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Song J, Song J, Mo B, Chen X. Uridylation and adenylation of RNAs. SCIENCE CHINA. LIFE SCIENCES 2015; 58:1057-66. [PMID: 26563174 PMCID: PMC5089844 DOI: 10.1007/s11427-015-4954-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 10/15/2015] [Indexed: 11/26/2022]
Abstract
The posttranscriptional addition of nontemplated nucleotides to the 3' ends of RNA molecules can have a significant impact on their stability and biological function. It has been recently discovered that nontemplated addition of uridine or adenosine to the 3' ends of RNAs occurs in different organisms ranging from algae to humans, and on different kinds of RNAs, such as histone mRNAs, mRNA fragments, U6 snRNA, mature small RNAs and their precursors etc. These modifications may lead to different outcomes, such as increasing RNA decay, promoting or inhibiting RNA processing, or changing RNA activity. Growing pieces of evidence have revealed that such modifications can be RNA sequence-specific and subjected to temporal or spatial regulation in development. RNA tailing and its outcomes have been associated with human diseases such as cancer. Here, we review recent developments in RNA uridylation and adenylation and discuss the future prospects in this research area.
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Affiliation(s)
- JianBo Song
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science, Shenzhen University, Shenzhen, 518060, China
- Department of Biochemistry and Molecular Biology, College of Science, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jun Song
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - BeiXin Mo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science, Shenzhen University, Shenzhen, 518060, China.
| | - XueMei Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science, Shenzhen University, Shenzhen, 518060, China.
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
- Howard Hughes Medical Institute, University of California, Riverside, CA, 92521, USA.
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52
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Sanei M, Chen X. Mechanisms of microRNA turnover. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:199-206. [PMID: 26342825 PMCID: PMC4618239 DOI: 10.1016/j.pbi.2015.07.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide (nt) RNAs that regulate gene expression by guiding Argonaute (AGO) proteins to specific target RNAs to cause their degradation or translational repression. The abundance of miRNAs is strictly controlled at the transcriptional or post-transcriptional levels. miRNA turnover is presumably a necessary means to regulate miRNA levels in response to physiological, developmental, and environmental changes. miRNA 3' end methylation, 3' end nucleotide addition, AGO and complementary target transcripts are known or probable processes/factors that affect miRNA stability and turnover. Here we discuss the mechanisms that control miRNA turnover in plants and, where applicable, make references to similarities and differences in these mechanisms between plants and animals.
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Affiliation(s)
- Maryam Sanei
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, United States
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, United States; Howard Hughes Medical Institute, University of California, Riverside, CA, United States.
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53
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Arrigo P, Pulliero A. Effect of Environmental Chemical Stress on Nuclear Noncoding RNA Involved in Epigenetic Control. BIOMED RESEARCH INTERNATIONAL 2015; 2015:761703. [PMID: 26339639 PMCID: PMC4538421 DOI: 10.1155/2015/761703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/11/2015] [Indexed: 11/18/2022]
Abstract
In the last decade the role of noncoding RNAs (ncRNAs) emerges not only as key elements of posttranscriptional gene silencing, but also as important players of epigenetic regulation. New kind and new functions of ncRNAs are continuously discovered and one of their most important roles is the mediation of environmental signals, both physical and chemical. The activity of cytoplasmic short ncRNA is extensively studied, in spite of the fact that their function and role in the nuclear compartment are not yet completely unraveled. Cellular nucleus contains a multiplicity of long and short ncRNAs controlling at different levels transcriptional and epigenetic processes. In addition, some ncRNAs are involved in RNA editing and quality control. In this paper we review the existing knowledge dealing with how chemical stressors can influence the functionality of short nuclear ncRNAs. Furthermore, we perform bioinformatics analyses indicating that chemical environmental stressors not only induce DNA damage but also influence the mechanism of ncRNAs production and control.
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Affiliation(s)
- Patrizio Arrigo
- National Research Council (CNR), Institute for Macromolecular Studies (ISMAC), Via De Marini 6, 16149 Genoa, Italy
| | - Alessandra Pulliero
- Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy
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54
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Noto T, Kataoka K, Suhren JH, Hayashi A, Woolcock KJ, Gorovsky MA, Mochizuki K. Small-RNA-Mediated Genome-wide trans-Recognition Network in Tetrahymena DNA Elimination. Mol Cell 2015; 59:229-42. [PMID: 26095658 PMCID: PMC4518040 DOI: 10.1016/j.molcel.2015.05.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/06/2015] [Accepted: 05/15/2015] [Indexed: 12/27/2022]
Abstract
Small RNAs are used to silence transposable elements (TEs) in many eukaryotes, which use diverse evolutionary solutions to identify TEs. In ciliated protozoans, small-RNA-mediated comparison of the germline and somatic genomes underlies identification of TE-related sequences, which are then eliminated from the soma. Here, we describe an additional mechanism of small-RNA-mediated identification of TE-related sequences in the ciliate Tetrahymena. We show that a limited set of internal eliminated sequences (IESs) containing potentially active TEs produces a class of small RNAs that recognize not only the IESs from which they are derived, but also other IESs in trans. This trans recognition triggers the expression of yet another class of small RNAs that identify other IESs. Therefore, TE-related sequences in Tetrahymena are robustly targeted for elimination by a genome-wide trans-recognition network accompanied by a chain reaction of small RNA production. Two types of siRNAs (scnRNAs) are expressed in Tetrahymena sexual reproduction Early-scnRNAs are produced from Type-A IESs containing potentially active transposons Early-scnRNAs trans-recognize Type-B IESs and trigger late-scnRNA production in cis Late-scnRNA production forms trans-recognition network for robust IES elimination
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Affiliation(s)
- Tomoko Noto
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Kensuke Kataoka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Jan H Suhren
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Azusa Hayashi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Katrina J Woolcock
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Martin A Gorovsky
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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55
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Chromodomain protein Tcd1 is required for macronuclear genome rearrangement and repair in Tetrahymena. Sci Rep 2015; 5:10243. [PMID: 25989344 PMCID: PMC4437310 DOI: 10.1038/srep10243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/07/2015] [Indexed: 11/25/2022] Open
Abstract
The survival of an organism’s progeny depends on the maintenance of its genome. Programmed DNA rearrangement and repair in Tetrahymena occur during the differentiation of the developing somatic macronuclear genome from the germ line micronuclear genome. Tetrahymena chromodomain protein (Tcd1) exhibited dynamic localization from the parental to the developing macronuclei. In the developing macronuclei, Tcd1 colocalized with Pdd1 and H3K9me3. Furthermore, Tcd1 colocalized with Pdd1 in the conjusome and “donut structure” of DNA elimination heterochromatin region. During the growth and conjugation stages, TCD1 knockout cells appeared normal and similar to wild-type strains. In addition, these knockout cells proceeded to the 2MAC-1MIC stage. However, the progeny of the TCD1 knockout cells did not grow upon return to SPP medium and eventually died. The deletion of the internal elimination sequence R element was partially disrupted in the developing new macronuclei. Gamma H2A staining showed that Tcd1 loss induced the accumulation of DNA double-strand breaks and the failure of genome repair. These results suggest that the chromodomain protein Tcd1 is required for the rearrangement and repair of new macronuclear genome in Tetrahymena.
