Exploring the Structure of Long Non-Coding Rnas, J
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Trans-Acting Antisense Rnas Mediate Transcriptional Gene Cosuppression in S
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae Jurgi Camblong,1 Nissrine Beyrouthy, Elisa Guffanti, Guillaume Schlaepfer, Lars M. Steinmetz,2 and Francxoise Stutz3 Department of Cell Biology and NCCR ‘‘Frontiers in Genetics’’ Program, University of Geneva, 1211 Geneva 4, Switzerland Homology-dependent gene silencing, a phenomenon described as cosuppression in plants, depends on siRNAs. We provide evidence that in Saccharomyces cerevisiae, which is missing the RNAi machinery, protein coding gene cosuppression exists. Indeed, introduction of an additional copy of PHO84 on a plasmid or within the genome results in the cosilencing of both the transgene and the endogenous gene. This repression is transcriptional and position-independent and requires trans-acting antisense RNAs. Antisense RNAs induce transcriptional gene silencing both in cis and in trans, and the two pathways differ by the implication of the Hda1/2/3 complex. We also show that trans-silencing is influenced by the Set1 histone methyltransferase, which promotes antisense RNA production. Finally we show that although antisense-mediated cis-silencing occurs in other genes, trans- silencing so far depends on features specific to PHO84. All together our data highlight the importance of noncoding RNAs in mediating RNAi-independent transcriptional gene silencing. [Keywords: Antisense RNA; cis and trans transcriptional gene silencing; PHO84; cosuppression; RNAi-independent TGS; noncoding RNA; S. cerevisiae] Supplemental material is available at http://www.genesdev.org. Received January 15, 2009; revised version accepted May 18, 2009. Eukaryotic gene expression is a complex process regu- recently reported (Camblong et al. -
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. -
Upstream Sequences Other Than AAUAAA Are Required for Efficient Messenger RNA 3’-End Formation in Plants
The Plant Cell, Vol. 2, 1261-1272, December 1990 O 1990 American Society of Plant Physiologists Upstream Sequences Other than AAUAAA Are Required for Efficient Messenger RNA 3’-End Formation in Plants Bradley D. Mogen, Margaret H. MacDonald, Robert Graybosch,’ and Arthur G. Hunt2 Plant Physiology/Biochemistry/MolecularBiology Program, Department of Agronomy, University of Kentucky, Lexington, Kentucky 40546-009 1 We have characterized the upstream nucleotide sequences involved in mRNA 3’-end formation in the 3‘ regions of the cauliflower mosaic virus (CaMV) 19S/35S transcription unit and a pea gene encoding ribulose-l,5-bisphosphate carboxylase small subunit (rbcs). Sequences between 57 bases and 181 bases upstream from the CaMV polyade- nylation site were required for efficient polyadenylation at this site. In addition, an AAUAAA sequence located 13 bases to 18 bases upstream from this site was also important for efficient mRNA 3’-end formation. An element located between 60 bases and 137 bases upstream from the poly(A) addition sites in a pea rbcS gene was needed for functioning of these sites. The CaMV -181/-57 and rbcS -137/-60 elements were different in location and sequence composition from upstream sequences needed for polyadenylation in mammalian genes, but resembled the signals that direct mRNA 3’-end formation in yeast. However, the role of the AAUAAA motif in 3’-end formation in the CaMV 3’ region was reminiscent of mRNA polyadenylation in animals. We suggest that multiple elements are involved in mRNA 3‘-end formation in plants, and that interactions of different components of the plant polyadenyl- ation apparatus with their respective sequence elements and with each other are needed for efficient mRNA 3‘-end formation. -
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. -
The Difficult Case of an RNA-Only Origin of Life
Emerging Topics in Life Sciences (2019) 3 469–475 https://doi.org/10.1042/ETLS20190024 Perspective The difficult case of an RNA-only origin of life Kristian Le Vay and Hannes Mutschler Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Downloaded from https://portlandpress.com/emergtoplifesci/article-pdf/3/5/469/859756/etls-2019-0024c.pdf by Max-Planck-Institut fur Biochemie user on 28 November 2019 Correspondence: Hannes Mutschler ([email protected]) The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of- equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems. The conjecture that life on Earth evolved from an ‘RNA World’ remains one of the most popular hypotheses for abiogenesis, even 60 years after Alex Rich first put the idea forward [1]. For some, evi- dence based upon ubiquitous molecular fossils and the elegance of the idea that RNA once had a dual role as information carrier and prebiotic catalyst provide overwhelming support for the theory. Nevertheless, doubts remain surrounding the chemical evolution of an RNA world, whose classical scenario is based on a temporal sequence of nucleotide formation, enzyme-free polymerisation/replica- tion, recombination, encapsulation in lipid vesicles (or other compartments), evolution of ribozymes and finally the innovation of the genetic code and its translation (Figure 1)[2,3]. -
