Non-Coding Rnas As Regulators in Epigenetics (Review)
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Comparison of the Effects on Mrna and Mirna Stability Arian Aryani and Bernd Denecke*
Aryani and Denecke BMC Research Notes (2015) 8:164 DOI 10.1186/s13104-015-1114-z RESEARCH ARTICLE Open Access In vitro application of ribonucleases: comparison of the effects on mRNA and miRNA stability Arian Aryani and Bernd Denecke* Abstract Background: MicroRNA has become important in a wide range of research interests. Due to the increasing number of known microRNAs, these molecules are likely to be increasingly seen as a new class of biomarkers. This is driven by the fact that microRNAs are relatively stable when circulating in the plasma. Despite extensive analysis of mechanisms involved in microRNA processing, relatively little is known about the in vitro decay of microRNAs under defined conditions or about the relative stabilities of mRNAs and microRNAs. Methods: In this in vitro study, equal amounts of total RNA of identical RNA pools were treated with different ribonucleases under defined conditions. Degradation of total RNA was assessed using microfluidic analysis mainly based on ribosomal RNA. To evaluate the influence of the specific RNases on the different classes of RNA (ribosomal RNA, mRNA, miRNA) ribosomal RNA as well as a pattern of specific mRNAs and miRNAs was quantified using RT-qPCR assays. By comparison to the untreated control sample the ribonuclease-specific degradation grade depending on the RNA class was determined. Results: In the present in vitro study we have investigated the stabilities of mRNA and microRNA with respect to the influence of ribonucleases used in laboratory practice. Total RNA was treated with specific ribonucleases and the decay of different kinds of RNA was analysed by RT-qPCR and miniaturized gel electrophoresis. -
Chapter 14: Functional Genomics Learning Objectives
Chapter 14: Functional Genomics Learning objectives Upon reading this chapter, you should be able to: ■ define functional genomics; ■ describe the key features of eight model organisms; ■ explain techniques of forward and reverse genetics; ■ discuss the relation between the central dogma and functional genomics; and ■ describe proteomics-based approaches to functional genomics. Outline : Functional genomics Introduction Relation between genotype and phenotype Eight model organisms E. coli; yeast; Arabidopsis; C. elegans; Drosophila; zebrafish; mouse; human Functional genomics using reverse and forward genetics Reverse genetics: mouse knockouts; yeast; gene trapping; insertional mutatgenesis; gene silencing Forward genetics: chemical mutagenesis Functional genomics and the central dogma Approaches to function; Functional genomics and DNA; …and RNA; …and protein Proteomic approaches to functional genomics CASP; protein-protein interactions; protein networks Perspective Albert Blakeslee (1874–1954) studied the effect of altered chromosome numbers on the phenotype of the jimson-weed Datura stramonium, a flowering plant. Introduction: Functional genomics Functional genomics is the genome-wide study of the function of DNA (including both genes and non-genic regions), as well as RNA and proteins encoded by DNA. The term “functional genomics” may apply to • the genome, transcriptome, or proteome • the use of high-throughput screens • the perturbation of gene function • the complex relationship of genotype and phenotype Functional genomics approaches to high throughput analyses Relationship between genotype and phenotype The genotype of an individual consists of the DNA that comprises the organism. The phenotype is the outward manifestation in terms of properties such as size, shape, movement, and physiology. We can consider the phenotype of a cell (e.g., a precursor cell may develop into a brain cell or liver cell) or the phenotype of an organism (e.g., a person may have a disease phenotype such as sickle‐cell anemia). -
Exploring the Structure of Long Non-Coding Rnas, J
IMF YJMBI-63988; No. of pages: 15; 4C: 3, 4, 7, 8, 10 1 2 Rise of the RNA Machines: Exploring the Structure of 3 Long Non-Coding RNAs 4 Irina V. Novikova, Scott P. Hennelly, Chang-Shung Tung and Karissa Y. Sanbonmatsu Q15 6 Los Alamos National Laboratory, Los Alamos, NM 87545, USA 7 Correspondence to Karissa Y. Sanbonmatsu: [email protected] 8 http://dx.doi.org/10.1016/j.jmb.2013.02.030 9 Edited by A. Pyle 1011 12 Abstract 13 Novel, profound and unexpected roles of long non-coding RNAs (lncRNAs) are emerging in critical aspects of 14 gene regulation. Thousands of lncRNAs have been recently discovered in a wide range of mammalian 15 systems, related to development, epigenetics, cancer, brain function and hereditary disease. The structural 16 biology of these lncRNAs presents a brave new RNA world, which may contain a diverse zoo of new 17 architectures and mechanisms. While structural studies of lncRNAs are in their infancy, we describe existing 18 structural data for lncRNAs, as well as crystallographic studies of other RNA machines and their implications 19 for lncRNAs. We also discuss the importance of dynamics in RNA machine mechanism. Determining 20 commonalities between lncRNA systems will help elucidate the evolution and mechanistic role of lncRNAs in 21 disease, creating a structural framework necessary to pursue lncRNA-based therapeutics. 22 © 2013 Published by Elsevier Ltd. 24 23 25 Introduction rather than the exception in the case of eukaryotic 50 organisms. 51 26 RNA is primarily known as an intermediary in gene LncRNAs are defined by the following: (i) lack of 52 11 27 expression between DNA and proteins. -
