Biogenesis of Small Rnas in Animals

Total Page:16

File Type:pdf, Size:1020Kb

Biogenesis of Small Rnas in Animals REVIEWS POST-TRANSCRIPTIONAL CONTROL Biogenesis of small RNAs in animals V. Narry Kim*, Jinju Han* and Mikiko C. Siomi‡ Abstract | Small RNAs of 20–30 nucleotides can target both chromatin and transcripts, and thereby keep both the genome and the transcriptome under extensive surveillance. Recent progress in high-throughput sequencing has uncovered an astounding landscape of small RNAs in eukaryotic cells. Various small RNAs of distinctive characteristics have been found and can be classified into three classes based on their biogenesis mechanism and the type of Argonaute protein that they are associated with: microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs) and Piwi-interacting RNAs (piRNAs). This Review summarizes our current knowledge of how these intriguing molecules are generated in animal cells. Heterochromatin The first small RNA, lin‑4, was discovered in 1993 by The best understood among the three classes, Highly condensed regions of genetic screens in nematode worms1,2. The number of miRNAs are generated from local hairpin structures by the genome in which known small RNAs has since expanded substantially, the action of two RNase III-type proteins, Drosha and Dicer transcription is generally mainly as a result of the cloning and sequencing of size‑ (BOX 2). Mature miRNAs of ~22 nt are then bound by limited. fractionated RNAs3–5. The recent development of deep‑ Ago‑subfamily proteins. miRNAs target mRNAs and 6,7 RNase III-type protein sequencing technologies and computational prediction thereby function as post‑transcriptional regulators. An endonuclease that cleaves methods8–11 has accelerated the discovery of less abun‑ The longest of the three classes, piRNAs (24–31 nt in double-stranded RNAs and dant small RNAs. The functions of small RNAs range length) are associated with Piwi‑subfamily proteins. creates 5′-phosphate and heterochromatin 3′-hydroxyl termini, leaving from formation to mRNA destabilization Intriguingly, the biogenesis of piRNAs does not depend 12,13 14 2-nucleotide 3′ overhangs. and translational control . Through such extensive on Dicer . piRNAs are highly abundant in germ cells patrolling across the genome and transcriptome, small and at least some of them are involved in transposon RNAs are involved in almost every biological process, silencing through heterochromatin formation or RNA including developmental timing, cell differentiation, cell destabilization. endo‑siRNAs have been studied mostly proliferation, cell death, metabolic control, transposon in Drosophila melanogaster, although they have also silencing and antiviral defence. been found in mouse oocytes and embryonic stem (ES) ‘Small RNA’ is a rather arbitrary term, because it was cells15–17. Despite their similarity with miRNAs in terms previously used for other non‑coding RNAs, such as small of their association with Ago‑subfamily proteins, endo‑ nuclear RNAs (snRNAs) and transfer RNAs (tRNAs). siRNAs differ from miRNAs in that they are derived *School of Biological Bacterial short regulatory RNAs have also been referred from long double‑stranded RNAs (dsRNAs) and are Sciences and Center for to as small RNAs, but they are not related to eukaryotic dependent only on Dicer and not on Drosha18–20. They National Creative Research, small RNAs. What distinguishes and defines eukaryo‑ are also slightly shorter (~21 nt) than miRNAs. At least Seoul National University, tic small RNAs in the RNA silencing pathway is their some of the endo‑siRNAs have been shown to function Seoul, 151-742, Korea. ‡Keio University School of limited size (~20–30 nucleotides (nt)) and their associa‑ as post‑transcriptional regulators that target RNAs. Medicine, 35 Shinanomachi, tion with Argonaute (Ago)‑family proteins (BOX 1; TABLE 1). This Review summarizes our current knowledge of Shinjuku-ku, Tokyo The Ago family can be grouped further into two clades: the biogenesis pathways of small RNAs. The focus of the 160-8582, and the Japan the Ago subfamily and the Piwi subfamily. At least three Review will remain on animal small RNAs, mainly in Science and Technology Agency (JST), Core Research classes of small RNAs are encoded in our genome, based mammals and flies. Several excellent reviews on small 21–24 for Evolutionary Science on their biogenesis mechanism