1
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Potužník JF, Cahova H. If the 5' cap fits (wear it) - Non-canonical RNA capping. RNA Biol 2024; 21:1-13. [PMID: 39007883 PMCID: PMC11253889 DOI: 10.1080/15476286.2024.2372138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
RNA capping is a prominent RNA modification that influences RNA stability, metabolism, and function. While it was long limited to the study of the most abundant eukaryotic canonical m7G cap, the field recently went through a large paradigm shift with the discovery of non-canonical RNA capping in bacteria and ultimately all domains of life. The repertoire of non-canonical caps has expanded to encompass metabolite caps, including NAD, FAD, CoA, UDP-Glucose, and ADP-ribose, alongside alarmone dinucleoside polyphosphate caps, and methylated phosphate cap-like structures. This review offers an introduction into the field, presenting a summary of the current knowledge about non-canonical RNA caps. We highlight the often still enigmatic biological roles of the caps together with their processing enzymes, focusing on the most recent discoveries. Furthermore, we present the methods used for the detection and analysis of these non-canonical RNA caps and thus provide an introduction into this dynamic new field.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
- Department of Cell Biology, Charles University, Faculty of Science, Prague 2, Czechia
| | - Hana Cahova
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
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2
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Wen X, Irshad A, Jin H. The Battle for Survival: The Role of RNA Non-Canonical Tails in the Virus-Host Interaction. Metabolites 2023; 13:1009. [PMID: 37755289 PMCID: PMC10537345 DOI: 10.3390/metabo13091009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Terminal nucleotidyltransferases (TENTs) could generate a 'mixed tail' or 'U-rich tail' consisting of different nucleotides at the 3' end of RNA by non-templated nucleotide addition to protect or degrade cellular messenger RNA. Recently, there has been increasing evidence that the decoration of virus RNA terminus with a mixed tail or U-rich tail is a critical way to affect viral RNA stability in virus-infected cells. This paper first briefly introduces the cellular function of the TENT family and non-canonical tails, then comprehensively reviews their roles in virus invasion and antiviral immunity, as well as the significance of the TENT family in antiviral therapy. This review will contribute to understanding the role and mechanism of non-canonical RNA tailing in survival competition between the virus and host.
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Affiliation(s)
| | | | - Hua Jin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China; (X.W.); (A.I.)
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3
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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4
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Falk F, Kamanyi Marucha K, Clayton C. The EIF4E1-4EIP cap-binding complex of Trypanosoma brucei interacts with the terminal uridylyl transferase TUT3. PLoS One 2021; 16:e0258903. [PMID: 34807934 PMCID: PMC8608314 DOI: 10.1371/journal.pone.0258903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Most transcription in Trypanosoma brucei is constitutive and polycistronic. Consequently, the parasite relies on post-transcriptional mechanisms, especially affecting translation initiation and mRNA decay, to control gene expression both at steady-state and for adaptation to different environments. The parasite has six isoforms of the cap-binding protein EIF4E as well as five EIF4Gs. EIF4E1 does not bind to any EIF4G, instead being associated with a 4E-binding protein, 4EIP. 4EIP represses translation and reduces the stability of a reporter mRNA when artificially tethered to the 3’-UTR, whether or not EIF4E1 is present. 4EIP is essential during the transition from the mammalian bloodstream form to the procyclic form that lives in the Tsetse vector. In contrast, EIF4E1 is dispensable during differentiation, but is required for establishment of growing procyclic forms. In Leishmania, there is some evidence that EIF4E1 might be active in translation initiation, via direct recruitment of EIF3. However in T. brucei, EIF4E1 showed no detectable association with other translation initiation factors, even in the complete absence of 4EIP. There was some evidence for interactions with NOT complex components, but if these occur they must be weak and transient. We found that EIF4E1is less abundant in the absence of 4EIP, and RNA pull-down results suggested this might occur through co-translational complex assembly. We also report that 4EIP directly recruits the cytosolic terminal uridylyl transferase TUT3 to EIF4E1/4EIP complexes. There was, however, no evidence that TUT3 is essential for 4EIP function.
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Affiliation(s)
- Franziska Falk
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Kevin Kamanyi Marucha
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- * E-mail:
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5
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Manavski N, Vicente A, Chi W, Meurer J. The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods. Genes (Basel) 2021; 12:genes12081121. [PMID: 34440296 PMCID: PMC8394491 DOI: 10.3390/genes12081121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.