Interplay Between Epigenetics and Metabolism in Oncogenesis: Mechanisms and Therapeutic Approaches
OPEN Oncogene (2017) 36, 3359–3374 www.nature.com/onc REVIEW Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches CC Wong1, Y Qian2,3 and J Yu1 Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer. Oncogene (2017) 36, 3359–3374; doi:10.1038/onc.2016.485; published online 16 January 2017 INTRODUCTION metabolic genes have also been identified as driver genes It has been appreciated since the early days of cancer research mutated in some cancers, such as isocitrate dehydrogenase 1 16 17 that the metabolic profiles of tumor cells differ significantly from and 2 (IDH1/2) in gliomas and acute myeloid leukemia (AML), 18 normal cells. Cancer cells have high metabolic demands and they succinate dehydrogenase (SDH) in paragangliomas and fuma- utilize nutrients with an altered metabolic program to support rate hydratase (FH) in hereditary leiomyomatosis and renal cell 19 their high proliferative rates and adapt to the hostile tumor cancer (HLRCC). -
RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases
G C A T T A C G G C A T genes Review RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases Amber Willbanks, Shaun Wood and Jason X. Cheng * Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL 60637, USA; [email protected] (A.W.); [email protected] (S.W.) * Correspondence: [email protected] Abstract: Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Keywords: 5’ cap (5’ cap); 7-methylguanosine (m7G); R-loops; N6-methyladenosine (m6A); RNA editing; A-to-I; C-to-U; 2’-O-methylation (Nm); 5-methylcytosine (m5C); NOL1/NOP2/sun domain Citation: Willbanks, A.; Wood, S.; (NSUN); MYC Cheng, J.X. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes 2021, 12, 627. -
SARS-Cov-2 RNA, Qualitative Real-Time RT-PCR (Test Code 39433)
SARS-CoV-2 RNA, Qualitative Real-Time RT-PCR (Test Code 39433) Package Insert For Emergency Use Only For In-vitro Diagnostic Use - Rx Only Intended Use The Quest Diagnostics SARS-CoV-2 RNA, Qualitative Real-Time RT-PCR (“Quest SARS-CoV-2 rRT-PCR”) is a real-time RT-PCR test intended for the qualitative detection of nucleic acid from the SARS-CoV-2 in upper and lower respiratory specimens (such as nasopharyngeal or oropharyngeal swabs, sputum, tracheal aspirates, and bronchoalveolar lavage) collected from individuals suspected of COVID-19 by their healthcare provider. This test is also for use with nasal swab specimens that are self-collected at home or in a healthcare setting by individuals using an authorized home-collection kit when determined to be appropriate by a healthcare provider. This test is for the qualitative detection of nucleic acid from the SARS-CoV-2 in pooled samples containing up to four of the individual upper respiratory swab specimens (nasopharyngeal, mid-turbinate, anterior nares or oropharyngeal swabs) that were collected in individual vials containing transport media from individuals suspected of COVID-19 by their healthcare provider. Negative results from pooled testing should not be treated as definitive. If patient’s clinical signs and symptoms are inconsistent with a negative result or results are necessary for patient management, then the patient should be considered for individual testing. Specimens included in pools with a positive, inconclusive, or invalid result must be tested individually prior to reporting a result. Specimens with low viral loads may not be detected in sample pools due to the decreased sensitivity of pooled testing. -
RNA Interference with Sirna
CANCER GENOMICS & PROTEOMICS 3: 127-136 (2006) Review RNA Interference with siRNA HELENA JOYCE*, ISABELLA BRAY* and MARTIN CLYNES National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland Abstract. Over the last decade, RNA interference has RNAs (13). Twenty-one different gene products with emerged as an effective mechanism for silencing gene different functions and subcellular localizations were expression. This ancient cellular antiviral response can be used studied. Knockdown experiments, monitored by to allow specific inhibition of the function of any chosen target immunofluorescence and immunoblotting, showed that even gene, including those involved in diseases such as cancer, major cellular proteins such as actin and vimentin could be AIDS and hepatitis. It has become an invaluable research tool silenced efficiently. Previous work had discovered that these to aid in the identification of novel genes involved in disease 22-nucleotide sequences served as guide sequences that processes. It has advanced from the use of synthetic RNA for instruct a multicomponent nuclease, RNA-induced silencing the endogenous production of small hairpin RNA by plasmid complex (RISC), to destroy specific messenger RNAs (7). and viral vectors, and from transient inhibition in vitro to It was then found that, in response to dsRNA, cells trigger longer-lasting effects in vivo. However, as with antisense and a two-step reaction. In the first step, long dsRNA is ribozymes, the efficient delivery of siRNA into cells is currently processed by a ribonuclease (RNase) III enzyme, called the limiting factor to successful gene expression inhibition in Dicer, into small interfering RNAs (siRNAs); these vivo. This review gives an overview of the mechanism of action subsequently serve as the sequence determinants of the of siRNA and its use in cancer research. -