and the type of Ago pro‑ RNAs in plants and yeast are available elsewhere . and Technology (CREST), tein that they are associated with: microRNAs (miRNA s), Saitama 332-0012, Japan. endo genous small interfering RNAs (endo‑siRNAs or microRNA biogenesis Correspondence to V.N.K. esiRNA s) and Piwi‑interacting RNAs (piRNAs). It should miRNAs are single‑stranded RNAs (ssRNAs) of ~22 nt and M.C.S. e-mails: [email protected]; be noted, however, that the recent discoveries of numerous in length that are generated from endogenous hair‑ 25 [email protected] non‑canonical small RNAs have blurred the boundaries pin‑shaped transcripts . miRNAs function as guide doi:10.1038/nrm2632 between the classes. molecules in post‑transcriptional gene regulation by 126 | FEBRUARY 2009 | VOLUME 10 www.nature.com/reviews/molcellbio © 2009 Macmillan Publishers Limited. All rights reserved REVIEWS Box 1 | Argonaute proteins and their associated small RNAs miRNA genes and their transcription. At present, the miRNA database contains 154 Caenorhabditis elegans, The Argonaute (Ago) a PAZ MID PIWI 152 D. melanogaster, 337 Danio rerio (zebrafish), 475 Gallus family can be classified N C gallus (chicken), 695 human and 187 Arabidopsis thal- into two subclades: the iana miRNAs. miRNAs are even present in simple multi‑ Ago subfamily and the b cellular organisms, such as poriferans (sponges) and Piwi subfamily (TABLE 1). Catalytic site PIWI 27 bilaterian The Ago proteins are cnidarians (starlet sea anemone) . Many of the expressed ubiquitously, animal miRNA s are phylogenetically conserved; ~55% interact with microRNAs of C. elegans miRNAs have homologues in humans, (miRNAs) or small MID which indicates that miRNAs have had important roles interfering RNAs PAZ throughout animal evolution28. Animal miRNAs seem (siRNAs), and function as 3′ end of to have evolved separately from those in plants because post-transcriptional guide strand 5′ end of their sequences, precursor structure and biogenesis regulators. The Piwi 29,30 guide strand mechanisms are distinct from those in plants . proteins are abundantly Most mammalian miRNA genes have multiple iso‑ expressed in germ cells and function in transposon silencing, together with forms (paralogues) that are probably the result of gene Piwi-interacting RNAs (piRNAs). Nature Reviews | Molecular Cell Biology Ago-family proteins are composed of three characteristic domains: the PAZ, MID duplications. For instance, the human genome has and PIWI domains (see the figure, part a). The PAZ domain serves as a docking site for 12 loci for let‑7‑family miRNAs. Paralogues often have the 3′ end of small RNA181–184, whereas the MID domain anchors the 5′ terminal identical sequences at nucleotide positions 2–7 relative nucleotide183–187 (see the figure, part b). Recent studies have determined the structure to the 5′ end of the miRNA. Because these six nucleo‑ of Thermus thermophilus Ago with a guide strand and target strand duplex183,184. The tides (called seed) are crucial in base pairing with the PIWI domain has a structure that is similar to RNase H, which cuts the RNA strand of target mRNA, the paralogues are thought to act redun‑ an RNA–DNA hybrid. Indeed, the PIWI domain of some Ago proteins can cleave the dantly. However, because the 3′ sequences of miRNAs target RNA bound to small RNA: this is called slicer activity. Of the four human Ago also contribute to target binding and because the expres‑ proteins (AGO1–4; also known as EIF2C1–4), only AGO2 has slicer activity, whereas in sion patterns of these sister miRNAs are often different Drosophila melanogaster all Ago and Piwi proteins possess slicer activity. Apart from from each other, members of the same seed family might the endonucleolytic cleavage that is mediated by the PIWI domain, the Ago proteins 31 can induce translational repression and exonucleolytic mRNA decay through have distinct roles in vivo . interaction with other protein factors13. Approximately 50% of mammalian miRNA loci The fly Piwi proteins Aubergine (AUB) and AGO3 can cleave target mRNAs, are found in close proximity to other miRNAs. These resulting in the silencing of retrotransposons, other intergenic repetitive elements clustered miRNAs are transcribed from a single poly- and protein-coding genes, such as Stellate (also known as SteXh)145,148. PIWI might cistronic transcription unit (TU)32, although there may function