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Affiliation(s)
- Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Alexandre Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
- Correspondence: ; Tel.: +49-89-218074556
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6
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Terminal uridyltransferase 7 regulates TLR4-triggered inflammation by controlling Regnase-1 mRNA uridylation and degradation. Nat Commun 2021; 12:3878. [PMID: 34188032 PMCID: PMC8241994 DOI: 10.1038/s41467-021-24177-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
Different levels of regulatory mechanisms, including posttranscriptional regulation, are needed to elaborately regulate inflammatory responses to prevent harmful effects. Terminal uridyltransferase 7 (TUT7) controls RNA stability by adding uridines to its 3′ ends, but its function in innate immune response remains obscure. Here we reveal that TLR4 activation induces TUT7, which in turn selectively regulates the production of a subset of cytokines, including Interleukin 6 (IL-6). TUT7 regulates IL-6 expression by controlling ribonuclease Regnase-1 mRNA (encoded by Zc3h12a gene) stability. Mechanistically, TLR4 activation causes TUT7 to bind directly to the stem-loop structure on Zc3h12a 3′-UTR, thereby promotes Zc3h12a uridylation and degradation. Zc3h12a from LPS-treated TUT7-sufficient macrophages possesses increased oligo-uridylated ends with shorter poly(A) tails, whereas oligo-uridylated Zc3h12a is significantly reduced in Tut7-/- cells after TLR4 activation. Together, our findings reveal the functional role of TUT7 in sculpting TLR4-driven responses by modulating mRNA stability of a selected set of inflammatory mediators. Terminal uridyltransferase 7 (TUT7) adds U-tails on diverse RNAs to promote degradation. Here the authors show that TUT7 is induced upon LPS treatment in macrophages and promotes decay of Regnase-1, thereby regulating the expression of a subset of cytokines, including IL-6.
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7
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Borbolis F, Syntichaki P. Biological implications of decapping: beyond bulk mRNA decay. FEBS J 2021; 289:1457-1475. [PMID: 33660392 DOI: 10.1111/febs.15798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022]
Abstract
It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
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8
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Zorn P, Misiak D, Gekle M, Köhn M. Identification and initial characterization of POLIII-driven transcripts by msRNA-sequencing. RNA Biol 2021; 18:1807-1817. [PMID: 33404286 PMCID: PMC8583065 DOI: 10.1080/15476286.2020.1871216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are powerful regulators of gene expression but medium-sized (50–300 nts in length) ncRNAs (msRNAs) are barely picked-up precisely by RNA-sequencing. Here we describe msRNA-sequencing (msRNAseq), a modified protocol that associated with a computational analyses pipeline identified about ~1800 msRNA loci, including over 300 putatively novel msRNAs, in human and murine cells. We focused on the identification and initial characterization of three POLIII-derived transcripts. The validation of these uncharacterized msRNAs identified an ncRNA in antisense orientation from the POLR3E locus transcribed by POLIII. This msRNA, termed POLAR (POLR3E Antisense RNA), has a strikingly short half-life, localizes to paraspeckles (PSPs) and associates with PSP-associated proteins indicating that msRNAseq identifies functional msRNAs. Thus, our analyses will pave the way for analysing the roles of msRNAs in cells, development and diseases.
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Affiliation(s)
| | - Danny Misiak
- Institute of Molecular Medicine, University of Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, University of Halle-Wittenberg, Germany
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9
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Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP. The genetic basis of aneuploidy tolerance in wild yeast. eLife 2020; 9:52063. [PMID: 31909711 PMCID: PMC6970514 DOI: 10.7554/elife.52063] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Aneuploidy is highly detrimental during development yet common in cancers and pathogenic fungi – what gives rise to differences in aneuploidy tolerance remains unclear. We previously showed that wild isolates of Saccharomyces cerevisiae tolerate chromosome amplification while laboratory strains used as a model for aneuploid syndromes do not. Here, we mapped the genetic basis to Ssd1, an RNA-binding translational regulator that is functional in wild aneuploids but defective in laboratory strain W303. Loss of SSD1 recapitulates myriad aneuploidy signatures previously taken as eukaryotic responses. We show that aneuploidy tolerance is enabled via a role for Ssd1 in mitochondrial physiology, including binding and regulating nuclear-encoded mitochondrial mRNAs, coupled with a role in mitigating proteostasis stress. Recapitulating ssd1Δ defects with combinatorial drug treatment selectively blocked proliferation of wild-type aneuploids compared to euploids. Our work adds to elegant studies in the sensitized laboratory strain to present a mechanistic understanding of eukaryotic aneuploidy tolerance.