Andrey L. Karamyshev
CURRICULUM VITAE Andrey L. Karamyshev Assistant Professor Department of Cell Biology and Biochemistry! Texas Tech University Health Sciences Center! 3601 4th Street, Mail Stop 6540! Lubbock, TX 79430 Phone: (806) 743-4102 Fax: (806) 743-2990 e-mail: [email protected] EDUCATION: Postdoctoral Studies: Department of Tumor Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan (Advisor: Dr. Yoshikazu Nakamura). Department of Medical Biochemistry and Genetics, College of Medicine, Texas A&M University, College Station, TX (Advisor: Dr. Arthur E. Johnson). Ph.D. in Biochemistry, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. M.S., Biology, Kuban State University, Krasnodar, Russia. FIELDS OF SPECIALIZATION: Biochemistry, Molecular and Cellular Biology. RESEARCH INTERESTS Molecular mechanisms of human diseases. Post-transcriptional regulation of gene expression. Gene silencing and translational repression. mRNA and protein quality control. RNA stability and degradation. siRNAs/miRNAs. Prolactin, CFTR, secretory and membrane proteins. Protein translation, folding and transport. Protein-protein interactions. SCIENTIFIC PUBLICATIONS (see list below) 31 publications (total), including 25 full-length peer-reviewed papers in scientific journals, 5 articles in the Encyclopedia of Molecular Biology (Publisher: John Wiley & Sons, Inc., N.Y.), and chapter in a book. PRESENTATIONS (90 total, see lists below) Results were presented at various international and national meetings, conferences and symposia (58 presentations), as well as during invited or selected talks (32 talks) at different universities and meetings around the world. Andrey L. Karamyshev, Ph.D. RESEARCH EXPERIENCE AND POSITIONS 2016-present Assistant Professor (Tenure track), Department of Cell Biology and Biochemistry!, Texas Tech University Health Sciences Center!, Lubbock, TX. 2009-2016 Assistant Professor (Research track), Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX. -
RNA Interference in the Nucleus: Roles for Small Rnas in Transcription, Epigenetics and Beyond
REVIEWS NON-CODING RNA RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond Stephane E. Castel1 and Robert A. Martienssen1,2 Abstract | A growing number of functions are emerging for RNA interference (RNAi) in the nucleus, in addition to well-characterized roles in post-transcriptional gene silencing in the cytoplasm. Epigenetic modifications directed by small RNAs have been shown to cause transcriptional repression in plants, fungi and animals. Additionally, increasing evidence indicates that RNAi regulates transcription through interaction with transcriptional machinery. Nuclear small RNAs include small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) and are implicated in nuclear processes such as transposon regulation, heterochromatin formation, developmental gene regulation and genome stability. RNA interference Since the discovery that double-stranded RNAs (dsRNAs) have revealed a conserved nuclear role for RNAi in (RNAi). Silencing at both the can robustly silence genes in Caenorhabditis elegans and transcriptional gene silencing (TGS). Because it occurs post-transcriptional and plants, RNA interference (RNAi) has become a new para- in the germ line, TGS can lead to transgenerational transcriptional levels that is digm for understanding gene regulation. The mecha- inheritance in the absence of the initiating RNA, but directed by small RNA molecules. nism is well-conserved across model organisms and it is dependent on endogenously produced small RNA. uses short antisense RNA to inhibit translation or to Such epigenetic inheritance is familiar in plants but has Post-transcriptional gene degrade cytoplasmic mRNA by post-transcriptional gene only recently been described in metazoans. silencing silencing (PTGS). PTGS protects against viral infection, In this Review, we cover the broad range of nuclear (PTGS). -
Zinc Fingers and a Green Thumb: Manipulating Gene Expression in Plants Segal, Stege and Barbas 165