differently from AUB and AGO3, as it associates with chromatin and be exceptional cases in which individual miRNAs are interacts with HP1a (heterochromatin protein 1a), which is involved in derived from separate gene promoters. Some miRNAs heterochromatin formation. Thus, PIWI might contribute to the epigenetic control of are generated from non‑coding TUs, whereas others are the fly genome188. Consistently, AUB and AGO3 are localized in the cytoplasm, encoded in protein‑coding TUs (FIG. 1). Approximately whereas PIWI is found in the nucleus145–148. The expression patterns are also different; 40% of miRNA loci are located in the intronic region of PIWI, but not AUB and AGO3, was detected in the soma of ovaries, indicating that PIWI has a function outside of germ cells. Epigenetic changes were observed non‑coding transcripts, whereas
Recommended publications
  • Patenting Interfering RNA
    Patenting Interfering RNA J. Douglas Schultz SPE Art Unit 1635 (571) 272-0763 [email protected] Oligonucleotide Inhibitors: Mechanisms of Action RNAi - Mechanism of Action • dsRNA induces sequence-specific degradation of homologous gene transcripts • RISC metabolizes dsRNA to small 21-23- nucleotide siRNAs – RISC contains dsRNase (“Dicer”), ssRNase (Argonaut 2 or Ago2) • RISC utilizes antisense strand as “guide” to find cleavable target siRNA Mechanism of Action miRNA Mechanism of Action Interfering RNA Glossary of Terms • RNAi – RNA interference • dsRNA – double stranded RNA • siRNA – small interfering RNA, double stranded, 21-23 nucleotides • shRNA – short hairpin RNA (doubled stranded by virtue of a ssRNA folding back on itself) • miRNA – micro RNA • RISC – RNA-induced silencing complex – Dicer – RNase endonuclease siRNA miRNA • Exogenously delivered • Endogenously produced • 21-23mer dsRNA • 21-23mer dsRNA • Acts through RISC • Acts through RISC • Induces homologous target • Induces homologous target cleavage cleavage • Perfect sequence match • Imperfect sequence match – Results in target degradation – Results in translation arrest RNAi Patentability issues Sample Claims: • A siRNA that inhibits expression of a nucleic acid encoding protein X. OR • A siRNA comprising a 2’-modification, wherein said modification comprises 2’-fluoro, 2’-O-methyl, or 2’- deoxy. (Note: no target recited) OR • A method of reducing tumor cell growth comprising administering siRNA targeting protein X. RNAi Patentability Issues 35 U.S.C. 101 – Utility • Credible/Specific/Substantial/Well Established. • Used to attempt modulation of gene expression in human diseases • Routinely investigate gene function in a high throughput fashion or to (see Rana RT, Nat. Rev. Mol. Cell Biol. 2007, Vol. 8:23-36).
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2004/0086860 A1 Sohail (43) Pub
    US 20040O86860A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2004/0086860 A1 Sohail (43) Pub. Date: May 6, 2004 (54) METHODS OF PRODUCING RNAS OF Publication Classification DEFINED LENGTH AND SEQUENCE (51) Int. Cl." .............................. C12Q 1/68; C12P 19/34 (76) Inventor: Muhammad Sohail, Marston (GB) (52) U.S. Cl. ............................................... 435/6; 435/91.2 Correspondence Address: MINTZ, LEVIN, COHN, FERRIS, GLOWSKY (57) ABSTRACT AND POPEO, PC. ONE FINANCIAL CENTER Methods of making RNA duplexes and single-stranded BOSTON, MA 02111 (US) RNAS of a desired length and Sequence based on cleavage of RNA molecules at a defined position, most preferably (21) Appl. No.: 10/264,748 with the use of deoxyribozymes. Novel deoxyribozymes capable of cleaving RNAS including a leader Sequence at a (22) Filed: Oct. 4, 2002 Site 3' to the leader Sequence are also described. Patent Application Publication May 6, 2004 Sheet 1 of 2 US 2004/0086860 A1 DNA Oligonucleotides T7 Promoter -TN-- OR 2N-2-N-to y Transcription Products GGGCGAAT-N-UU GGGCGAAT-N-UU w N Deoxyribozyme Cleavage - Q GGGCGAAT -------' Racction GGGCGAAT N-- UU N-UU ssRNA products N-UU Anneal ssRNA UU S-2N- UU siRNA product FIGURE 1: Flowchart summarising the procedure for siRNA synthesis. Patent Application Publication May 6, 2004 Sheet 2 of 2 US 2004/0086860 A1 Full-length transcript 3'-digestion product 5'-digestion product (5'GGGCGAATA) A: Production of single-stranded RNA templates by in vitro transcription and digestion With a deoxyribozyme V 2- 2 V 22inv 22 * 2 &3 S/AS - 88.8x, *...* or as IGFR -- is as 4.
