51
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Wang X, Leung FS, Bush JO, Conti M. Alternative cleavage and polyadenylation of the Ccnb1 mRNA defines accumulation of cyclin protein during the meiotic cell cycle. Nucleic Acids Res 2024; 52:1258-1271. [PMID: 38048302 PMCID: PMC10853788 DOI: 10.1093/nar/gkad1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023] Open
Abstract
Progression through the mitotic and meiotic cell cycle is driven by fluctuations in the levels of cyclins, the regulatory subunits controlling the localization and activity of CDK1 kinases. Cyclin levels are regulated through a precise balance of synthesis and degradation. Here we demonstrate that the synthesis of Cyclin B1 during the oocyte meiotic cell cycle is defined by the selective translation of mRNA variants generated through alternative cleavage and polyadenylation (APA). Using gene editing in mice, we introduced mutations into the proximal and distal polyadenylation elements of the 3' untranslated region (UTR) of the Ccnb1 mRNA. Through in vivo loss-of-function experiments, we demonstrate that the translation of mRNA with a short 3' UTR specifies Cyclin B1 protein levels that set the timing of meiotic re-entry. In contrast, translation directed by a long 3' UTR is necessary to direct Cyclin B1 protein accumulation during the MI/MII transition. These findings establish that the progression through the cell cycle is dependent on the selective translation of multiple mRNA variants generated by APA.
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Affiliation(s)
- Xiaotian Wang
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Fang-Shiuan Leung
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey O Bush
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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52
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Hansel-Frose AFF, Allmer J, Friedrichs M, dos Santos HG, Dallagiovanna B, Spangenberg L. Alternative polyadenylation and dynamic 3' UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs. Front Mol Biosci 2024; 11:1336336. [PMID: 38380430 PMCID: PMC10877728 DOI: 10.3389/fmolb.2024.1336336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
Alternative polyadenylation (APA) increases transcript diversity through the generation of isoforms with varying 3' untranslated region (3' UTR) lengths. As the 3' UTR harbors regulatory element target sites, such as miRNAs or RNA-binding proteins, changes in this region can impact post-transcriptional regulation and translation. Moreover, the APA landscape can change based on the cell type, cell state, or condition. Given that APA events can impact protein expression, investigating translational control is crucial for comprehending the overall cellular regulation process. Revisiting data from polysome profiling followed by RNA sequencing, we investigated the cardiomyogenic differentiation of pluripotent stem cells by identifying the transcripts that show dynamic 3' UTR lengthening or shortening, which are being actively recruited to ribosome complexes. Our findings indicate that dynamic 3' UTR lengthening is not exclusively associated with differential expression during cardiomyogenesis but rather with recruitment to polysomes. We confirm that the differentiated state of cardiomyocytes shows a preference for shorter 3' UTR in comparison to the pluripotent stage although preferences vary during the days of the differentiation process. The most distinct regulatory changes are seen in day 4 of differentiation, which is the mesoderm commitment time point of cardiomyogenesis. After identifying the miRNAs that would target specifically the alternative 3' UTR region of the isoforms, we constructed a gene regulatory network for the cardiomyogenesis process, in which genes related to the cell cycle were identified. Altogether, our work sheds light on the regulation and dynamic 3' UTR changes of polysome-recruited transcripts that take place during the cardiomyogenic differentiation of pluripotent stem cells.