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Affiliation(s)
- James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States
| | - Leah E Escalante
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Katie J Clowers
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - DeElegant Robinson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States
| | - Venera Bouriakov
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Great Lakes Bioenergy Research Center, Madison, United States
| | - Joshua J Coon
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Great Lakes Bioenergy Research Center, Madison, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, Madison, United States
| | - Evgenia Shishkova
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, Madison, United States
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Great Lakes Bioenergy Research Center, Madison, United States
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10
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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11
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Pirouz M, Ebrahimi AG, Gregory RI. Unraveling 3'-end RNA uridylation at nucleotide resolution. Methods 2019; 155:10-19. [PMID: 30395968 PMCID: PMC6387850 DOI: 10.1016/j.ymeth.2018.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional modification of RNA, the so-called 'Epitranscriptome', can regulate RNA structure, stability, localization, and function. Numerous modifications have been identified in virtually all classes of RNAs, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), microRNAs (miRNAs), and other noncoding RNAs (ncRNAs). These modifications may occur internally (by base or sugar modifications) and include RNA methylation at different nucleotide positions, or by the addition of various nucleotides at the 3'-end of certain transcripts by a family of terminal nucleotidylyl transferases. Developing methods to specifically and accurately detect and map these modifications is essential for understanding the molecular function(s) of individual RNA modifications and also for identifying and characterizing the proteins that may read, write, or erase them. Here, we focus on the characterization of RNA species targeted by 3' terminal uridylyl transferases (TUTases) (TUT4/7, also known as Zcchc11/6) and a 3'-5' exoribonuclease, Dis3l2, in the recently identified Dis3l2-mediated decay (DMD) pathway - a dedicated quality control pathway for a subset of ncRNAs. We describe the detailed methods used to precisely identify 3'-end modifications at nucleotide level resolution with a particular focus on the U1 and U2 small nuclear RNA (snRNA) components of the Spliceosome. These tools can be applied to investigate any RNA of interest and should facilitate studies aimed at elucidating the functional relevance of 3'-end modifications.
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Affiliation(s)
- Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Aref G Ebrahimi
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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12
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Saramago M, da Costa PJ, Viegas SC, Arraiano CM. The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:85-98. [PMID: 31342438 DOI: 10.1007/978-3-030-19966-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA degradation is considered a critical posttranscriptional regulatory checkpoint, maintaining the correct functioning of organisms. When a specific RNA transcript is no longer required in the cell, it is signaled for degradation through a number of highly regulated steps. Ribonucleases (or simply RNases) are key enzymes involved in the control of RNA stability. These enzymes can perform the RNA degradation alone or cooperate with other proteins in RNA degradation complexes. Important findings over the last years have shed light into eukaryotic RNA degradation by members of the RNase II/RNB family of enzymes. DIS3 enzyme belongs to this family and represents one of the catalytic subunits of the multiprotein complex exosome. This RNase has a diverse range of functions, mainly within nuclear RNA metabolism. Humans encode two other DIS3-like enzymes: DIS3L (DIS3L1) and DIS3L2. DIS3L1 also acts in association with the exosome but is strictly cytoplasmic. In contrast, DIS3L2 acts independently of the exosome and shows a distinctive preference for uridylated RNAs. These enzymes have been shown to be involved in important cellular processes, such as mitotic control, and associated with human disorders like cancer. This review shows how the impairment of function of each of these enzymes is implicated in human disease.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisboa, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisbon, Lisboa, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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13
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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14
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Cerezo E, Plisson-Chastang C, Henras AK, Lebaron S, Gleizes PE, O'Donohue MF, Romeo Y, Henry Y. Maturation of pre-40S particles in yeast and humans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1516. [PMID: 30406965 DOI: 10.1002/wrna.1516] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/02/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022]
Abstract
The synthesis of ribosomal subunits in eukaryotes requires the interplay of numerous maturation and assembly factors (AFs) that intervene in the insertion of ribosomal proteins within pre-ribosomal particles, the ribosomal subunit precursors, as well as in pre-ribosomal RNA (rRNA) processing and folding. Here, we review the intricate nuclear and cytoplasmic maturation steps of pre-40S particles, the precursors to the small ribosomal subunits, in both yeast and human cells, with particular emphasis on the timing and mechanisms of AF association with and dissociation from pre-40S particles and the roles of these AFs in the maturation process. We highlight the particularly complex pre-rRNA processing pathway in human cells, compared to yeast, to generate the mature 18S rRNA. We discuss the information gained from the recently published cryo-electron microscopy atomic models of yeast and human pre-40S particles, as well as the checkpoint/quality control systems that seem to operate to probe functional sites within yeast cytoplasmic pre-40S particles. This article is categorized under: RNA Processing > rRNA Processing Translation > Ribosome Biogenesis.
