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Muscle Development/genetics
- Muscular Atrophy, Spinal/genetics
- Muscular Atrophy, Spinal/metabolism
- Muscular Atrophy, Spinal/pathology
- Muscular Atrophy, Spinal/therapy
- Myocardium/cytology
- Myocardium/metabolism
- Myocytes, Cardiac/cytology
- Myocytes, Cardiac/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplasms/therapy
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Neurogenesis/genetics
- Neurons/cytology
- Neurons/metabolism
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Double-Stranded/therapeutic use
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Small Untranslated/therapeutic use
- Survival of Motor Neuron 1 Protein/genetics
- Survival of Motor Neuron 1 Protein/metabolism
Collapse
Affiliation(s)
- Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran 19857-17443, Iran;
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran;
| | - Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran;
| | - Mohamad Eftekhary
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran;
| | - Nicole Wagner
- Université Côte d’Azur, CNRS, INSERM, iBV, 06107 Nice, France
- Correspondence: (N.W.); (K.-D.W.); Tel.: +33-493-3776-65 (K.-D.W.)
| | - Kay-Dietrich Wagner
- Université Côte d’Azur, CNRS, INSERM, iBV, 06107 Nice, France
- Correspondence: (N.W.); (K.-D.W.); Tel.: +33-493-3776-65 (K.-D.W.)
| |
Collapse
|
10
|
Ali Hosseini Rad SM, Min Yi Tan G, Poudel A, He K, McLellan AD. Regulation of human Mcl-1 by a divergently-expressed antisense transcript. Gene 2020; 762:145016. [PMID: 32777522 DOI: 10.1016/j.gene.2020.145016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/21/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
Mcl-1 is a member of the Bcl-2 anti-apoptotic protein family with important roles in the development, lifespan and metabolism of lymphocytes, as well as oncogenesis. Mcl-1 displays the shortest half-life of all Bcl-2 family members, with miRNA interference and proteasomal degradation being major pathways for Mcl-1 downregulation. In this study, we have identified a previously undescribed control mechanism active at the RNA level. A divergently transcribed lncRNA LOC107985203 (named here mcl1-AS1) negatively modulated Mcl-1 expression resulting in downregulation of Mcl-1 at both mRNA and protein level in a time-dependent manner. Using reporter assays, we confirmed that the mcl1-AS1 lncRNA promoter was located within Mcl-1 coding region. We next placed mcl1-AS1 under tetracycline-inducible control and demonstrated decreased viability in HEK293 cells upon doxycycline induction. Inhibition of mcl1-AS1 with shRNA reversed drug sensitivity. Bioinformatics surveys predicted direct mcl1-AS1 lncRNA binding to Mcl-1 transcripts, suggesting its mechanism in Mcl-1 expression is at the transcriptional level, consistent with a common role for anti-sense transcripts. The identification of a bi-directional promoter and lncRNA controlling Mcl-1 expression will have implications for controlling Mcl-1 activity in cancer cells, or for the purpose of enhancing the lifespan and quality of anti-cancer T lymphocytes.
Collapse
Affiliation(s)
- S M Ali Hosseini Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand.
| | - Grace Min Yi Tan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand
| | - Aarati Poudel
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand
| | - Kevin He
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand
| | - Alexander D McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand.
| |
Collapse
|
11
|
Chen L, Bao Y, Jiang S, Zhong XB. The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases. Noncoding RNA 2020; 6:ncrna6020024. [PMID: 32599764 PMCID: PMC7345002 DOI: 10.3390/ncrna6020024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and HNF4α-AS1, which are antisense lncRNA genes located in the neighborhood regions of the transcription factor (TF) genes HNF1α and HNF4α, respectively. HNF1α-AS1 and HNF4α-AS1 have been reported to be involved in several important functions in human physiological activities and diseases. In the liver, HNF1α-AS1 and HNF4α-AS1 regulate the expression and function of several drug-metabolizing cytochrome P450 (P450) enzymes, which also further impact P450-mediated drug metabolism and drug toxicity. In addition, HNF1α-AS1 and HNF4α-AS1 also play important roles in the tumorigenesis, progression, invasion, and treatment outcome of several cancers. Through interacting with different molecules, including miRNAs and proteins, HNF1α-AS1 and HNF4α-AS1 can regulate their target genes in several different mechanisms including miRNA sponge, decoy, or scaffold. The purpose of the current review is to summarize the identified functions and mechanisms of HNF1α-AS1 and HNF4α-AS1 and to discuss the future directions of research of these two lncRNAs.