    [Show full text]
  • INTRODUCTION Sirna and Rnai
    J Korean Med Sci 2003; 18: 309-18 Copyright The Korean Academy ISSN 1011-8934 of Medical Sciences RNA interference (RNAi) is the sequence-specific gene silencing induced by dou- ble-stranded RNA (dsRNA). Being a highly specific and efficient knockdown tech- nique, RNAi not only provides a powerful tool for functional genomics but also holds Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National a promise for gene therapy. The key player in RNAi is small RNA (~22-nt) termed University, Seoul, Korea siRNA. Small RNAs are involved not only in RNAi but also in basic cellular pro- cesses, such as developmental control and heterochromatin formation. The inter- Received : 19 May 2003 esting biology as well as the remarkable technical value has been drawing wide- Accepted : 23 May 2003 spread attention to this exciting new field. V. Narry Kim, D.Phil. Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, San 56-1, Shillim-dong, Gwanak-gu, Seoul 151-742, Korea Key Words : RNA Interference (RNAi); RNA, Small interfering (siRNA); MicroRNAs (miRNA); Small Tel : +82.2-887-8734, Fax : +82.2-875-0907 hairpin RNA (shRNA); mRNA degradation; Translation; Functional genomics; Gene therapy E-mail : [email protected] INTRODUCTION established yet, testing 3-4 candidates are usually sufficient to find effective molecules. Technical expertise accumulated The RNA interference (RNAi) pathway was originally re- in the field of antisense oligonucleotide and ribozyme is now cognized in Caenorhabditis elegans as a response to double- being quickly applied to RNAi, rapidly improving RNAi stranded RNA (dsRNA) leading to sequence-specific gene techniques.
    [Show full text]
  • Small Interfering RNA-Mediated Translation Repression Alters Ribosome Sensitivity to Inhibition by Cycloheximide in Chlamydomonas Reinhardtii
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Dissertations and Theses in Biological Sciences Biological Sciences, School of Spring 2013 Small Interfering RNA-Mediated Translation Repression Alters Ribosome Sensitivity to Inhibition by Cycloheximide in Chlamydomonas reinhardtii Xinrong Ma University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/bioscidiss Part of the Biology Commons, Cellular and Molecular Physiology Commons, Microbiology Commons, and the Molecular Genetics Commons Ma, Xinrong, "Small Interfering RNA-Mediated Translation Repression Alters Ribosome Sensitivity to Inhibition by Cycloheximide in Chlamydomonas reinhardtii" (2013). Dissertations and Theses in Biological Sciences. 51. https://digitalcommons.unl.edu/bioscidiss/51 This Article is brought to you for free and open access by the Biological Sciences, School of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Dissertations and Theses in Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. SMALL INTERFERING RNA-MEDIATED TRANSLATION REPRESSION ALTERS RIBOSOME SENSITIVITY TO INHIBITION BY CYCLOHEXIMIDE IN CHLAMYDOMONAS REINHARDTII by Xinrong Ma A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Biological Sciences Under the Supervision of Professor Heriberto Cerutti Lincoln, Nebraska May, 2013 SMALL INTERFERING RNA-MEDIATED TRANSLATION REPRESSION ALTERS RIBOSOME SENSITIVITY TO INHIBITION BY CYCLOHEXIMIDE IN CHLAMYDOMONAS REINHARDTII Xinrong Ma, Ph.D. University of Nebraska, 2013 Advisor: Heriberto Cerutti RNA interference (RNAi) is an evolutionarily conserved gene silencing mechanism in eukaryotes, with regulatory roles in a variety of biological processes, including cell cycle, cell differentiation, physiological and metabolic pathways, and stress responses.