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56
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Polyuridylation in Eukaryotes: A 3'-End Modification Regulating RNA Life. BIOMED RESEARCH INTERNATIONAL 2015; 2015:968127. [PMID: 26078976 PMCID: PMC4442281 DOI: 10.1155/2015/968127] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/23/2015] [Accepted: 04/15/2015] [Indexed: 12/22/2022]
Abstract
In eukaryotes, mRNA polyadenylation is a well-known modification that is essential for many aspects of the protein-coding RNAs life cycle. However, modification of the 3′ terminal nucleotide within various RNA molecules is a general and conserved process that broadly modulates RNA function in all kingdoms of life. Numerous types of modifications have been characterized, which are generally specific for a given type of RNA such as the CCA addition found in tRNAs. In recent years, the addition of nontemplated uridine nucleotides or uridylation has been shown to occur in various types of RNA molecules and in various cellular compartments with significantly different outcomes. Indeed, uridylation is able to alter RNA half-life both in positive and in negative ways, highlighting the importance of the enzymes in charge of performing this modification. The present review aims at summarizing the current knowledge on the various processes leading to RNA 3′-end uridylation and on their potential impacts in various diseases.
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Tu B, Liu L, Xu C, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ramachandran V, Ren G, Yu B, Li S, Meyers BC, Mo B, Chen X. Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genet 2015; 11:e1005119. [PMID: 25928405 PMCID: PMC4415760 DOI: 10.1371/journal.pgen.1005119] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 03/03/2015] [Indexed: 12/31/2022] Open
Abstract
3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine other potential nucleotidyl transferases, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. Moreover, tailing of AGO1-bound miRNA165/6 drastically reduces the slicing activity of AGO1-miR165/6, suggesting that tailing reduces miRNA activity. However, monouridylation of miR171a by URT1 endows the miRNA the ability to trigger the biogenesis of secondary siRNAs. Therefore, 3’ tailing could affect the activities of miRNAs in addition to leading to miRNA degradation. The tailing of RNAs with non-templated uridines, known as uridylation, is often associated with RNA degradation. We previously identified HESO1 as a nucleotidyl transferase that uridylates microRNAs (miRNAs) to lead to their degradation in Arabidopsis. But HESO1 cannot account for all the miRNA uridylation activity in vivo. Here, we have uncovered UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) as another nucleotidyl transferase that uridylates miRNAs. HESO1 and URT1 have different substrate preferences and act cooperatively to tail miRNAs. We show that both enzymes are able to act on ARGONAUTE1 (AGO1)-bound miRNAs and that the tailed miRNAs stay bound by AGO1. We show that URT1-mediated tailing affects the activities of miR165/6 and miR171a differently. This study reveals intricate miRNA uridylation processes as well as functional outcomes of miRNA uridylation.
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Affiliation(s)
- Bin Tu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
- Rice Research Institute, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan, China
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Chi Xu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Jixian Zhai
- Department of Plant & Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Shengben Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Miguel A. Lopez
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Vanitharani Ramachandran
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Guodong Ren
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Bin Yu
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Shigui Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan, China
| | - Blake C. Meyers
- Department of Plant & Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Beixin Mo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, China
- * E-mail: (BM); (XC)
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, United States of America
- * E-mail: (BM); (XC)
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58
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MacColl E, Therkelsen MD, Sherpa T, Ellerbrock H, Johnston LA, Jariwala RH, Chang W, Gurtowski J, Schatz MC, Mozammal Hossain M, Cassidy-Hanley DM, Clark TG, Chang WJ. Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis. Mol Phylogenet Evol 2015; 86:1-7. [PMID: 25743182 DOI: 10.1016/j.ympev.2015.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/14/2015] [Accepted: 02/22/2015] [Indexed: 12/23/2022]
Abstract
Ichthyophthirius multifiliis is the etiologic agent of "white spot", a commercially important disease of freshwater fish. As a parasitic ciliate, I. multifiliis infects numerous host species across a broad geographic range. Although Ichthyophthirius outbreaks are difficult to control, recent sequencing of the I. multifiliis genome has revealed a number of potential metabolic pathways for therapeutic intervention, along with likely vaccine targets for disease prevention. Nonetheless, major gaps exist in our understanding of both the life cycle and population structure of I. multifiliis in the wild. For example, conjugation has never been described in this species, and it is unclear whether I. multifiliis undergoes sexual reproduction, despite the presence of a germline micronucleus. In addition, no good methods exist to distinguish strains, leaving phylogenetic relationships between geographic isolates completely unresolved. Here, we compared nucleotide sequences of SSUrDNA, mitochondrial NADH dehydrogenase subunit I and cox-1 genes, and 14 somatic SNP sites from nine I. multifiliis isolates obtained from four different states in the US since 1995. The mitochondrial sequences effectively distinguished the isolates from one another and divided them into at least two genetically distinct groups. Furthermore, none of the nine isolates shared the same composition of the 14 somatic SNP sites, suggesting that I. multifiliis undergoes sexual reproduction at some point in its life cycle. Finally, compared to the well-studied free-living ciliates Tetrahymena thermophila and Paramecium tetraurelia, I. multifiliis has lost 38% and 29%, respectively, of 16 experimentally confirmed conjugation-related genes, indicating that mechanistic differences in sexual reproduction are likely to exist between I. multifiliis and other ciliate species.
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Affiliation(s)
| | | | - Tshering Sherpa
- Department of Biology, Hamilton College, Clinton, NY 13323, USA
| | | | - Lily A Johnston
- Department of Biology, Hamilton College, Clinton, NY 13323, USA
| | - Ravi H Jariwala
- Department of Biology, Hamilton College, Clinton, NY 13323, USA
| | - WeiShu Chang
- Department of Biology, Hamilton College, Clinton, NY 13323, USA
| | - James Gurtowski
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - M Mozammal Hossain
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Donna M Cassidy-Hanley
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Theodore G Clark
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
| | - Wei-Jen Chang
- Department of Biology, Hamilton College, Clinton, NY 13323, USA.
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59
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Gou LT, Dai P, Liu MF. Small noncoding RNAs and male infertility. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:733-45. [PMID: 25044449 DOI: 10.1002/wrna.1252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Abstract
Small noncoding RNAs (ncRNAs) are a novel class of gene regulators that modulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, and they play crucial roles in almost all cellular processes in eukaryotes. Recent studies have indicated that several types of small noncoding RNAs, including microRNAs (miRNAs), endo-small interference RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs), are expressed in the male germline and are required for spermatogenesis in animals. In this review, we summarize the recent knowledge of these small noncoding RNAs in male germ cells and their biological functions and mechanisms of action in animal spermatogenesis.
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Affiliation(s)
- Lan-Tao Gou
- Center for RNA Research, State Key Laboratory of Molecular Biology-University of Chinese Academy of Sciences, Shanghai, China; Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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60
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Noto T, Kurth HM, Mochizuki K. Analysis of Piwi-loaded small RNAs in Tetrahymena. Methods Mol Biol 2014; 1093:209-24. [PMID: 24178568 DOI: 10.1007/978-1-62703-694-8_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Scan RNAs (scnRNAs) are developmentally regulated siRNAs of ~26-32 nucleotides in length that are involved in programmed DNA elimination in Tetrahymena. scnRNAs are loaded onto the Piwi-related protein Twi1p and 2'-O-methylated at their 3' termini. We describe two alternative strategies for analyzing the Twi1p-loaded scnRNAs: preparation of loaded scnRNAs by immuno-purification of the Twi1p-scnRNA complex and exclusion of non-methylated scnRNAs during cDNA library construction using periodate oxidation.
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Affiliation(s)
- Tomoko Noto
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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61
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Dueck A, Meister G. Assembly and function of small RNA – Argonaute protein complexes. Biol Chem 2014; 395:611-29. [DOI: 10.1515/hsz-2014-0116] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
Abstract
Abstract
Small RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs) or Piwi-interacting RNAs (piRNAs) are important regulators of gene expression in various organisms. Small RNAs bind to a member of the Argonaute protein family and are incorporated into larger structures that mediate diverse gene silencing events. The loading of Argonaute proteins with small RNAs is aided by a number of auxiliary factors as well as ATP hydrolysis. This review will focus on the mechanisms of Argonaute loading in different organisms. Furthermore, we highlight the versatile functions of small RNA-Argonaute protein complexes in organisms from all three kingdoms of life.