Collapse
Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Suzhen Jiang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, China
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- Correspondence: ; Tel.: +01-860-486-3697
| |
Collapse
|
12
|
Kim S, Shin W, Lee YM, Mun S, Han K. Differential expressions of L1-chimeric transcripts in normal and matched-cancer tissues. Anal Biochem 2020; 600:113769. [PMID: 32430276 DOI: 10.1016/j.ab.2020.113769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/25/2020] [Accepted: 05/05/2020] [Indexed: 01/20/2023]
Abstract
L1s are a cis-regulatory elements and contain bidirectional internal promoters within the 5' untranslated region (UTR). L1s provide bidirectional promoters that generate alternative transcripts and affect differential expressions in the human genome. In particular, L1 antisense promoters (L1ASPs) could produce aberrant transcripts in cancer tissues compared to normal tissues. In this study, we identified the L1-chimeric transcripts derived from L1ASPs and analyzed relative expression of L1-chimeric transcripts between normal and matched-cancer tissues. First, we collected 425 L1-chimeric transcripts by referring to previous studies. Through the manual inspection, we identified 144 L1-chimeric transcripts derived from 44 L1 antisense promoters, suggesting that the antisense promoter acted as an alternative promoter. We analyzed relative gene expression levels of 16 L1-chimeric transcripts between matched cancer-normal tissue pair (lung, liver, gastric, kidney, thyroid, breast, ovary, uterus, and prostate) using real-time quantitative PCR (RT-qPCR) and investigated putative transcription factor binding motifs to determine activity of L1ASPs. Taken together, we propose that L1ASPs could contribute to the differential gene expression between normal and cancer tissues.
Collapse
Affiliation(s)
- Songmi Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea
| | - Yong-Moon Lee
- Department of Pathology, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
| |
Collapse
|
13
|
Functions and mechanism of noncoding RNA in the somatic cells of the testis. ZYGOTE 2019; 28:87-92. [PMID: 31787116 DOI: 10.1017/s0967199419000650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ncRNAs are involved in numerous biological processes by regulating gene expression and cell stability. Studies have shown that ncRNAs also contribute to spermatogenesis. Leydig cells (LCs) and Sertoli cells (SCs) are somatic cells of the testis that support spermatogenesis and are vital to male fertility. In this review, we summarized the findings from studies on ncRNAs in SCs and LCs. In SCs, ncRNAs play key roles in phagocytosis, immunoprotection and development of SCs. In LCs, ncRNAs are involved in steroidogenesis, in particular production of testosterone as well as development of LCs. Here, we discuss the possible target genes and functions of ncRNAs in both types of cells. These ncRNAs regulate the expression of target genes or mRNA coding sequence regions, resulting in a chain reaction that influences cell function. In addition, microRNAs, lncRNAs, piRNA-like RNAs (pilRNAs) and natural antisense transcripts (NATs) are discussed in this review. In summary, we suggest that these ncRNAs might act in coordination to control spermatogenesis and maintain the environmental homeostasis of the testis.
Collapse
|
14
|
Eftekhary M, Mohammadi-Yeganeh S, Bolandi Z, Hashemi SM, Mokhberian N, Sharifi K, Ghanbarian H. A novel natural antisense transcript at human SOX9 locus is down-regulated in cancer and stem cells. Biotechnol Lett 2019; 42:329-339. [DOI: 10.1007/s10529-019-02774-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/24/2019] [Indexed: 12/12/2022]
|
15
|
Mourão K, Schurch NJ, Lucoszek R, Froussios K, MacKinnon K, Duc C, Simpson G, Barton GJ. Detection and mitigation of spurious antisense expression with RoSA. F1000Res 2019. [DOI: 10.12688/f1000research.18952.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antisense transcription is known to have a range of impacts on sense gene expression, including (but not limited to) impeding transcription initiation, disrupting post-transcriptional processes, and enhancing, slowing, or even preventing transcription of the sense gene. Strand-specific RNA-Seq protocols preserve the strand information of the original RNA in the data, and so can be used to identify where antisense transcription may be implicated in regulating gene expression. However, our analysis of 199 strand-specific RNA-Seq experiments reveals that spurious antisense reads are often present in these datasets at levels greater than 1% of sense gene expression levels. Furthermore, these levels can vary substantially even between replicates in the same experiment, potentially disrupting any downstream analysis, if the incorrectly assigned antisense counts dominate the set of genes with high antisense transcription levels. Currently, no tools exist to detect or correct for this spurious antisense signal. Our tool, RoSA (Removal of Spurious Antisense), detects the presence of high levels of spurious antisense read alignments in strand-specific RNA-Seq datasets. It uses incorrectly spliced reads on the antisense strand and/or ERCC spikeins (if present in the data) to calculate both global and gene-specific antisense correction factors. We demonstrate the utility of our tool to filter out spurious antisense transcript counts in an Arabidopsis thaliana RNA-Seq experiment. Availability: RoSA is open source software available under the GPL licence via the Barton Group GitHub page https://github.com/bartongroup.