    [Show full text]
  • Annale D890ahlfors.Pdf (5.211Mb)
    TURUN YLIOPISTON JULKAISUJA ANNALES UNIVERSITATIS TURKUENSIS SARJA - SER. D OSA - TOM. 890 MEDICA - ODONTOLOGICA INTERLEUKIN-4 INDUCED LEUKOCYTE DIFFERENTIATION by Helena Ahlfors TURUN YLIOPISTO UNIVERSITY OF TURKU Turku 2009 From Turku Centre for Biotechnology, University of Turku and Åbo Akademi University; Department of Medical Biochemistry and Molecular Biology, University of Turku and National Graduate School of Informational and Structural Biology Supervised by Professor Riitta Lahesmaa, M.D., Ph.D. Turku Centre for Biotechnology University of Turku and Åbo Akademi University Turku, Finland Reviewed by Professor Risto Renkonen M.D., Ph.D. Transplantation laboratory Haartman Institute University of Helsinki Helsinki, Finland and Docent Panu Kovanen, M.D., Ph.D. Haartman Institute Department of Pathology University of Helsinki Helsinki, Finland Opponent Assistant Professor Mohamed Oukka, Ph.D. Seattle Children’s Research Institute Department of Immunology University of Washington Seattle, USA ISBN 978-951-29-4183-4 (PRINT) ISBN 978-951-29-4184-1 (PDF) ISSN 0355-9483 Painosalama Oy – Turku, Finland 2009 Think where mans glory most begins and ends, and say my glory was I had such friends. William Butler Yeats (1865 – 1939) ABSTRACT Helena Ahlfors Interleukin-4 induced leukocyte differentiation Turku Centre for Biotechnology, University of Turku and Åbo Akademi University Department of Medical Biochemistry and Genetics, University of Turku National Graduate School of Informational and Structural Biology, 2009 Monocytes, macrophages and dendritic cells (DCs) are important mediators of innate immune system, whereas T lymphocytes are the effector cells of adaptive immune responses. DCs play a crucial role in bridging innate and adaptive immunity. Naïve CD4+ Th progenitors (Thp) differentiate to functionally distinct effector T cell subsets including Th1, Th2 and Th17 cells, which while being responsible for specific immune functions have also been implicated in pathological responses, such as autoimmunity, asthma and allergy.
    [Show full text]
  • Retroviral Delivery of Small Interfering RNA Into Primary Cells
    Retroviral delivery of small interfering RNA into primary cells Gregory M. Barton and Ruslan Medzhitov* Section of Immunobiology and The Howard Hughes Medical Institute, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520 Communicated by Peter Cresswell, Yale University School of Medicine, New Haven, CT, October 2, 2002 (received for review August 9, 2002) RNA interference is an evolutionarily conserved process in which gene was replaced with the human CD4 gene, which was cloned recognition of double-stranded RNA ultimately leads to posttran- from splenic cDNA. To eliminate any potential signaling, a scriptional suppression of gene expression. This suppression is premature stop codon was introduced after amino acid 425, just mediated by short (21- to 22-nt) small interfering RNAs (siRNAs), after the transmembrane domain. The human H1 promoter was which induce degradation of mRNA based on complementary base cloned from genomic DNA and inserted either upstream of the pairing. The silencing of gene expression by siRNAs is emerging cytomegalovirus (CMV) promoter (RVH1) by using previously rapidly as a powerful method for genetic analysis. Recently, several introduced XhoI and EcoRI sites or within the 3Ј LTR by groups have reported systems designed to express siRNAs in using SalI. The oligonucleotides encoding the human p53 mammalian cells through transfection of either oligonucleotides or siRNA, described by Brummelkamp et al. (6), were 5Ј-GATC- plasmids encoding siRNAs. Because these systems rely on trans- CCCGACTCCAGTGGTAATCTACTTCAAGAGAGTA- fection for delivery, the cell types available for study are restricted GATTACCACTGGAGTCTTTTTGGAAC-3Ј and 5Ј-TCGA- generally to transformed cell lines. Here, we describe a retroviral GTTCCAAAAAGACTCCAGTGGTAATCTACTCTCTTG- system for delivery of siRNA into cells.