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62
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Abstract
Cell identities can be stable over a long time due to a “cellular memory” of expression profiles achieved through epigenetic mechanisms. In this review, Stuwe et al. describe recent studies demonstrating that short noncoding RNAs can also provide molecular signals that define epigenetic states of cells, leading to transgenerational epigenetic inheritance. Cells in multicellular organisms have distinct identities characterized by their profiles of expressed genes. Cell identities can be stable over a long time and through multiple cellular divisions but are also responsive to extracellular signals. Since the DNA sequence is identical in all cells, a “cellular memory” of expression profiles is achieved by what are defined as epigenetic mechanisms. Two major molecular principles—networks of transcription factors and maintenance of cis-chromatin modifications—have been implicated in maintaining cellular memory. Here we describe recent studies demonstrating that short noncoding RNAs can also provide molecular signals that define epigenetic states of cells. Small RNAs can act independently or cooperate with chromatin modifications to achieve long-lasting effects necessary for cellular memory and transgenerational inheritance.
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Affiliation(s)
- Evelyn Stuwe
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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63
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Abe M, Naqvi A, Hendriks GJ, Feltzin V, Zhu Y, Grigoriev A, Bonini NM. Impact of age-associated increase in 2'-O-methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes Dev 2014; 28:44-57. [PMID: 24395246 PMCID: PMC3894412 DOI: 10.1101/gad.226654.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
miRNAs exhibit heterogeneity in length and sequence in different biological contexts. Abe et al. found that Drosophila miRNAs undergo isoform pattern changes with age, and an increase of some miRNAs reflects increased 2′-O-methylation of select isoforms. Loading of miRNAs into Ago2, but not Ago1, increased with age. Hen1 and Ago2 mutations caused accelerated neurodegeneration and shorter life span, suggesting that the age-associated increase of 2′-O-methylation of miRNAs affects age-associated processes. MicroRNAs (miRNAs) are 20- to ∼24-nucleotide (nt) small RNAs that impact a variety of biological processes, from development to age-associated events. To study the role of miRNAs in aging, studies have profiled the levels of miRNAs with time. However, evidence suggests that miRNAs show heterogeneity in length and sequence in different biological contexts. Here, by examining the expression pattern of miRNAs by Northern blot analysis, we found that Drosophila miRNAs show distinct isoform pattern changes with age. Surprisingly, an increase of some miRNAs reflects increased 2′-O-methylation of select isoforms. Small RNA deep sequencing revealed a global increase of miRNAs loaded into Ago2, but not into Ago1, with age. Our data suggest increased loading of miRNAs into Ago2, but not Ago1, with age, indicating a mechanism for differential loading of miRNAs with age between Ago1 and Ago2. Mutations in Hen1 and Ago2, which lack 2′-O-methylation of miRNAs, result in accelerated neurodegeneration and shorter life span, suggesting a potential impact of the age-associated increase of 2′-O-methylation of small RNAs on age-associated processes. Our study highlights that miRNA 2′-O-methylation at the 3′ end is modulated by differential partitioning of miRNAs between Ago1 and Ago2 with age and that this process, along with other functions of Ago2, might impact age-associated events in Drosophila.
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Affiliation(s)
- Masashi Abe
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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64
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Burroughs AM, Ando Y, Aravind L. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:141-81. [PMID: 24311560 DOI: 10.1002/wrna.1210] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022]
Abstract
Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense-antisense transcriptional products, (2) genome-encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNAi. They were recruited alongside RNaseIII domains and RNA-dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs.
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Affiliation(s)
- Alexander Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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65
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Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
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Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
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66
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Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res 2013; 42:1414-26. [PMID: 24198247 PMCID: PMC3919602 DOI: 10.1093/nar/gkt1021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany and Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
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67
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Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification. EUKARYOTIC CELL 2013; 13:77-86. [PMID: 24186950 DOI: 10.1128/ec.00233-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Parasitic protozoa of the flagellate order Kinetoplastida represent one of the deepest branches of the eukaryotic tree. Among this group of organisms, the mechanism of RNA interference (RNAi) has been investigated in Trypanosoma brucei and to a lesser degree in Leishmania (Viannia) spp. The pathway is triggered by long double-stranded RNA (dsRNA) and in T. brucei requires a set of five core genes, including a single Argonaute (AGO) protein, T. brucei AGO1 (TbAGO1). The five genes are conserved in Leishmania (Viannia) spp. but are absent in other major kinetoplastid species, such as Trypanosoma cruzi and Leishmania major. In T. brucei small interfering RNAs (siRNAs) are methylated at the 3' end, whereas Leishmania (Viannia) sp. siRNAs are not. Here we report that T. brucei HEN1, an ortholog of the metazoan HEN1 2'-O-methyltransferases, is required for methylation of siRNAs. Loss of TbHEN1 causes a reduction in the length of siRNAs. The shorter siRNAs in hen1(-/-) parasites are single stranded and associated with TbAGO1, and a subset carry a nontemplated uridine at the 3' end. These findings support a model wherein TbHEN1 methylates siRNA 3' ends after they are loaded into TbAGO1 and this methylation protects siRNAs from uridylation and 3' trimming. Moreover, expression of TbHEN1 in Leishmania (Viannia) panamensis did not result in siRNA 3' end methylation, further emphasizing mechanistic differences in the trypanosome and Leishmania RNAi mechanisms.
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68
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Mechanistic insights into small RNA recognition and modification by the HEN1 methyltransferase. Biochem J 2013; 453:281-90. [PMID: 23621770 DOI: 10.1042/bj20121699] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The HEN1 methyltransferase from Arabidopsis thaliana modifies the 3'-terminal nucleotides of small regulatory RNAs. Although it is one of the best characterized members of the 2'-O-methyltransferase family, many aspects of its interactions with the cofactor and substrate RNA remained unresolved. To better understand the substrate interactions and contributions of individual steps during HEN1 catalysis, we studied the binding and methylation kinetics of the enzyme using a series of unmethylated, hemimethylated and doubly methylated miRNA and siRNA substrates. The present study shows that HEN1 specifically binds double-stranded unmethylated or hemimethylated miR173/miR173* substrates with a subnanomolar affinity in a cofactor-dependent manner. Kinetic studies under single turnover and pre-steady state conditions in combination with isotope partitioning analysis showed that the binary HEN1-miRNA/miRNA* complex is catalytically competent; however, successive methylation of the two strands in a RNA duplex occurs in a non-processive (distributive) manner. We also find that the observed moderate methylation strand preference is largely exerted at the RNA-binding step and is fairly independent of the nature of the 3'-terminal nucleobase, but shows some dependency on proximal nucleotide mispairs. The results of the present study thus provide novel insights into the mechanism of RNA recognition and modification by a representative small RNA 2'-O-methyltransferase.
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69
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Feng X, Guang S. Non-coding RNAs mediate the rearrangements of genomic DNA in ciliates. SCIENCE CHINA-LIFE SCIENCES 2013; 56:937-43. [PMID: 24008384 DOI: 10.1007/s11427-013-4539-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/10/2013] [Indexed: 01/24/2023]
Abstract
Most eukaryotes employ a variety of mechanisms to defend the integrity of their genome by recognizing and silencing parasitic mobile nucleic acids. However, recent studies have shown that genomic DNA undergoes extensive rearrangements, including DNA elimination, fragmentation, and unscrambling, during the sexual reproduction of ciliated protozoa. Non-coding RNAs have been identified to program and regulate genome rearrangement events. In Paramecium and Tetrahymena, scan RNAs (scnRNAs) are produced from micronuclei and transported to vegetative macronuclei, in which scnRNA elicits the elimination of cognate genomic DNA. In contrast, Piwi-interacting RNAs (piRNAs) in Oxytricha enable the retention of genomic DNA that exhibits sequence complementarity in macronuclei. An RNA interference (RNAi)-like mechanism has been found to direct these genomic rearrangements. Furthermore, in Oxytricha, maternal RNA templates can guide the unscrambling process of genomic DNA. The non-coding RNA-directed genome rearrangements may have profound evolutionary implications, for example, eliciting the multigenerational inheritance of acquired adaptive traits.