POST-TRANSCRIPTIONAL REGULATION of AFP and Igm GENES
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2011 POST-TRANSCRIPTIONAL REGULATION OF AFP AND IgM GENES Lilia M. Turcios University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Turcios, Lilia M., "POST-TRANSCRIPTIONAL REGULATION OF AFP AND IgM GENES" (2011). University of Kentucky Doctoral Dissertations. 210. https://uknowledge.uky.edu/gradschool_diss/210 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Lilia M. Turcios The Graduate School University of Kentucky 2011 POST-TRANSCRIPTIONAL REGULATION OF AFP AND IgM GENES ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Medicine at the University of Kentucky By Lilia M. Turcios Director: Dr. Martha Peterson Lexington, KY 2011 Copyright © Lilia M. Turcios 2011 ABSTRACT OF DISSERTATION POST-TRANSCRIPTIONAL REGULATION OF AFP AND IgM GENES Gene expression can be regulated at multiple steps once transcription is initiated. I have studied two different gene models, the α-Fetoprotein (AFP) and the immunoglobulin heavy chain (IgM) genes, to better understand post-transcriptional gene regulation mechanisms. The AFP gene is highly expressed during fetal liver development and dramatically repressed after birth. There is a mouse strain-specific difference between adult levels of AFP, with BALB/cJ mice expressing 10 to 20-fold higher levels compared to other mouse strains. -
A Group Ill Twintron Encoding a Maturase-Like Gene Excises Through Lariat Intermediates
I.=) 1994 Oxford University Press Nucleic Acids Research, 1994, Vol. 22, No. 6 1029-1036 A group Ill twintron encoding a maturase-like gene excises through lariat intermediates Donald W.Copertino1 2+, Edina T.Hall2,§, Fredrick W.Van Hook2, Kristin P.Jenkins2 and Richard B.Hallick1,2* 1Departments of Biochemistry and 2Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA Received December 9, 1993; Revised and Accepted February 10, 1994 ABSTRACT The 1605 bp intron 4 of the Euglena gracilis chloroplast the closely related nonphotosynthetic euglenoid Astasia longa psbC gene was characterized as a group Ill twintron (8, 9). composed of an internal 1503 nt group Ill intron with Euglena chloroplast genes also contain 15 twintrons, introns- an open reading frame of 1374 nt (ycfl3, 458 amino within-introns, that are sequentially spliced (3). There are acids), and an external group Ill intron of 102 nt. twintrons with one intron internal to another intron (2, 6, 10), Twintron excision proceeds by a sequential splicing and complex twintrons with multiple internal introns (11; for pathway. The splicing of the internal and external group review, see 3). Group II and group III introns can occur as Ill introns occurs via lariat intermediates. Branch sites internal and/or external introns of twintrons. Excision of internal were mapped by primer extension RNA sequencing. introns occurs prior to excision of external introns. The excision The unpaired adenosines in domains VI of the internal of internal group IH introns of twintrons can proceed from and external introns are covalently linked to the 5' multiple 5' and 3' splice sites (6, 1 1). -
The Association of Group IIB Intron with Integrons in Hypersaline Environments Sarah Sonbol1 and Rania Siam1,2*
Sonbol and Siam Mobile DNA (2021) 12:8 https://doi.org/10.1186/s13100-021-00234-2 RESEARCH Open Access The association of group IIB intron with integrons in hypersaline environments Sarah Sonbol1 and Rania Siam1,2* Abstract Background: Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated with integrons. In order to identify group II introns linked with integrons and CALINS (cluster of attC sites lacking a neighboring integron integrase) within halophiles, we mined for integrons in 28 assembled metagenomes from hypersaline environments and publically available 104 halophilic genomes using Integron Finder followed by blast search for group II intron reverse transcriptases (RT)s. Results: We report the presence of different group II introns associated with integrons and integron-related sequences denoted by UHB.F1, UHB.I2, H.ha.F1 and H.ha.F2. The first two were identified within putative integrons in the metagenome of Tanatar-5 hypersaline soda lake, belonging to IIC and IIB intron classes, respectively at which the first was a truncated intron. Other truncated introns H.ha.F1 and H.ha.F2 were also detected in a CALIN within the extreme halophile Halorhodospira halochloris, both belonging to group IIB introns. The intron-encoded proteins (IEP) s identified within group IIB introns belonged to different classes: CL1 class in UHB.I2 and bacterial class E in H.ha.Fa1 and H.ha.F2. A newly identified insertion sequence (ISHahl1)ofIS200/605 superfamily was also identified adjacent to H. -
The Excludon: a New Concept in Bacterial Antisense RNA-Mediated
