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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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Bopst M, Dinklo T, Funk J, Greiter-Wilke A, Lenz B, Kustermann S, Jiang T, Xie J. Unexpected neurotoxicity in chronic toxicity studies with a HBV viral expression inhibitor. Regul Toxicol Pharmacol 2023; 141:105407. [PMID: 37141985 DOI: 10.1016/j.yrtph.2023.105407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/12/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
The non-clinical safety profile of the small molecule hepatitis B virus viral expression inhibitor RG7834 was studied in a package consisting of safety pharmacology, genotoxicity, repeat dose toxicity and reproductive toxicity studies. The chronic monkey toxicity study identified dose- and time-dependent symptoms of polyneuropathy, with correlating nerve conduction velocity reductions and axonal degeneration in peripheral nerves and spinal cord, in all compound treatment groups with no evidence of reversibility after approximately 3 months of treatment cessation. Similar histopathological findings were observed in the chronic rat toxicity study. Subsequent in vitro neurotoxicity investigations and ion channel electrophysiology did not elucidate a potential mechanism for the late toxicity. However, based on similar findings observed with a structurally different molecule, an inhibition of their common pharmacological targets, PAPD5 & PAPD 7, was considered as a possible mechanism of toxicity. In conclusion, the marked neuropathies, only observed after chronic dosing, did not support further clinical development of RG7834 because of its foreseen clinical treatment duration of up to 48 weeks in chronic HBV patients.
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Affiliation(s)
- Martin Bopst
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Theo Dinklo
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Juergen Funk
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Andrea Greiter-Wilke
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Barbara Lenz
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Stefan Kustermann
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Tianyi Jiang
- Roche Pharma and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Shanghai, 201023, China
| | - Jianxun Xie
- Roche Pharma and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Shanghai, 201023, China
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Halabian R, Makałowski W. A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes. BIOLOGY 2022; 11:1032. [PMID: 36101413 PMCID: PMC9311842 DOI: 10.3390/biology11071032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 05/03/2023]
Abstract
As one of the major structural constituents, mobile elements comprise more than half of the human genome, among which Alu, L1, and SVA elements are still active and continue to generate new offspring. One of the major characteristics of L1 and SVA elements is their ability to co-mobilize adjacent downstream sequences to new loci in a process called 3' DNA transduction. Transductions influence the structure and content of the genome in different ways, such as increasing genome variation, exon shuffling, and gene duplication. Moreover, given their mutagenicity capability, 3' transductions are often involved in tumorigenesis or in the development of some diseases. In this study, we analyzed 3202 genomes sequenced at high coverage by the New York Genome Center to catalog and characterize putative 3' transduced segments mediated by L1s and SVAs. Here, we present a genome-wide map of inter/intrachromosomal 3' transduction variants, including their genomic and functional location, length, progenitor location, and allelic frequency across 26 populations. In total, we identified 7103 polymorphic L1s and 3040 polymorphic SVAs. Of these, 268 and 162 variants were annotated as high-confidence L1 and SVA 3' transductions, respectively, with lengths that ranged from 7 to 997 nucleotides. We found specific loci within chromosomes X, 6, 7, and 6_GL000253v2_alt as master L1s and SVAs that had yielded more transductions, among others. Together, our results demonstrate the dynamic nature of transduction events within the genome and among individuals and their contribution to the structural variations of the human genome.
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Affiliation(s)
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149 Münster, Germany;
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Tamaddon M, Shokri G, Hosseini Rad SMA, Rad I, Emami Razavi À, Kouhkan F. Involved microRNAs in alternative polyadenylation intervene in breast cancer via regulation of cleavage factor "CFIm25". Sci Rep 2020; 10:11608. [PMID: 32665581 PMCID: PMC7360588 DOI: 10.1038/s41598-020-68406-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 06/24/2020] [Indexed: 12/22/2022] Open
Abstract
Cleavage factor “CFIm25”, as a key repressor at proximal poly (A) site, negatively correlates to cell proliferation and tumorigenicity in various cancers. Hence, understanding CFIm25 mechanism of action in breast cancer would be a great benefit. To this aim four steps were designed. First, potential miRNAs that target 3′-UTR of CFIm25 mRNA, retrieved from Targetscan web server. Second, screened miRNAs were profiled in 100 breast cancer and 100 normal adjacent samples. Third, miRNAs that their expression was inversely correlated to the CFIm25, overexpressed in MDA-MB-231 cell line, and their effect on proliferation and migration monitored via MTT and wound healing assays, respectively. Fourth, interaction of miRNAs of interest with 3′-UTR of CFIm25 confirmed via luciferase assay and western blot. Our results indicate that CFIm25 considerably down-regulates in human breast cancer tissue. qRT-PCR assay, luciferase test, and western blotting confirm that CFIm25 itself could be directly regulated by oncomiRs such as miR-23, -24, -27, -135, -182 and -374. Besides, according to MTT and wound healing assays of cell lines, CFIm25 knockdown intensifies cell growth, proliferation and migration. Our results also confirm indirect impact of CFIm25 on regulation of mRNA’s 3′–UTR length, which then control corresponding miRNAs’ action. miRNAs directly control CFIm25 expression level, which then tunes expression of the oncogenes and tumor proliferation. Therefore, regulation of CFIm25 expression level via miRNAs is expected to improve treatment responses in breast cancer.