    [Show full text]
  • Viral Vectors Applied for Rnai-Based Antiviral Therapy
    viruses Review Viral Vectors Applied for RNAi-Based Antiviral Therapy Kenneth Lundstrom PanTherapeutics, CH1095 Lutry, Switzerland; [email protected] Received: 30 July 2020; Accepted: 21 August 2020; Published: 23 August 2020 Abstract: RNA interference (RNAi) provides the means for alternative antiviral therapy. Delivery of RNAi in the form of short interfering RNA (siRNA), short hairpin RNA (shRNA) and micro-RNA (miRNA) have demonstrated efficacy in gene silencing for therapeutic applications against viral diseases. Bioinformatics has played an important role in the design of efficient RNAi sequences targeting various pathogenic viruses. However, stability and delivery of RNAi molecules have presented serious obstacles for reaching therapeutic efficacy. For this reason, RNA modifications and formulation of nanoparticles have proven useful for non-viral delivery of RNAi molecules. On the other hand, utilization of viral vectors and particularly self-replicating RNA virus vectors can be considered as an attractive alternative. In this review, examples of antiviral therapy applying RNAi-based approaches in various animal models will be described. Due to the current coronavirus pandemic, a special emphasis will be dedicated to targeting Coronavirus Disease-19 (COVID-19). Keywords: RNA interference; shRNA; siRNA; miRNA; gene silencing; viral vectors; RNA replicons; COVID-19 1. Introduction Since idoxuridine, the first anti-herpesvirus antiviral drug, reached the market in 1963 more than one hundred antiviral drugs have been formally approved [1]. Despite that, there is a serious need for development of novel, more efficient antiviral therapies, including drugs and vaccines, which has become even more evident all around the world today due to the recent coronavirus pandemic [2].
    [Show full text]
  • Advances in Oligonucleotide Drug Delivery
    REVIEWS Advances in oligonucleotide drug delivery Thomas C. Roberts 1,2 ✉ , Robert Langer 3 and Matthew J. A. Wood 1,2 ✉ Abstract | Oligonucleotides can be used to modulate gene expression via a range of processes including RNAi, target degradation by RNase H-mediated cleavage, splicing modulation, non-coding RNA inhibition, gene activation and programmed gene editing. As such, these molecules have potential therapeutic applications for myriad indications, with several oligonucleotide drugs recently gaining approval. However, despite recent technological advances, achieving efficient oligonucleotide delivery, particularly to extrahepatic tissues, remains a major translational limitation. Here, we provide an overview of oligonucleotide-based drug platforms, focusing on key approaches — including chemical modification, bioconjugation and the use of nanocarriers — which aim to address the delivery challenge. Oligonucleotides are nucleic acid polymers with the In addition to their ability to recognize specific tar- potential to treat or manage a wide range of diseases. get sequences via complementary base pairing, nucleic Although the majority of oligonucleotide therapeutics acids can also interact with proteins through the for- have focused on gene silencing, other strategies are being mation of three-dimensional secondary structures — a pursued, including splice modulation and gene activa- property that is also being exploited therapeutically. For tion, expanding the range of possible targets beyond example, nucleic acid aptamers are structured
    [Show full text]
  • Ribozyme-Enhanced Single-Stranded Ago2-Processed Interfering RNA Triggers Efficient Gene Silencing with Fewer Off-Target Effects
    ARTICLE Received 9 Dec 2014 | Accepted 21 Aug 2015 | Published 12 Oct 2015 DOI: 10.1038/ncomms9430 OPEN Ribozyme-enhanced single-stranded Ago2-processed interfering RNA triggers efficient gene silencing with fewer off-target effects Renfu Shang1,2,3, Fengjuan Zhang1,2,3, Beiying Xu1,2,3, Hairui Xi4, Xue Zhang1,2,3, Weihua Wang1,2,3 & Ligang Wu1,2,3 Short-hairpin RNAs (shRNAs) are widely used to produce small-interfering RNAs (siRNAs) for gene silencing. Here we design an alternative siRNA precursor, named single-stranded, Argonaute 2 (Ago2)-processed interfering RNA (saiRNA), containing a 16–18 bp stem and a loop complementary to the target transcript. The introduction of a self-cleaving ribozyme derived from hepatitis delta virus to the 30 end of the transcribed saiRNA dramatically improves its silencing activity by generating a short 30 overhang that facilitates the efficient binding of saiRNA to Ago2. The same ribozyme also enhances the activity of Dicer-dependent shRNAs. Unlike a classical shRNA, the strand-specific cleavage of saiRNA by Ago2 during processing eliminates the passenger strand and prevents the association of siRNA with non-nucleolytic Ago proteins. As a result, off-target effects are reduced. In addition, saiRNA exhibits less competition with the biogenesis of endogenous miRNAs. Therefore, ribozyme-enhanced saiRNA provides a reliable tool for RNA interference applications. 1 National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. 2 Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.