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Affiliation(s)
- Emilie Cerezo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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15
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Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:a032839. [PMID: 29311343 PMCID: PMC5932591 DOI: 10.1101/cshperspect.a032839] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.
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Affiliation(s)
- Adam M Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
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16
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Kobyłecki K, Kuchta K, Dziembowski A, Ginalski K, Tomecki R. Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3'-terminal positions of synthesized tails. RNA (NEW YORK, N.Y.) 2017; 23:1902-1926. [PMID: 28947555 PMCID: PMC5689010 DOI: 10.1261/rna.061010.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/12/2017] [Indexed: 05/25/2023]
Abstract
Noncanonical RNA nucleotidyltransferases (NTases), including poly(A), poly(U) polymerases (PAPs/PUPs), and C/U-adding enzymes, modify 3'-ends of different transcripts affecting their functionality and stability. They contain PAP/OAS1 substrate-binding domain (SBD) with inserted NTase domain. Aspergillus nidulans CutA (AnCutA), synthesizes C/U-rich 3'-terminal extensions in vivo. Here, using high-throughput sequencing of the 3'-RACE products for tails generated by CutA proteins in vitro in the presence of all four NTPs, we show that even upon physiological ATP excess synthesized tails indeed contain an unprecedented number of cytidines interrupted by uridines and stretches of adenosines, and that the majority end with two cytidines. Strikingly, processivity assays documented that in the presence of CTP as a sole nucleotide, the enzyme terminates after adding two cytidines only. Comparison of our CutA 3D model to selected noncanonical NTases of known structures revealed substantial differences in the nucleotide recognition motif (NRM) within PAP/OAS1 SBD. We demonstrate that CutA specificity toward CTP can be partially changed to PAP or PUP by rational mutagenesis within NRM and, analogously, Cid1 PUP can be converted into a C/U-adding enzyme. Collectively, we suggest that a short cluster of amino acids within NRM is a determinant of NTases' substrate preference, which may allow us to predict their specificity.
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Affiliation(s)
- Kamil Kobyłecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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17
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De Almeida C, Scheer H, Zuber H, Gagliardi D. RNA uridylation: a key posttranscriptional modification shaping the coding and noncoding transcriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 28984054 DOI: 10.1002/wrna.1440] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 12/27/2022]
Abstract
RNA uridylation is a potent and widespread posttranscriptional regulator of gene expression. RNA uridylation has been detected in a range of eukaryotes including trypanosomes, animals, plants, and fungi, but with the noticeable exception of budding yeast. Virtually all classes of eukaryotic RNAs can be uridylated and uridylation can also tag viral RNAs. The untemplated addition of a few uridines at the 3' end of a transcript can have a decisive impact on RNA's fate. In rare instances, uridylation is an intrinsic step in the maturation of noncoding RNAs like for the U6 spliceosomal RNA or mitochondrial guide RNAs in trypanosomes. Uridylation can also switch specific miRNA precursors from a degradative to a processing mode. This switch depends on the number of uridines added which is regulated by the cellular context. Yet, the typical consequence of uridylation on mature noncoding RNAs or their precursors is to accelerate decay. Importantly, mRNAs are also tagged by uridylation. In fact, the advent of novel high throughput sequencing protocols has recently revealed the pervasiveness of mRNA uridylation, from plants to humans. As for noncoding RNAs, the main function to date for mRNA uridylation is to promote degradation. Yet, additional roles begin to be ascribed to U-tailing such as the control of mRNA deadenylation, translation control and possibly storage. All these new findings illustrate that we are just beginning to appreciate the diversity of roles played by RNA uridylation and its full temporal and spatial implication in regulating gene expression. WIREs RNA 2018, 9:e1440. doi: 10.1002/wrna.1440 This article is categorized under: RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Caroline De Almeida
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Hélène Scheer
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
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18
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Nowak JS, Hobor F, Downie Ruiz Velasco A, Choudhury NR, Heikel G, Kerr A, Ramos A, Michlewski G. Lin28a uses distinct mechanisms of binding to RNA and affects miRNA levels positively and negatively. RNA (NEW YORK, N.Y.) 2017; 23:317-332. [PMID: 27881476 PMCID: PMC5311490 DOI: 10.1261/rna.059196.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2016] [Indexed: 05/29/2023]
Abstract
Lin28a inhibits the biogenesis of let-7 miRNAs by triggering the polyuridylation and degradation of their precursors by terminal uridylyltransferases TUT4/7 and 3'-5' exoribonuclease Dis3l2, respectively. Previously, we showed that Lin28a also controls the production of neuro-specific miRNA-9 via a polyuridylation-independent mechanism. Here we reveal that the sequences and structural characteristics of pre-let-7 and pre-miRNA-9 are eliciting two distinct modes of binding to Lin28a. We present evidence that Dis3l2 controls miRNA-9 production. Finally, we show that the constitutive expression of untagged Lin28a during neuronal differentiation in vitro positively and negatively affects numerous other miRNAs. Our findings shed light on the role of Lin28a in differentiating cells and on the ways in which one RNA-binding protein can perform multiple roles in the regulation of RNA processing.