Collapse
|
16
|
Nonogaki H. Seed germination and dormancy: The classic story, new puzzles, and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:541-563. [PMID: 30565406 DOI: 10.1111/jipb.12762] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.
Collapse
|
17
|
Lin S, Zhang Z, Xie T, Hu B, Ruan Z, Zhang L, Li C, Li C, Luo W, Nie Q, Zhang X. Identification of a novel antisense RNA that regulates growth hormone receptor expression in chickens. RNA Biol 2019; 16:626-638. [PMID: 30764709 PMCID: PMC6546403 DOI: 10.1080/15476286.2019.1572440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identified a novel antisense transcript in the chicken, designated GHR-AS-EST, transcribed from the growth hormone receptor (GHR) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. GHR-AS-EST is predominantly expressed in the chicken liver and muscle tissues. GHR-AS-EST sequence conservation among vertebrates is weak. GHR-AS-EST forms an RNA-RNA duplex with GHBP to increase its stability, and regulates the expression of GHR sense transcripts at both the mRNA and protein levels. Further, GHR-AS-EST promotes cell proliferation by stimulating the expression of signaling factors in the JAK2/STAT pathway, and contributes to fat deposition via downregulating the expression of signaling factors in the JAK2/SOCS pathway in LMH hepatocellular carcinoma cells. We expect that the discovery of a NAT for a regulatory gene associated with cell proliferation and lipolysis will further our understanding of the molecular regulation of both muscle development and fat deposition.
Collapse
Affiliation(s)
- Shudai Lin
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China.,b Animal Genomics and Improvement Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA.,c Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Zihao Zhang
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Tingting Xie
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Bowen Hu
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Zhuohao Ruan
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Li Zhang
- d Agricultural College , Guangdong Ocean University , Zhanjiang , P.R. China
| | - Congjun Li
- b Animal Genomics and Improvement Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Charles Li
- c Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Wen Luo
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Qinghua Nie
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Xiquan Zhang
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| |
Collapse
|
18
|
Latgé G, Poulet C, Bours V, Josse C, Jerusalem G. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers. Int J Mol Sci 2018; 19:ijms19010123. [PMID: 29301303 PMCID: PMC5796072 DOI: 10.3390/ijms19010123] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.
Collapse
Affiliation(s)
- Guillaume Latgé
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Christophe Poulet
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Center of Genetics, University Hospital (CHU), 4500 Liège, Belgium.
| | - Claire Josse
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Guy Jerusalem
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| |
Collapse
|
19
|
Yatusevich R, Fedak H, Ciesielski A, Krzyczmonik K, Kulik A, Dobrowolska G, Swiezewski S. Antisense transcription represses Arabidopsis seed dormancy QTL DOG1 to regulate drought tolerance. EMBO Rep 2017; 18:2186-2196. [PMID: 29030481 PMCID: PMC5709759 DOI: 10.15252/embr.201744862] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022] Open
Abstract
Plants have developed multiple strategies to sense the external environment and to adapt growth accordingly. Delay of germination 1 (DOG1) is a major quantitative trait locus (QTL) for seed dormancy strength in Arabidopsis thaliana that is reported to be expressed exclusively in seeds. DOG1 is extensively regulated, with an antisense transcript (asDOG1) suppressing its expression in seeds. Here, we show that asDOG1 shows high levels in mature plants where it suppresses DOG1 expression under standard growth conditions. Suppression is released by shutting down antisense transcription, which is induced by the plant hormone abscisic acid (ABA) and drought. Loss of asDOG1 results in constitutive high-level DOG1 expression, conferring increased drought tolerance, while inactivation of DOG1 causes enhanced drought sensitivity. The unexpected role of DOG1 in environmental adaptation of mature plants is separate from its function in seed dormancy regulation. The requirement of asDOG1 to respond to ABA and drought demonstrates that antisense transcription is important for sensing and responding to environmental changes in plants.