    [Show full text]
  • Beyond Microrna Â
    Cancer Letters xxx (2013) xxx–xxx Contents lists available at SciVerse ScienceDirect Cancer Letters journal homepage: www.elsevier.com/locate/canlet Mini-review Beyond microRNA – Novel RNAs derived from small non-coding RNA and their implication in cancer ⇑ Elena S. Martens-Uzunova , Michael Olvedy, Guido Jenster Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands article info abstract Article history: Over the recent years, Next Generation Sequencing (NGS) technologies targeting the microRNA transcrip- Available online xxxx tome revealed the existence of many different RNA fragments derived from small RNA species other than microRNA. Although initially discarded as RNA turnover artifacts, accumulating evidence suggests that Keywords: RNA fragments derived from small nucleolar RNA (snoRNA) and transfer RNA (tRNA) are not just random snoRNA-derived RNA (sdRNA) degradation products but rather stable entities, which may have functional activity in the normal and tRNA fragment (tRF) malignant cell. Next generation sequencing This review summarizes new findings describing the detection and alterations in expression of Cancer snoRNA-derived (sdRNA) and tRNA-derived (tRF) RNAs. We focus on the possible interactions of sdRNAs microRNA Non-coding RNA and tRFs with the canonical microRNA pathways in the cell and present current hypotheses on the func- tion of these RNAs. Ó 2013 Elsevier Ireland Ltd. All rights reserved. 1. Introduction Alongside with miRNA, other types of small regulatory ncRNAs like exogenous and endogenous small interfering RNAs (siRNAs Within less than a decade since the sequencing of the human and endo-siRNAs) [6–8] and PiWi-interacting RNAs (piRNAs) [9] genome it became clear that over ninety percent of our genes en- are also involved in gene regulation and genome defense and share code for RNA transcripts that never get translated to protein.
    [Show full text]
  • Ribonucleic Acid (RNA)
    AccessScience from McGraw-Hill Education Page 1 of 11 www.accessscience.com Ribonucleic acid (RNA) Contributed by: Michael W. Gray, Ann L. Beyer Publication year: 2014 One of the two major classes of nucleic acid, mainly involved in translating the genetic information carried in deoxyribonucleic acid (DNA) into proteins. Various types of ribonucleic acids (RNAs) [see table] function in protein synthesis: transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) function in the synthesis of all proteins, whereas messenger RNAs (mRNAs) are a diverse set, with each member specifically directing the synthesis of one protein. Messenger RNA is the intermediate in the usual biological pathway of DNA → RNA → protein. However, RNA is a very versatile molecule. Other types of RNA serve other important functions for cells and viruses, such as the involvement of small nuclear RNAs (snRNAs) in mRNA splicing. In some cases, RNA performs functions typically considered DNA-like, such as serving as the genetic material for certain viruses, or roles typically carried out by proteins, such as RNA enzymes or ribozymes. See also: DEOXYRIBONUCLEIC ACID (DNA); NUCLEIC ACID. Structure and synthesis RNA is a linear polymer of four different nucleotides (Fig. 1). Each nucleotide is composed of three parts: a five-carbon sugar known as ribose; a phosphate group; and one of four bases attached to each ribose, that is, adenine (A), cytosine (C), guanine (G), or uracil (U). The combination of base and sugar constitutes a nucleoside. The structure of RNA is basically a repeating chain of ribose and phosphate moieties, with one of the four bases attached to each ribose.
    [Show full text]
  • Interference Interfering RNA-Mediated RNA Inhibition Of
    Inhibition of HIV-1 Infection by Small Interfering RNA-Mediated RNA Interference John Capodici, Katalin Karikó and Drew Weissman This information is current as J Immunol 2002; 169:5196-5201; ; of September 29, 2021. doi: 10.4049/jimmunol.169.9.5196 http://www.jimmunol.org/content/169/9/5196 Downloaded from References This article cites 27 articles, 9 of which you can access for free at: http://www.jimmunol.org/content/169/9/5196.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on September 29, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2002 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Inhibition of HIV-1 Infection by Small Interfering RNA-Mediated RNA Interference1 John Capodici,* Katalin Kariko´,† and Drew Weissman2* RNA interference (RNAi) is an ancient antiviral response that processes dsRNA and associates it into a nuclease complex that identifies RNA with sequence homology and specifically cleaves it.
    [Show full text]