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Affiliation(s)
- Xuezhu Feng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
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70
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Luteijn MJ, Ketting RF. PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat Rev Genet 2013; 14:523-34. [PMID: 23797853 DOI: 10.1038/nrg3495] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small-RNA-guided gene regulation is a recurring theme in biology. Animal germ cells are characterized by an intriguing small-RNA-mediated gene-silencing mechanism known as the PIWI pathway. For a long time, both the biogenesis of PIWI-interacting RNAs (piRNAs) as well as their mode of gene silencing has remained elusive. A recent body of work is shedding more light on both aspects and implicates PIWI in the establishment of transgenerational epigenetic states. In fact, the epigenetic states imposed by PIWI on targets may actually drive piRNA production itself. These findings start to couple small RNA biogenesis with small-RNA-mediated epigenetics.
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Affiliation(s)
- Maartje J Luteijn
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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71
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Mochizuki K, Kurth HM. Loading and pre-loading processes generate a distinct siRNA population in Tetrahymena. Biochem Biophys Res Commun 2013; 436:497-502. [PMID: 23770361 PMCID: PMC3714595 DOI: 10.1016/j.bbrc.2013.05.133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 05/30/2013] [Indexed: 12/04/2022]
Abstract
The various properties of small RNAs, such as length, terminal nucleotide, thermodynamic asymmetry and duplex mismatches, can impact their sorting into different Argonaute proteins in diverse eukaryotes. The developmentally regulated 26- to 32-nt siRNAs (scnRNAs) are loaded to the Argonaute protein Twi1p and display a strong bias for uracil at the 5′ end. In this study, we used deep sequencing to analyze loaded and unloaded populations of scnRNAs. We show that the size of the scnRNA is determined during a pre-loading process, whereas their 5′ uracil bias is attributed to both pre-loading and loading processes. We also demonstrate that scnRNAs have a strong bias for adenine at the third base from the 3′ terminus, suggesting that most scnRNAs are direct Dicer products. Furthermore, we show that the thermodynamic asymmetry of the scnRNA duplex does not affect the guide and passenger strand decision. Finally, we show that scnRNAs frequently have templated uracil at the last base without a strong bias for adenine at the second base indicating non-sequential production of scnRNAs from substrates. These findings provide a biochemical basis for the varying attributes of scnRNAs, which should help improve our understanding of the production and turnover of scnRNAs in vivo.
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Affiliation(s)
- Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria.
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72
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microRNAs and the regulation of neuronal plasticity under stress conditions. Neuroscience 2013; 241:188-205. [DOI: 10.1016/j.neuroscience.2013.02.065] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/26/2013] [Accepted: 02/26/2013] [Indexed: 12/21/2022]
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Abstract
Ciliates are an ancient and diverse group of microbial eukaryotes that have emerged as powerful models for RNA-mediated epigenetic inheritance. They possess extensive sets of both tiny and long noncoding RNAs that, together with a suite of proteins that includes transposases, orchestrate a broad cascade of genome rearrangements during somatic nuclear development. This Review emphasizes three important themes: the remarkable role of RNA in shaping genome structure, recent discoveries that unify many deeply diverged ciliate genetic systems, and a surprising evolutionary "sign change" in the role of small RNAs between major species groups.
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Billi AC, Freeberg MA, Day AM, Chun SY, Khivansara V, Kim JK. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet 2013; 9:e1003392. [PMID: 23516384 PMCID: PMC3597512 DOI: 10.1371/journal.pgen.1003392] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 01/21/2013] [Indexed: 11/21/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) fulfill a critical, conserved role in defending the genome against foreign genetic elements. In many organisms, piRNAs appear to be derived from processing of a long, polycistronic RNA precursor. Here, we establish that each Caenorhabditis elegans piRNA represents a tiny, autonomous transcriptional unit. Remarkably, the minimal C. elegans piRNA cassette requires only a 21 nucleotide (nt) piRNA sequence and an ∼50 nt upstream motif with limited genomic context for expression. Combining computational analyses with a novel, in vivo transgenic system, we demonstrate that this upstream motif is necessary for independent expression of a germline-enriched, Piwi-dependent piRNA. We further show that a single nucleotide position within this motif directs differential germline enrichment. Accordingly, over 70% of C. elegans piRNAs are selectively expressed in male or female germline, and comparison of the genes they target suggests that these two populations have evolved independently. Together, our results indicate that C. elegans piRNA upstream motifs act as independent promoters to specify which sequences are expressed as piRNAs, how abundantly they are expressed, and in what germline. As the genome encodes well over 15,000 unique piRNA sequences, our study reveals that the number of transcriptional units encoding piRNAs rivals the number of mRNA coding genes in the C. elegans genome. Across the animal kingdom, Piwi-interacting small RNAs (piRNAs) protect genome integrity and promote fertility. While the functions of piRNAs are well-characterized, far less is known about how they are generated and how their expression is regulated. In the Caenorhabditis elegans genome, a conserved sequence motif lies upstream of many piRNA loci and appears to regulate their expression. We combined computational and experimental approaches to investigate the role of this motif in the expression of C. elegans piRNAs. We discovered that >70% of piRNAs are differentially enriched in male versus female germline, and these male and female piRNAs show different upstream motifs. Using a transgenic system for expressing synthetic piRNAs in vivo, we demonstrate that variation of a single nucleotide within this motif influences piRNA germline enrichment. We further show that the conserved motif is capable of driving piRNA expression in genomic isolation. Accordingly, the genomic distribution of these motifs determines which sequences are expressed as piRNAs in C. elegans. Our results suggest that each C. elegans piRNA represents an independent transcript whose sequence, abundance, and germline enrichment are encoded by a variant upstream motif, defining a novel modality for expression of piRNAs.
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Affiliation(s)
- Allison C. Billi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mallory A. Freeberg
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amanda M. Day
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sang Young Chun
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Vishal Khivansara
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John K. Kim
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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75
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Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell 2013; 151:1243-55. [PMID: 23217708 DOI: 10.1016/j.cell.2012.10.045] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/19/2012] [Accepted: 10/04/2012] [Indexed: 10/27/2022]
Abstract
Genome duality in ciliated protozoa offers a unique system to showcase their epigenome as a model of inheritance. In Oxytricha, the somatic genome is responsible for vegetative growth, whereas the germline contributes DNA to the next sexual generation. Somatic nuclear development removes all transposons and other so-called "junk" DNA, which comprise ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. Oxytricha piRNAs map primarily to the somatic genome, representing the ~5% of the germline that is retained. Furthermore, injection of synthetic piRNAs corresponding to normally deleted regions leads to their retention in later generations. Our findings highlight small RNAs as powerful transgenerational carriers of epigenetic information for genome programming.