163 Zinc fingers and a green thumb: manipulating gene expression in plants David J Segaly, Justin T Stegez and Carlos F Barbas IIIç Artificial transcription factors can be rapidly constructed A variety of techniques have been developed to manip- from predefined zinc-finger modules to regulate virtually any ulate gene expression in plants. Increased expression of gene. Stable, heritable up- and downregulation of endogenous genes is most commonly achieved through endogenous genes has been demonstrated in transgenic transgene overexpression [1]. The introduction of tissue- plants. These advances promise new approaches for creating specific and inducible promoters has improved the utility functional knockouts and conditional overexpression, and of this approach, and efficient and robust plant transforma- for other gene discovery and manipulation applications in tion techniques have made the construction of transgenes plants. a relatively routine task. However, variable expression and co-suppression of transgenes often complicate this process. Addresses Furthermore, transgenes cannot accommodate alternative ÃThe Skaggs Institute for Chemical Biology and the Department of splicing, which may be important for the appropriate Molecular Biology, The Scripps Research Institute, La Jolla, function of some transgenes [2]. California 92037, USA yDepartment of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, USA Reducing or eliminating the expression of a gene in plants zDiversa Corporation, San Diego, California 92121, USA is not as simple as overexpressing a gene. Gene disruption §The Scripps Research Institute, BCC-550, North Torrey Pines Road, by homologous recombination, tDNA insertions and che- La Jolla, California 92037, USA mical mutagenesis has been used successfully, but these e-mail: [email protected] Correspondence: Carlos F Barbas III approaches are inefficient and time-consuming technolo- gies. -
Switch from Translation Initiation to Elongation Needs Not4 and Not5 Collaboration
bioRxiv preprint doi: https://doi.org/10.1101/850859; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Switch from translation initiation to elongation needs Not4 and Not5 collaboration George E Allen1°, Olesya O Panasenko1°, Zoltan Villanyi1,&, Marina Zagatti1, Benjamin Weiss1, 2 2 1* 5 Christine Polte , Zoya Ignatova , Martine A Collart 1Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Switzerland 2Biochemistry and Molecular Biology, University of Hamburg, Germany °Equally contributing first authors 10 *Correspondence to: [email protected] &Current Address: Dept of Biochemistry and Molecular Biology, University of Szeged Abstract: Not4 and Not5 are crucial components of the Ccr4-Not complex with pivotal functions in mRNA metabolism. Both associate with ribosomes but mechanistic insights on their 15 function remain elusive. Here we determine that Not5 and Not4 synchronously impact translation initiation and Not5 alone alters translation elongation. Deletion of Not5 causes elongation defects in a codon-dependent fashion, increasing and decreasing the ribosome dwelling occupancy at minor and major codons, respectively. This larger difference in codons’ translation velocities alters translation globally and enables kinetically unfavorable processes 20 such as nascent chain deubiquitination to take place. In turn, this leads to abortive translation and favors protein aggregation. These findings highlight the global impact of Not4 and Not5 in controlling the speed of mRNA translation and transition from initiation to elongation. Summary: Not4 and Not5 regulate translation synchronously but distinguishably, facilitating 25 smooth transition from initiation to elongation Results and discussion The Ccr4-Not complex is a global regulator of mRNA metabolism in eukaryotic cells (for review see (1)). -
REVIEW Chromatin Modifications and DNA Double-Strand Breaks
Leukemia (2007) 21, 195–200 & 2007 Nature Publishing Group All rights reserved 0887-6924/07 $30.00 www.nature.com/leu REVIEW Chromatin modifications and DNA double-strand breaks: the current state of play TC Karagiannis1,2 and A El-Osta3 1Molecular Radiation Biology, Trescowthick Research Laboratories, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; 2Department of Pathology, The University of Melbourne, Parkville, Melbourne, Victoria, Australia and 3Epigenetics in Human Health and Disease, Baker Medical Research Institute, The Alfred Medical Research and Education Precinct, Prahran, Victoria, Australia The packaging and compaction of DNA into chromatin is mutated (ATM) and ataxia telangiectasia-related (also known as important for all DNA-metabolism processes such as transcrip- Rad3-related, ATR), which are members of the phosphoinositide tion, replication and repair. The involvement of chromatin 4,5 modifications in transcriptional regulation is relatively well 3-kinase (PI(3)K) superfamily. They catalyse the phosphoryla- characterized, and the distinct patterns of chromatin transitions tion of numerous downstream substrates that are involved in 4,5 that guide the process are thought to be the result of a code on cell-cycle regulation, DNA repair and apoptosis. the histone proteins (histone code). In contrast to transcription, In mammalian cells, DSBs are repaired by one of two distinct the intricate link between chromatin and responses to DNA and complementary pathways – homologous recombination damage has been given attention only recently. It is now (HR) and non-homologous end-joining (NHEJ).6,7 Briefly, NHEJ emerging that specific ATP-dependent chromatin remodeling involves processing of the broken DNA terminii to make them complexes (including the Ino80, Swi/Snf and RSC remodelers) 3 and certain constitutive (methylation of lysine 79 of histone H3) compatible, followed by a ligation step.