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Affiliation(s)
- Mona Tamaddon
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | - Gelareh Shokri
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | | | - Iman Rad
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | - Àmirnader Emami Razavi
- Ìran National Tumor Bank, Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Kouhkan
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran.
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Ustyantsev IG, Tatosyan KA, Stasenko DV, Kochanova NY, Borodulina OR, Kramerov DA. Polyadenylation of Sine Transcripts Generated by RNA Polymerase III Dramatically Prolongs Their Lifetime in Cells. Mol Biol 2020. [DOI: 10.1134/s0026893319040150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mueller H, Lopez A, Tropberger P, Wildum S, Schmaler J, Pedersen L, Han X, Wang Y, Ottosen S, Yang S, Young JAT, Javanbakht H. PAPD5/7 Are Host Factors That Are Required for Hepatitis B Virus RNA Stabilization. Hepatology 2019; 69:1398-1411. [PMID: 30365161 DOI: 10.1002/hep.30329] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Abstract
RG7834 is a potent, orally bioavailable small-molecule inhibitor of hepatitis B virus (HBV) gene expression that belongs to the dihydroquinolizinone (DHQ) chemical class and uniquely blocks production of both viral DNA and antigens. In this study, we used DHQ compounds as tools in a compound-based adaptation version of the yeast three-hybrid screen to identify the cognate cellular protein targets, the non-canonical poly(A) RNA polymerase associated domain containing proteins 5 and 7 (PAPD5 and PAPD7). Interaction with RG7834 was mapped to the catalytic domains of the two cellular enzymes. The role of PAPD5 and PAPD7 in HBV replication was confirmed by oligonucleotide-mediated knockdown studies that phenocopied the result seen with RG7834-treated HBV-infected hepatocytes. The greatest effect on HBV gene expression was seen when PAPD5 and PAPD7 mRNAs were simultaneously knocked down, suggesting that the two cellular proteins play a redundant role in maintaining HBV mRNA levels. In addition, as seen previously with RG7834 treatment, PAPD5 and PAPD7 knockdown led to destabilization and degradation of HBV mRNA without impacting production of viral RNA transcripts. Conclusion: We identify PAPD5 and PAPD7 as cellular host factors required for HBV RNA stabilization and as therapeutic targets for the HBV cure.
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Affiliation(s)
- Henrik Mueller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Anaïs Lopez
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Philipp Tropberger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Steffen Wildum
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Josephine Schmaler
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Lykke Pedersen
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Copenhagen, Denmark
| | - Xingchun Han
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, Shanghai, China
| | - Yongguang Wang
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, Shanghai, China
| | - Søren Ottosen
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Copenhagen, Denmark
| | - Song Yang
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, Shanghai, China
| | - John A T Young
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Hassan Javanbakht
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
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Rodríguez-Romero J, Marconi M, Ortega-Campayo V, Demuez M, Wilkinson MD, Sesma A. Virulence- and signaling-associated genes display a preference for long 3'UTRs during rice infection and metabolic stress in the rice blast fungus. THE NEW PHYTOLOGIST 2019; 221:399-414. [PMID: 30169888 DOI: 10.1111/nph.15405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Generation of mRNA isoforms by alternative polyadenylation (APA) and their involvement in regulation of fungal cellular processes, including virulence, remains elusive. Here, we investigated genome-wide polyadenylation site (PAS) selection in the rice blast fungus to understand how APA regulates pathogenicity. More than half of Magnaporthe oryzae transcripts undergo APA and show novel motifs in their PAS region. Transcripts with shorter 3'UTRs are more stable and abundant in polysomal fractions, suggesting they are being translated more efficiently. Importantly, rice colonization increases the use of distal PASs of pathogenicity genes, especially those participating in signalling pathways like 14-3-3B, whose long 3'UTR is required for infection. Cleavage factor I (CFI) Rbp35 regulates expression and distal PAS selection of virulence and signalling-associated genes, tRNAs and transposable elements, pointing its potential to drive genomic rearrangements and pathogen evolution. We propose a noncanonical PAS selection mechanism for Rbp35 that recognizes UGUAH, unlike humans, without CFI25. Our results showed that APA controls turnover and translation of transcripts involved in fungal growth and environmental adaptation. Furthermore, these data provide useful information for enhancing genome annotations and for cross-species comparisons of PASs and PAS usage within the fungal kingdom and the tree of life.
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Affiliation(s)
- Julio Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marco Marconi
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Víctor Ortega-Campayo
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marie Demuez
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Mark D Wilkinson
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Ane Sesma
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
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