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Affiliation(s)
- Wenwen Fang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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76
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Scott DD, Norbury CJ. RNA decay via 3' uridylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:654-65. [PMID: 23385389 DOI: 10.1016/j.bbagrm.2013.01.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 01/22/2013] [Accepted: 01/24/2013] [Indexed: 11/30/2022]
Abstract
The post-transcriptional addition of non-templated nucleotides to the 3' ends of RNA molecules can have a profound impact on their stability and biological function. Evidence accumulated over the past few decades has identified roles for polyadenylation in RNA stabilisation, degradation and, in the case of eukaryotic mRNAs, translational competence. By contrast, the biological significance of RNA 3' modification by uridylation has only recently started to become apparent. The evolutionary origin of eukaryotic RNA terminal uridyltransferases can be traced to an ancestral poly(A) polymerase. Here we review what is currently known about the biological roles of these enzymes, the ways in which their activity is regulated and the consequences of this covalent modification for the target RNA molecule, with a focus on those instances where uridylation has been found to contribute to RNA degradation. Roles for uridylation have been identified in the turnover of mRNAs, pre-microRNAs, piwi-interacting RNAs and the products of microRNA-directed mRNA cleavage; many mature microRNAs are also modified by uridylation, though the consequences in this case are currently less well understood. In the case of piwi-interacting RNAs, modification of the 3'-terminal nucleotide by the HEN1 methyltransferase blocks uridylation and so stabilises the small RNA. The extent to which other uridylation-dependent mechanisms of RNA decay are similarly regulated awaits further investigation. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Daniel D Scott
- University of Oxford, Sir William Dunn School of Pathology, Oxford, UK.
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77
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Atayde VD, Shi H, Franklin JB, Carriero N, Notton T, Lye LF, Owens K, Beverley SM, Tschudi C, Ullu E. The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway. Mol Microbiol 2012; 87:580-93. [PMID: 23217017 DOI: 10.1111/mmi.12117] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2012] [Indexed: 12/01/2022]
Abstract
Among trypanosomatid protozoa the mechanism of RNA interference (RNAi) has been investigated in Trypanosoma brucei and to a lesser extent in Leishmania braziliensis. Although these two parasitic organisms belong to the same family, they are evolutionarily distantly related raising questions about the conservation of the RNAi pathway. Here we carried out an in-depth analysis of small interfering RNAs (siRNAs) associated with L. braziliensis Argonaute1 (LbrAGO1). In contrast to T. brucei, Leishmania siRNAs are sensitive to 3' end oxidation, indicating the absence of blocking groups, and the Leishmania genome does not code for a HEN1 RNA 2'-O-methyltransferase, which modifies small RNA 3' ends. Consistent with this observation, ~20% of siRNA 3' ends carry non-templated uridines. Thus siRNA biogenesis, and most likely their metabolism, is different in these organisms. Similarly to T. brucei, putative mobile elements and repeats constitute the major Leishmania siRNA-producing loci and AGO1 ablation leads to accumulation of long transcripts derived from putative mobile elements. However, contrary to T. brucei, no siRNAs were detected from other genomic regions with the potential to form double-stranded RNA, namely sites of convergent transcription and inverted repeats. Thus, our results indicate that organism-specific diversification has occurred in the RNAi pathway during evolution of the trypanosomatid lineage.
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Affiliation(s)
- Vanessa D Atayde
- Departments of Internal Medicine, Yale University, New Haven, CT 06536, USA
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78
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Abstract
There is growing evidence to support the notion that small RNAs derived from noncoding RNAs (ncRNAs) are mobile carriers of epigenetic information in diverse eukaryotic systems. However, challenges remain in defining what messages are being sent and how. In the August 1, 2012, issue of Genes & Development, Schoeberl and colleagues (pp. 1729-1742) reported a detailed analysis of the turnover of small RNAs during the sexual reproduction of the ciliated protozoan Tetrahymena. The results revealed surprisingly complicated roles played by small RNAs in shaping the communication between the germline and the soma.
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Affiliation(s)
- Shan Gao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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79
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Abstract
microRNAs (miRNAs) are 20-24 nucleotide RNAs that regulate a variety of developmental and metabolic processes. The accumulation of miRNAs in vivo can be controlled at multiple levels. In addition to miRNA biogenesis, mechanisms that lead to RNA degradation, such as 3' uridylation and 3' truncation, also affect the steady-state levels of miRNAs. On the other hand, 2'-O-methylation in plant miRNAs protects their 3' ends from truncation and uridylation. The recent identification of HESO1 as the key enzyme responsible for miRNA uridylation in Arabidopsis was a first step toward a full understanding of the mechanisms underlying miRNA turnover. Analyses of the heso1 mutant predicted the existence of another uridylation activity and a previously unknown nuclease that act on miRNAs. The future identification of these enzymes will enrich our understanding of miRNA turnover.
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Affiliation(s)
- Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
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80
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Beyret E, Liu N, Lin H. piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism. Cell Res 2012; 22:1429-39. [PMID: 22907665 DOI: 10.1038/cr.2012.120] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
piRNAs, a class of small non-coding RNAs associated with PIWI proteins, have broad functions in germline development, transposon silencing, and epigenetic regulation. In diverse organisms, a subset of piRNAs derived from repeat sequences are produced via the interplay between two PIWI proteins. This mechanism, termed "ping-pong" cycle, operates among the PIWI proteins of the primordial mouse testis; however, its involvement in postnatal testes remains elusive. Here we show that adult testicular piRNAs are produced independent of the ping-pong mechanism. We identified and characterized large populations of piRNAs in the adult and postnatal developing testes associated with MILI and MIWI, the only PIWI proteins detectable in these testes. No interaction between MILI and MIWI or sequence feature for the ping-pong mechanism among their piRNAs was detected in the adult testis. The majority of MILI- and MIWI-associated piRNAs originate from the same DNA strands within the same loci. Both populations of piRNAs are biased for 5' Uracil but not for Adenine on the 10th nucleotide position, and display no complementarity. Furthermore, in Miwi mutants, MILI-associated piRNAs are not downregulated, but instead upregulated. These results indicate that the adult testicular piRNAs are predominantly, if not exclusively, produced by a primary processing mechanism instead of the ping-pong mechanism. In this primary pathway, biogenesis of MILI- and MIWI-associated piRNAs may compete for the same precursors; the types of piRNAs produced tend to be non-selectively dictated by the available precursors in the cell; and precursors with introns tend to be spliced before processed into piRNAs.
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Affiliation(s)
- Ergin Beyret
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06509, USA
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81
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Zahler AM, Neeb ZT, Lin A, Katzman S. Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus. PLoS One 2012; 7:e42371. [PMID: 22900016 PMCID: PMC3416858 DOI: 10.1371/journal.pone.0042371] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/06/2012] [Indexed: 01/04/2023] Open
Abstract
Ciliated protozoans possess two types of nuclei; a transcriptionally silent micronucleus, which serves as the germ line nucleus, and a transcriptionally active macronucleus, which serves as the somatic nucleus. The macronucleus is derived from a new diploid micronucleus after mating, with epigenetic information contributed by the parental macronucleus serving to guide the formation of the new macronucleus. In the stichotrichous ciliate Oxytricha trifallax, the macronuclear DNA is highly processed to yield gene-sized nanochromosomes with telomeres at each end. Here we report that soon after mating of Oxytricha trifallax, abundant 27 nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of Oxytricha small RNAs from vegetative and mating cells. Using sequence comparisons between macronuclear and micronuclear versions of genes, we found that the 27 nt RNA class derives from the parental macronucleus, not the developing macronucleus. These small RNAs are produced equally from both strands of macronuclear nanochromosomes, but in a highly non-uniform distribution along the length of the nanochromosome, and with a particular depletion in the 30 nt telomere-proximal positions. This production of small RNAs from the parental macronucleus during macronuclear development stands in contrast to the mechanism of epigenetic control in the distantly related ciliate Tetrahymena. In that species, 28-29 nt scanRNAs are produced from the micronucleus and these micronuclear-derived RNAs serve as epigenetic controllers of macronuclear development. Unlike the Tetrahymena scanRNAs, the Oxytricha macronuclear-derived 27 mers are not modified by 2'O-methylation at their 3' ends. We propose models for the role of these "27macRNAs" in macronuclear development.
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Affiliation(s)
- Alan M Zahler
- Department of Molecular, Cell and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America.