Nature Reviews Microbiology | AOP, published online 24 December 2013; doi:10.1038/nrmicro2934 PROGRESS this paradigm in the context of other, better characterized asRNA-mediated regulatory The excludon: a new concept in mechanisms. The excludon concept describes unusually long asRNAs that inhibit the bacterial antisense RNA-mediated expression of one group of genes while enhancing the expression of a second group gene regulation of genes. Thus, single transcripts have the ability to control divergent operons that often have opposing functions. Nina Sesto, Omri Wurtzel, Cristel Archambaud, Rotem Sorek and Pascale Cossart asRNAs in microbial transcriptomes Abstract | In recent years, non-coding RNAs have emerged as key regulators of gene asRNAs are encoded on one strand of the DNA and overlap a gene that is encoded on expression. Among these RNAs, the antisense RNAs (asRNAs) are particularly the opposite strand. Therefore, these cis- abundant, but in most cases the function and mechanism of action for a particular encoded asRNAs have perfect complementa‑ asRNA remains elusive. Here, we highlight a recently discovered paradigm termed rity to the sense transcript from the opposite the excludon, which defines a genomic locus encoding an unusually long asRNA that DNA strand. The regulatory role of asRNAs spans divergent genes or operons with related or opposing functions. Because these was first reported more than 30 years ago, in the case of plasmid- and transposon-encoded asRNAs can inhibit the expression of one operon while functioning as an mRNA for asRNAs in Escherichia coli, when the asRNAs the adjacent operon, they act as fine-tuning regulatory switches in bacteria. -
Antisense RNA Insert Design for Plasmid Construction to Knockdown Target Gene Expression
Vol. 1:7-15 Antisense RNA Insert Design for Plasmid Construction to Knockdown Target Gene Expression Ji, Tom, Lu, Aneka, Wu, Kaylee Department of Microbiology and Immunology, University of British Columbia Regulatory RNA molecules are common tools used in bacterial gene regulation. This paper focuses on the steps in designing an antisense RNA component for insertion into a plasmid in order to silence a gene in the plasmid host cell. By hybridizing to the ribosomal binding site of the target gene mRNA transcript, the antisense RNA transcript from the plasmid is able to inhibit gene translation and lead to eventual mRNA degradation. By regulating or silencing the gene of interest, further experiments could be used to confirm or reject proposed roles for undefined genes. In this paper, wecD silencing using pHN678 plasmid in Escherichia Coli will be used as an example. The design of the antisense RNA component involves three main steps: identification of the gene of interest, selection of the antisense target sequence of the gene, and modification of the target sequence to generate the antisense sequence. In addition, a sense RNA insert could be used as an orientation control in the experiment. The vector plasmid without any sequence insertion should also be included as a negative control. As a result, a successfully designed antisense RNA insert should allow knockdown of the target gene through hybridization to the mRNA transcript and therefore inhibiting gene translation. INTRODUCTION Bacteria possess many diverse means of gene regulation regions containing the ribosomal binding site (RBS) and using RNA molecules. More specifically, RNA the start site of the wecD mRNA. -
RNA Regulatory Elements Play a Significant Role in Gene
Ab initio IDENTIFICATION OF REGULATORY RNAS USING INFORMATION-THEORETIC UNCERTAINTY by AMIRHOSSEIN MANZOUROLAJDAD (Under the Direction of Dr. Jonathan Arnold) ABSTRACT RNA regulatory elements play a significant role in gene regulation. Riboswitches are regulatory elements which function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Traditionally, riboswitches have been identified based on sequence and structural homology. In this work, in an attempt to devise an ab initio method for identification of regulatory elements, mainly riboswitches, we derive and implement Shannon’s entropy of the SCFG ensemble on an RNA sequence in polynomial time for both structurally ambiguous and unambiguous grammars. We then evaluate the significance of this new measure of structural entropy in identifying riboswitches. Finally, sim- ple lightweight stochastic context-free grammar folding models assign significant values to long extensive secondary structures in Bacillus subtilis. INDEX WORDS: Riboswitch, RNA Secondary Structure, Stochastic Context-free Grammars, Information Theory Ab initio IDENTIFICATION OF REGULATORY RNAS USING INFORMATION-THEORETIC UNCERTAINTY by AMIRHOSSEIN MANZOUROLAJDAD BS, The University of Guilan, Rasht, Iran, 2004 MS, Isfahan University of Technology, Isfahan, Iran, 2007 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS,GEORGIA 2014 ⃝c 2014 Amirhossein Manzourolajdad All Rights Reserved Ab initio IDENTIFICATION OF REGULATORY RNAS USING INFORMATION-THEORETIC UNCERTAINTY by AMIRHOSSEIN MANZOUROLAJDAD Approved: Major Professor: Jonathan Arnold Committee: Sidney Kushner Russell L. Malmberg Jan Mrazek Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia May 2014 I dedicate this work to my mother, Roya iv ACKNOWLEGEMENTS I will be eternally indebted to my major advisor Dr.