Collapse
Affiliation(s)
- Ruslan Yatusevich
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Halina Fedak
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | | | - Katarzyna Krzyczmonik
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Anna Kulik
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Grazyna Dobrowolska
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Szymon Swiezewski
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| |
Collapse
|
20
|
Huang X, Chen K. Differential Expression of Long Noncoding RNAs in Normal and Inflamed Human Dental Pulp. J Endod 2017; 44:62-72. [PMID: 29079059 DOI: 10.1016/j.joen.2017.08.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 08/08/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Dental pulp inflammation is an excellent model for the interaction between tissue inflammation and regenerative processes. It is worthwhile to better understand molecular signaling of repair and regeneration in inflammatory processes. Emerging evidence suggests that long noncoding RNA (lncRNA) participates in immune system inflammatory processes. Here we investigate the expression of lncRNAs in pulpitis, the inflammation of dental pulp tissue, and identify lncRNAs that possibly participate in inflammation responses and odontogenesis. METHODS Integrated comparative lncRNA microarray was used to examine lncRNA and mRNA expression between inflamed and normal human pulp tissue. The differential expression of lncRNAs and mRNAs was then validated by quantitative real-time polymerase chain reaction. A bioinformatics analysis was performed to predict the function of differentially expressed lncRNAs and mRNAs. RESULTS Our data indicated 752 lncRNAs were significantly differentially expressed (fold change > 2.0; P < .05) in inflamed pulp tissues compared with normal pulp tissues, including 338 upregulated and 414 downregulated lncRNAs. Among the 646 differentially expressed mRNAs (fold change > 2.0; P < .05), 460 were upregulated, and 186 were downregulated. The differentially downregulated genes are enriched for gene ontology terms related to odontogenesis and cell development in biological processes, whereas the differentially upregulated genes are related to immune and inflammation processes. CONCLUSIONS LncRNAs are differentially expressed in inflamed human pulp tissue compared with normal pulp tissue, indicating that lncRNAs may play key roles in pulpitis pathogenesis and development.
Collapse
Affiliation(s)
- Xin Huang
- Department of Stomatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ke Chen
- Department of Stomatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
| |
Collapse
|
21
|
Chicken CCDC152 shares an NFYB-regulated bidirectional promoter with a growth hormone receptor antisense transcript and inhibits cells proliferation and migration. Oncotarget 2017; 8:84039-84053. [PMID: 29137403 PMCID: PMC5663575 DOI: 10.18632/oncotarget.21091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 09/04/2017] [Indexed: 12/11/2022] Open
Abstract
The chicken coiled-coil domain-containing protein 152 (CCDC152) recently has been identified as a novel one implicated in cell cycle regulation, cellular proliferation and migration by us. Here we demonstrate that CCDC152 is oriented in a head-to-head configuration with the antisense transcript of growth hormone receptor (GHR) gene. Through serial luciferase reporter assays, we firstly identified a minimal 102 bp intergenic region as a core bidirectional promoter to drive basal transcription in divergent orientations. And site mutation and transient transfected assays showed that nuclear transcription factor Y subunit beta (NFYB) could bind to the CCAAT box and directly transactivate this bidirectional promoter. SiRNA-mediated NFYB depletion could significantly down-regulate the expression of both GHR-AS-I6 and CCDC152. Additionally, the expression of GHR-AS-I6 was significantly up-regulated after CCDC152 overexpression. Overexpression of CCDC152 remarkably reduced cell proliferation and migration through JAK2/STAT signaling pathway. Thus, the GHR-AS-I6-CCDC152 bidirectional transcription unit, as a novel direct target of NFYB, is possibly essential for the accelerated proliferation and motility of different cells.