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82
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Schoeberl UE, Kurth HM, Noto T, Mochizuki K. Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena. Genes Dev 2012; 26:1729-42. [PMID: 22855833 PMCID: PMC3418590 DOI: 10.1101/gad.196493.112] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/21/2012] [Indexed: 01/05/2023]
Abstract
The ciliated protozoan Tetrahymena undergoes extensive programmed DNA elimination when the germline micronucleus produces the new macronucleus during sexual reproduction. DNA elimination is epigenetically controlled by DNA sequences of the parental macronuclear genome, and this epigenetic regulation is mediated by small RNAs (scan RNAs [scnRNAs]) of ∼28-30 nucleotides that are produced and function by an RNAi-related mechanism. Here, we examine scnRNA production and turnover by deep sequencing. scnRNAs are produced exclusively from the micronucleus and nonhomogeneously from a variety of chromosomal locations. scnRNAs are preferentially derived from the eliminated sequences, and this preference is mainly determined at the level of transcription. Despite this bias, a significant fraction of scnRNAs is also derived from the macronuclear-destined sequences, and these scnRNAs are degraded during the course of sexual reproduction. These results indicate that the pattern of DNA elimination in the new macronucleus is shaped by the biased transcription in the micronucleus and the selective degradation of scnRNAs in the parental macronucleus.
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Affiliation(s)
| | | | | | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
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83
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Differential impact of the HEN1 homolog HENN-1 on 21U and 26G RNAs in the germline of Caenorhabditis elegans. PLoS Genet 2012; 8:e1002702. [PMID: 22829772 PMCID: PMC3400576 DOI: 10.1371/journal.pgen.1002702] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 02/21/2012] [Indexed: 02/07/2023] Open
Abstract
RNA interference (RNAi)–related pathways affect gene activity by sequence-specific recruitment of Ago proteins to mRNA target molecules. The sequence specificity of this process stems from small RNA (sRNA) co-factors bound by the Ago protein. Stability of sRNA molecules in some pathways is in part regulated by Hen1-mediated methylation of their 3′ ends. Here we describe the effects of the Caenorhabditis elegans HEN1 RNA–methyl-transferase homolog, HENN-1, on the different RNAi pathways in this nematode. We reveal differential effects of HENN-1 on the two pathways that are known to employ methylated sRNA molecules: the 26G and 21U pathways. Surprisingly, in the germline, stability of 21U RNAs, the C. elegans piRNAs, is only mildly affected by loss of methylation; and introduction of artificial 21U target RNA does not further destabilize non-methylated 21U RNAs. In contrast, most 26G RNAs display reduced stability and respond to loss of HENN-1 by displaying increased 3′-uridylation frequencies. Within the 26G RNA class, we find that specifically ERGO-1–bound 26G RNAs are modified by HENN-1, while ALG-3/ALG-4–bound 26G RNAs are not. Global gene expression analysis of henn-1 mutants reveals mild effects, including down-regulation of many germline-expressed genes. Our data suggest that, apart from direct effects of reduced 26G RNA levels of henn-1 on gene expression, most effects on global gene expression are indirect. These studies further refine our understanding of endogenous RNAi in C. elegans and the roles for Hen1 like enzymes in these pathways. Small RNAs (sRNAs) have been shown to be potent regulators of gene expression in many different systems. They act by providing sequence specificity to Argonaute (Ago) proteins that in turn affect the expression and/or stability of mRNAs, or affect chromatin structures through recognition of nascent transcripts. Stability of sRNAs can be regulated by methylation of their 3′ end. This modification prevents addition of uridine residues that can destabilize the sRNA. The enzyme that catalyzes the methylation of sRNAs has been identified in Arabidopsis: HEN1. We describe studies on the C. elegans homolog of Hen1, henn-1. Our findings show that HENN-1 protein does not stably associate with the Ago proteins binding methylated sRNAs, but that HENN-1 does localize to subcellular regions known to host these factors. We find that the two known methylated sRNA species in C. elegans (21U and 26G) respond differently to loss of henn-1. While HENN-1 is required for 26G RNA stability in the germline, it has limited impact on 21U RNAs. In addition, we demonstrate that only ERGO-1–bound 26G RNAs are methylated, while those bound by ALG-3/4, are not. Our findings further refine the general understanding of 21U and 26G RNA pathways and identify two separable effects of HENN-1 on these RNAi–related mechanisms.
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84
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Shen Y, Zheng KX, Duan D, Jiang L, Li J. Label-Free MicroRNA Profiling Not Biased by 3′ End 2′-O-Methylation. Anal Chem 2012; 84:6361-5. [DOI: 10.1021/ac301360z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ye Shen
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ke-xiao Zheng
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Demin Duan
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Jiang
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Jiong Li
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
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85
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Huang RH. Unique 2'-O-methylation by Hen1 in eukaryotic RNA interference and bacterial RNA repair. Biochemistry 2012; 51:4087-95. [PMID: 22564049 DOI: 10.1021/bi300497x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In an RNA transcript, the 2'-OH group at the 3'-terminal nucleotide is unique as it is the only 2'-OH group that is adjacent to a 3'-OH group instead of a phosphate backbone. The 2'-OH group at the 3'-terminal nucleotide of certain RNAs is methylated in vivo, which is acheived by a methyltransferase named Hen1 that is mechanistically distinct from other known RNA 2'-O-methyltransferases. In eukaryotic organisms, 3'-terminal 2'-O-methylation of small RNAs stabilizes these small RNAs for RNA interference (RNAi). In bacteria, the same methylation during RNA repair results in repaired RNA resisting future damage at the site of repair. Although the chemistry performed by the eukaryotic and bacterial Hen1 is the same, the mechanisms of how RNA is stabilized as a result of the 3'-terminal 2'-O-methylation are different between the eukaryotic RNAi and the bacterial RNA repair. In this review, I will discuss the distribution of Hen1 in living organisms, the classification of Hen1 into four subfamilies, the structure and mechanism of Hen1 that allows it to conduct RNA 3'-terminal 2'-O-methylation, and the possible evolutionary origin of Hen1 present in bacterial and eukaryotic organisms.
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Affiliation(s)
- Raven H Huang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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86
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Montgomery TA, Rim YS, Zhang C, Dowen RH, Phillips CM, Fischer SEJ, Ruvkun G. PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PLoS Genet 2012; 8:e1002616. [PMID: 22536158 PMCID: PMC3334881 DOI: 10.1371/journal.pgen.1002616] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 02/03/2012] [Indexed: 12/29/2022] Open
Abstract
Small RNAs--including piRNAs, miRNAs, and endogenous siRNAs--bind Argonaute proteins to form RNA silencing complexes that target coding genes, transposons, and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in Caenorhabditis elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. Silencing of the sensor is also dependent on the partially complementary, unlinked 26G siR-O7 siRNA. We show that 26G siR-O7 acts in trans to initiate 22G siRNA formation from the X-cluster. The presence of several mispairs between 26G siR-O7 and the X-cluster mRNA, as well as mutagenesis of the siRNA sensor, indicates that siRNA target recognition is permissive to a degree of mispairing. From a candidate reverse genetic screen, we identified several factors required for 22G siR-1 activity, including the chromatin factors mes-4 and gfl-1, the Argonaute ergo-1, and the 3' methyltransferase henn-1. Quantitative RT-PCR of small RNAs in a henn-1 mutant and deep sequencing of methylated small RNAs indicate that siRNAs and piRNAs that associate with PIWI clade Argonautes are methylated by HENN-1, while siRNAs and miRNAs that associate with non-PIWI clade Argonautes are not. Thus, PIWI-class Argonaute proteins are specifically adapted to associate with methylated small RNAs in C. elegans.