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Affiliation(s)
- Jakub Stanislaw Nowak
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Fruzsina Hobor
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6XA, United Kingdom
| | | | - Nila Roy Choudhury
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Gregory Heikel
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Alastair Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6XA, United Kingdom
| | - Gracjan Michlewski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
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19
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Boehm V, Gerbracht JV, Marx MC, Gehring NH. Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences. Nat Commun 2016; 7:13691. [PMID: 27917860 PMCID: PMC5150221 DOI: 10.1038/ncomms13691] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5'-3' mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3' UTRs of cytokine mRNAs reveals the contribution of 5'-3' decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Jennifer V Gerbracht
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Marie-Charlotte Marx
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
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20
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Łabno A, Tomecki R, Dziembowski A. Cytoplasmic RNA decay pathways - Enzymes and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3125-3147. [PMID: 27713097 DOI: 10.1016/j.bbamcr.2016.09.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
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21
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Widespread 3'-end uridylation in eukaryotic RNA viruses. Sci Rep 2016; 6:25454. [PMID: 27151171 PMCID: PMC4858684 DOI: 10.1038/srep25454] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
RNA 3′ uridylation occurs pervasively in eukaryotes, but is poorly characterized in viruses. In this study, we demonstrate that a broad array of RNA viruses, including mycoviruses, plant viruses and animal viruses, possess a novel population of RNA species bearing nontemplated oligo(U) or (U)-rich tails, suggesting widespread 3′ uridylation in eukaryotic viruses. Given the biological relevance of 3′ uridylation to eukaryotic RNA degradation, we propose a conserved but as-yet-unknown mechanism in virus-host interaction.
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22
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Zuber H, Scheer H, Ferrier E, Sement FM, Mercier P, Stupfler B, Gagliardi D. Uridylation and PABP Cooperate to Repair mRNA Deadenylated Ends in Arabidopsis. Cell Rep 2016; 14:2707-17. [PMID: 26972004 DOI: 10.1016/j.celrep.2016.02.060] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/08/2015] [Accepted: 02/11/2016] [Indexed: 11/30/2022] Open
Abstract
Uridylation emerges as a key modification promoting mRNA degradation in eukaryotes. In addition, uridylation by URT1 prevents the accumulation of excessively deadenylated mRNAs in Arabidopsis. Here, we show that the extent of mRNA deadenylation is controlled by URT1. By using TAIL-seq analysis, we demonstrate the prevalence of mRNA uridylation and the existence, at lower frequencies, of mRNA cytidylation and guanylation in Arabidopsis. Both URT1-dependent and URT1-independent types of uridylation co-exist but only URT1-mediated uridylation prevents the accumulation of excessively deadenylated mRNAs. Importantly, uridylation repairs deadenylated extremities to restore the size distribution observed for non-uridylated oligo(A) tails. In vivo and in vitro data indicate that Poly(A) Binding Protein (PABP) binds to uridylated oligo(A) tails and determines the length of U-extensions added by URT1. Taken together, our results uncover a role for uridylation and PABP in repairing mRNA deadenylated ends and reveal that uridylation plays diverse roles in eukaryotic mRNA metabolism.
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Affiliation(s)
- Hélène Zuber
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
| | - Hélène Scheer
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
| | - Emilie Ferrier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
| | - François Michaël Sement
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
| | - Pierre Mercier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
| | - Benjamin Stupfler
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France.
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