Collapse
|
22
|
Zelinger L, Karakülah G, Chaitankar V, Kim JW, Yang HJ, Brooks MJ, Swaroop A. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Invest Ophthalmol Vis Sci 2017; 58:4422-4435. [PMID: 28863214 PMCID: PMC5584472 DOI: 10.1167/iovs.17-21805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023] Open
Abstract
Purpose Transcriptome analysis by next generation sequencing allows qualitative and quantitative profiling of expression patterns associated with development and disease. However, most transcribed sequences do not encode proteins, and little is known about the functional relevance of noncoding (nc) transcriptome in neuronal subtypes. The goal of this study was to perform a comprehensive analysis of long noncoding (lncRNAs) and antisense (asRNAs) RNAs expressed in mouse retinal photoreceptors. Methods Transcriptomic profiles were generated at six developmental time points from flow-sorted Nrlp-GFP (rods) and Nrlp-GFP;Nrl-/- (S-cone like) mouse photoreceptors. Bioinformatic analysis was performed to identify novel noncoding transcripts and assess their regulation by rod differentiation factor neural retina leucine zipper (NRL). In situ hybridization (ISH) was used for validation and cellular localization. Results NcRNA profiles demonstrated dynamic yet specific expression signature and coexpression clusters during rod development. In addition to currently annotated 586 lncRNAs and 454 asRNAs, we identified 1037 lncRNAs and 243 asRNAs by de novo assembly. Of these, 119 lncRNAs showed altered expression in the absence of NRL and included NRL binding sites in their promoter/enhancer regions. ISH studies validated the expression of 24 lncRNAs (including 12 previously unannotated) and 4 asRNAs in photoreceptors. Coexpression analysis demonstrated 63 functional modules and 209 significant antisense-gene correlations, allowing us to predict possible role of these lncRNAs in rods. Conclusions Our studies reveal coregulation of coding and noncoding transcripts in rod photoreceptors by NRL and establish the framework for deciphering the function of ncRNAs during retinal development.
Collapse
Affiliation(s)
- Lina Zelinger
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Gökhan Karakülah
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Vijender Chaitankar
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Matthew J. Brooks
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| |
Collapse
|
23
|
Krzyczmonik K, Wroblewska-Swiniarska A, Swiezewski S. Developmental transitions in Arabidopsis are regulated by antisense RNAs resulting from bidirectionally transcribed genes. RNA Biol 2017; 14:838-842. [PMID: 28513325 DOI: 10.1080/15476286.2017.1327112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Transcription terminators are DNA elements located at the 3' end of genes that ensure efficient cleavage of nascent RNA generating the 3' end of mRNA, as well as facilitating disengagement of elongating DNA-dependent RNA polymerase II. Surprisingly, terminators are also a potent source of antisense transcription. We have recently described an Arabidopsis antisense transcript originating from the 3' end of a master regulator of Arabidopsis thaliana seed dormancy DOG1. In this review, we discuss the broader implications of our discovery in light of recent developments in yeast and Arabidopsis. We show that, surprisingly, the key features of terminators that give rise to antisense transcription are preserved between Arabidopsis and yeast, suggesting a conserved mechanism. We also compare our discovery to known antisense-based regulatory mechanisms, highlighting the link between antisense-based gene expression regulation and major developmental transitions in plants.
Collapse
Affiliation(s)
| | | | - Szymon Swiezewski
- a Department of Protein Biosynthesis , Institute of Biochemistry and Biophysics , Warsaw , Poland
| |
Collapse
|
24
|
Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Sakamoto T, Kurata T, Yamamoto YY. Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:587-605. [PMID: 28214361 DOI: 10.1111/tpj.13511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.
Collapse
Affiliation(s)
- Mutsutomo Tokizawa
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Kazutaka Kusunoki
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Hiroyuki Koyama
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yutaka Suzuki
- Institute of Medical Science, University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Yoshiharu Y Yamamoto
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- JST ALCA, Tokyo, Japan
| |
Collapse
|
25
|
Manghera M, Magnusson A, Douville RN. The sense behind retroviral anti-sense transcription. Virol J 2017; 14:9. [PMID: 28088235 PMCID: PMC5237517 DOI: 10.1186/s12985-016-0667-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 12/15/2022] Open
Abstract
Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.
Collapse
Affiliation(s)
- Mamneet Manghera
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Alycia Magnusson
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Renée N Douville
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada.
| |
Collapse
|