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Affiliation(s)
| | | | | | | | | | | | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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87
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The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. PLoS Genet 2012; 8:e1002617. [PMID: 22548001 PMCID: PMC3330095 DOI: 10.1371/journal.pgen.1002617] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 02/03/2012] [Indexed: 01/01/2023] Open
Abstract
Small RNAs regulate diverse biological processes by directing effector proteins called Argonautes to silence complementary mRNAs. Maturation of some classes of small RNAs involves terminal 2'-O-methylation to prevent degradation. This modification is catalyzed by members of the conserved HEN1 RNA methyltransferase family. In animals, Piwi-interacting RNAs (piRNAs) and some endogenous and exogenous small interfering RNAs (siRNAs) are methylated, whereas microRNAs are not. However, the mechanisms that determine animal HEN1 substrate specificity have yet to be fully resolved. In Caenorhabditis elegans, a HEN1 ortholog has not been studied, but there is evidence for methylation of piRNAs and some endogenous siRNAs. Here, we report that the worm HEN1 ortholog, HENN-1 (HEN of Nematode), is required for methylation of C. elegans small RNAs. Our results indicate that piRNAs are universally methylated by HENN-1. In contrast, 26G RNAs, a class of primary endogenous siRNAs, are methylated in female germline and embryo, but not in male germline. Intriguingly, the methylation pattern of 26G RNAs correlates with the expression of distinct male and female germline Argonautes. Moreover, loss of the female germline Argonaute results in loss of 26G RNA methylation altogether. These findings support a model wherein methylation status of a metazoan small RNA is dictated by the Argonaute to which it binds. Loss of henn-1 results in phenotypes that reflect destabilization of substrate small RNAs: dysregulation of target mRNAs, impaired fertility, and enhanced somatic RNAi. Additionally, the henn-1 mutant shows a weakened response to RNAi knockdown of germline genes, suggesting that HENN-1 may also function in canonical RNAi. Together, our results indicate a broad role for HENN-1 in both endogenous and exogenous gene silencing pathways and provide further insight into the mechanisms of HEN1 substrate discrimination and the diversity within the Argonaute family.
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88
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Coyne RS, Lhuillier-Akakpo M, Duharcourt S. RNA-guided DNA rearrangements in ciliates: is the best genome defence a good offence? Biol Cell 2012; 104:309-25. [PMID: 22352444 DOI: 10.1111/boc.201100057] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/15/2012] [Indexed: 12/13/2022]
Abstract
Genomes, like crazy patchwork quilts, are stitched together over evolutionary time from diverse elements, including some unwelcome invaders. To deal with parasitic mobile elements, most eukaryotes employ a genome self-defensive manoeuvre to recognise and silence such elements by homology-dependent interactions with RNA-protein complexes that alter chromatin. Ciliated protozoa employ more 'offensive' tactics by actually unstitching and reassembling their somatic genomes at every sexual generation to eliminate transposons and their remnants, using as patterns the maternal genomes that were rearranged in the previous cycle. Genetic and genomic studies of the distant relatives Paramecium and Tetrahymena have begun to reveal how such events are carried out with remarkable precision. Whole genome, non-coding transcripts from the maternal genome are compared with transcripts from the zygotic genome that are processed through an RNA interference (RNAi)-related process. Sequences found only in the latter are targeted for elimination by the resulting short 'scanRNAs' in many thousand DNA splicing reactions initiated by a domesticated transposase. The involvement of widely conserved mechanisms and protein factors clearly shows the relatedness of these phenomena to RNAi-mediated heterochromatic gene silencing. Such malleability of the genome on a generational time scale also has profound evolutionary implications, possibly including the epigenetic inheritance of acquired adaptive traits.
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89
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Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh TT, Meyers BC, Mo B, Chen X. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol 2012; 22:689-94. [PMID: 22464194 DOI: 10.1016/j.cub.2012.02.051] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
MicroRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs) impact numerous biological processes in eukaryotes. In addition to biogenesis, turnover contributes to the steady-state levels of small RNAs. One major factor that stabilizes miRNAs and siRNAs in plants as well as siRNAs and piRNAs in animals is 2'-O-methylation on the 3' terminal ribose by the methyltransferase HUA ENHANCER1 (HEN1) [1-6]. Genetic studies with Arabidopsis, Drosophila, and zebrafish hen1 mutants show that 2'-O-methylation protects small RNAs from 3'-to-5' truncation and 3' uridylation, the addition of nontemplated nucleotides, predominantly uridine [2, 7, 8]. Uridylation is a widespread phenomenon that is not restricted to small RNAs in hen1 mutants and is often associated with their reduced accumulation ([7, 9, 10]; reviewed in [11]). The enzymes responsible for 3' uridylation of small RNAs when they lack methylation in plants or animals have remained elusive. Here, we identify the Arabidopsis HEN1 SUPPRESSOR1 (HESO1) gene as responsible for small RNA uridylation in hen1 mutants. HESO1 exhibits terminal nucleotidyl transferase activity, prefers uridine as the substrate nucleotide, and is completely inhibited by 2'-O-methylation. We show that uridylation leads to miRNA degradation, and the degradation is most likely through an enzyme that is distinct from that causing the 3' truncation in hen1 mutants.
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Affiliation(s)
- Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Biology, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
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90
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Tetrahymena thermophila JMJD3 homolog regulates H3K27 methylation and nuclear differentiation. EUKARYOTIC CELL 2012; 11:601-14. [PMID: 22427430 DOI: 10.1128/ec.05290-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histone H3K27me3 modification is an important regulator for development and gene expression. In Tetrahymena thermophila, the complex chromatin dynamics of H3K27me3 marks during nuclear development suggested that an H3K27me3 demethylase might exist. Here, we report an H3K27me3 demethylase homolog, JMJ1, in Tetrahymena. During conjugation, JMJ1 expression is upregulated and the protein is localized first in the parental macronucleus and then in the new macronucleus. In conjugating cells, knockdown of JMJ1 expression resulted in a severe reduction in the production of progeny, suggesting that JMJ1 is essential for Tetrahymena conjugation. Furthermore, knockdown of JMJ1 resulted in increased H3K27 trimethylation in the new macronucleus and reduced transcription of genes related to DNA elimination, while the DNA elimination process was also partially blocked. Knockdown of the H3K27 methyltransferase EZL2 but not that of EZL1 partially restored progeny production in JMJ1-knockdown cells and reduced abnormal H3K27me3 accumulation in the new macronucleus. Taken together, these results demonstrate a critical role for JMJ1 in regulating H3K27me3 during conjugation and the importance of JMJ1 in regulating gene expression in the new macronucleus but not in regulating the formation of heterochromatin associated with programmed DNA deletion.
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91
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Abstract
As central components of RNA silencing, small RNAs play diverse and important roles in many biological processes in eukaryotes. Aberrant reduction or elevation in the levels of small RNAs is associated with many developmental and physiological defects. The in vivo levels of small RNAs are precisely regulated through modulating the rates of their biogenesis and turnover. 2'-O-methylation on the 3' terminal ribose is a major mechanism that increases the stability of small RNAs. The small RNA methyltransferase HUA ENHANCER1 (HEN1) and its homologs methylate microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs (piRNAs) in animals, and siRNAs in Drosophila. 3' nucleotide addition, especially uridylation, and 3'-5' exonucleolytic degradation are major mechanisms that turnover small RNAs. Other mechanisms impacting small RNA stability include complementary RNAs, cis-elements in small RNA sequences and RNA-binding proteins. Investigations are ongoing to further understand how small RNA stability impacts their accumulation in vivo in order to improve the utilization of RNA silencing in biotechnology and therapeutic applications.
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92
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Kawaoka S, Mitsutake H, Kiuchi T, Kobayashi M, Yoshikawa M, Suzuki Y, Sugano S, Shimada T, Kobayashi J, Tomari Y, Katsuma S. A role for transcription from a piRNA cluster in de novo piRNA production. RNA (NEW YORK, N.Y.) 2012; 18:265-73. [PMID: 22194309 PMCID: PMC3264913 DOI: 10.1261/rna.029777.111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are at the heart of the nucleic acid-based adaptive immune system against transposons in animal gonads. To date, how the piRNA pathway senses an element as a substrate and how de novo piRNA production is initiated remain elusive. Here, by utilizing a GFP transgene, we screened and obtained clonal silkworm BmN4 cell lines producing massively amplified GFP-derived piRNAs capable of silencing GFP in trans. In multiple independent cell lines where GFP expression was silenced by the piRNA pathway, we detected a common transcript from an endogenous piRNA cluster, in which a part of the cluster is uniquely fused with an antisense GFP sequence. Bioinformatic analyses suggest that the fusion transcript is a source of GFP primary piRNAs. Our data implicate a role for transcription from a piRNA cluster in initiating de novo piRNA production against a new insertion.
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Affiliation(s)
- Shinpei Kawaoka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroshi Mitsutake
- The United Graduate School of Agricultural Sciences, Tottori University, Koyama-cho, Minami 4-101, Tottori 680-8553, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Maki Kobayashi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mayu Yoshikawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toru Shimada
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun Kobayashi
- The United Graduate School of Agricultural Sciences, Tottori University, Koyama-cho, Minami 4-101, Tottori 680-8553, Japan
- Faculty of Agriculture, Yamaguchi University, Yoshida 1677-1, Yamaguchi 753-8515, Japan
- Corresponding authors.E-mail .E-mail .E-mail .
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding authors.E-mail .E-mail .E-mail .
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding authors.E-mail .E-mail .E-mail .
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93
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Abstract
Nuclear dualism is a characteristic feature of the ciliated protozoa. Tetrahymena have two different nuclei in each cell. The larger, polyploid, somatic macronucleus (MAC) is the site of transcriptional activity in the vegetatively growing cell. The smaller, diploid micronucleus (MIC) is transcriptionally inactive in vegetative cells, but is transcriptionally active in mating cells and responsible for the genetic continuity during sexual reproduction. Although the MICs and MACs develop from mitotic products of a common progenitor and reside in a common cytoplasm, they are different from one another in almost every respect.
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Affiliation(s)
- Kathleen M Karrer
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
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94
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Meng Y, Shao C, Wang H, Chen M. The regulatory activities of plant microRNAs: a more dynamic perspective. PLANT PHYSIOLOGY 2011; 157:1583-95. [PMID: 22003084 PMCID: PMC3327222 DOI: 10.1104/pp.111.187088] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 10/13/2011] [Indexed: 05/19/2023]
Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, People's Republic of China.
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95
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Mochizuki K. Developmentally programmed, RNA-directed genome rearrangement in Tetrahymena. Dev Growth Differ 2011; 54:108-19. [PMID: 22103557 DOI: 10.1111/j.1440-169x.2011.01305.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Developmentally programmed genome rearrangement has been observed in a variety of eukaryotes from vertebrates to worms to protists, and it provides an interesting exception to the general rule of the constancy of the genome. DNA elimination in the ciliated protozoan Tetrahymena is one of the most well-characterized programmed genome rearrangement events. DNA elimination in the newly formed macronucleus of Tetrahymena is epigenetically regulated by the DNA sequence of the parental macronucleus. Dicer-produced, Piwi-associated small RNAs mediate this epigenetic regulation, probably through a whole-genome comparison of the germline micronucleus to the somatic macronucleus. However, a correlation between small RNAs and programmed genome rearrangement could not be detected in the worm Ascaris suum. Therefore, different types of eukaryotes may have developed unique solutions to perform genome rearrangement.
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Affiliation(s)
- Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
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96
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Juliano C, Wang J, Lin H. Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Annu Rev Genet 2011; 45:447-69. [PMID: 21942366 DOI: 10.1146/annurev-genet-110410-132541] [Citation(s) in RCA: 265] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The topipotency of the germline is the full manifestation of the pluri- and multipotency of embryonic and adult stem cells, thus the germline and stem cells must share common mechanisms that guarantee their multipotentials in development. One of the few such known shared mechanisms is represented by Piwi proteins, which constitute one of the two subfamilies of the Argonaute protein family. Piwi proteins bind to Piwi-interacting RNAs (piRNAs) that are generally 26 to 31 nucleotides in length. Both Piwi proteins and piRNAs are most abundantly expressed in the germline. Moreover, Piwi proteins are expressed broadly in certain types of somatic stem/progenitor cells and other somatic cells across animal phylogeny. Recent studies indicate that the Piwi-piRNA pathway mediates epigenetic programming and posttranscriptional regulation, which may be responsible for its function in germline specification, gametogenesis, stem cell maintenance, transposon silencing, and genome integrity in diverse organisms.
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Affiliation(s)
- Celina Juliano
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06509, USA.
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97
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Schoeberl UE, Mochizuki K. Keeping the soma free of transposons: programmed DNA elimination in ciliates. J Biol Chem 2011; 286:37045-52. [PMID: 21914793 DOI: 10.1074/jbc.r111.276964] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Many transposon-related sequences are removed from the somatic macronucleus of ciliates during sexual reproduction. In the ciliate Tetrahymena, an RNAi-related mechanism produces small noncoding RNAs that induce heterochromatin formation, which is followed by DNA elimination. Because RNAi-related mechanisms repress transposon activities in a variety of eukaryotes, the DNA elimination mechanism of ciliates might have evolved from these types of transposon-silencing mechanisms. Nuclear dimorphism allows ciliates to identify any DNA that has invaded the germ-line micronucleus using small RNAs and a whole genome comparison of the micronucleus and the somatic macronucleus.
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Affiliation(s)
- Ursula E Schoeberl
- Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
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98
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Meikar O, Da Ros M, Korhonen H, Kotaja N. Chromatoid body and small RNAs in male germ cells. Reproduction 2011; 142:195-209. [DOI: 10.1530/rep-11-0057] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The chromatoid body (CB) is a germ granule in the cytoplasm of postmeiotic haploid round spermatids that is loaded with RNA and RNA-binding proteins. Following the discovery of small non-coding RNA-mediated gene regulation and the identification of PIWI-interacting RNAs (piRNAs) that have crucial roles in germ line development, the function of the CB has slowly begun to be revealed. Male germ cells utilise small RNAs to control the complex and specialised process of sperm production. Several microRNAs have been identified during spermatogenesis. In addition, a high number of piRNAs are present both in embryonic and postnatal male germ cells, with their expression being impressively induced in late meiotic cells and haploid round spermatids. At postmeiotic stage of germ cell differentiation, the CB accumulates piRNAs and proteins of piRNA machinery, as well as several other proteins involved in distinct RNA regulation pathways. All existing evidence suggests a role for the CB in mRNA regulation and small RNA-mediated gene control, but the mechanisms remain uncharacterised. In this review, we summarise the current knowledge of the CB and its association with small RNA pathways.
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99
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Sperling L. Remembrance of things past retrieved from the Paramecium genome. Res Microbiol 2011; 162:587-97. [DOI: 10.1016/j.resmic.2011.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 02/17/2011] [Indexed: 11/30/2022]
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100
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Xiong J, Yuan D, Fillingham JS, Garg J, Lu X, Chang Y, Liu Y, Fu C, Pearlman RE, Miao W. Gene network landscape of the ciliate Tetrahymena thermophila. PLoS One 2011; 6:e20124. [PMID: 21637855 PMCID: PMC3102692 DOI: 10.1371/journal.pone.0020124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/13/2011] [Indexed: 01/03/2023] Open
Abstract
Background Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Methodology/Principal Findings Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. Conclusions/Significance This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
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Affiliation(s)
- Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Dongxia Yuan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Jyoti Garg
- Department of Biology and Center for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - Xingyi Lu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Yue Chang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Yifan Liu
- Pathology Department, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Chengjie Fu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ronald E. Pearlman
- Department of Biology and Center for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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