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Affiliation(s)
- Aruana F. F. Hansel-Frose
- Laboratory of Basic Stem Cell Biology, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ/PR), Curitiba, Brazil
| | - Jens Allmer
- Department of Medical Informatics and Bioinformatics, University of Applied Sciences Ruhr West, Mülheim, Germany
| | - Marcel Friedrichs
- Bioinformatics and Medical Informatics Department, University of Bielefeld, Bielefeld, Germany
| | | | - Bruno Dallagiovanna
- Laboratory of Basic Stem Cell Biology, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ/PR), Curitiba, Brazil
| | - Lucía Spangenberg
- Bioinformatics Unit, Pasteur Institute of Montevideo, Montevideo, Uruguay
- Departamento Basico de Medicina, Hospital de Clinicas, Universidad de la República (Udelar), Montevideo, Uruguay
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53
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Meng X, Li C, Hei Y, Zhou X, Zhou G. Comparative alternative polyadenylation profiles in differentiated adipocytes of subcutaneous and intramuscular fat tissue in cattle. Gene 2024; 894:147949. [PMID: 37918547 DOI: 10.1016/j.gene.2023.147949] [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: 05/15/2023] [Revised: 09/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Alternative polyadenylation (APA) is a key molecular mechanism involved in the post-transcriptional regulation of gene expression, which has been proven to play a critical role in cell differentiation. In the present study, we performed IVT-SAPAS sequencing to profile the dynamic changes of APA sites in bovine subcutaneous preadipocytes and intramuscular preadipocytes during adipogenesis. A total of 52621 high quality APA sites were identified in preadipocytes and adipocytes. Compared with preadipocytes, the increased usage of canonical AATAAA was observed in the cell-biased APA sites of adipocytes. Furthermore, 1933 and 2140 differentially expressed APA (DE-APA) sites, as well as 341 and 337 untranslated region-APA (UTR-APA) switching genes were identified in subcutaneous preadipocytes and intramuscular preadipocytes during adipogenesis, respectively. The UTR-APA switching genes showed divergent trends in preadipocytes, among which UTR-APA switching genes in intramuscular preadipocytes tended to use shorter 3'UTR for differentiation into mature adipocytes. APA events mediated by UTR-APA switching in intramuscular adipocytes were enriched in lipid synthesis and adipocyte differentiation. TRIB3, WWTR1, and INSIG1 played important roles in the differentiation of intramuscular preadipocytes. Briefly, our results provided new insights into understanding the mechanisms of bovine adipocyte differentiation.
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Affiliation(s)
- Xiangge Meng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengping Li
- College of Life Science, Liaocheng University, Liaocheng, China
| | - Yu Hei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Guoli Zhou
- College of Life Science, Liaocheng University, Liaocheng, China.
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54
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Ge Y, Huang J, Chen R, Fu Y, Ling T, Ou X, Rong X, Cheng Y, Lin Y, Zhou F, Lu C, Yuan S, Xu A. Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses. PLoS Pathog 2024; 20:e1012061. [PMID: 38416782 PMCID: PMC10927093 DOI: 10.1371/journal.ppat.1012061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/11/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024] Open
Abstract
Alternative polyadenylation (APA) is a widespread mechanism of gene regulation that generates mRNA isoforms with alternative 3' untranslated regions (3' UTRs). Our previous study has revealed the global 3' UTR shortening of host mRNAs through APA upon viral infection. However, how the dynamic changes in the APA landscape occur upon viral infection remains largely unknown. Here we further found that, the reduced protein abundance of CPSF6, one of the core 3' processing factors, promotes the usage of proximal poly(A) sites (pPASs) of many immune related genes in macrophages and fibroblasts upon viral infection. Shortening of the 3' UTR of these transcripts may improve their mRNA stability and translation efficiency, leading to the promotion of type I IFN (IFN-I) signalling-based antiviral immune responses. In addition, dysregulated expression of CPSF6 is also observed in many immune related physiological and pathological conditions, especially in various infections and cancers. Thus, the global APA dynamics of immune genes regulated by CPSF6, can fine-tune the antiviral response as well as the responses to other cellular stresses to maintain the tissue homeostasis, which may represent a novel regulatory mechanism for antiviral immunity.
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Affiliation(s)
- Yong Ge
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingrong Huang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Rong Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yonggui Fu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Tao Ling
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xin Ou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiaohui Rong
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Youxiang Cheng
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yi Lin
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Fengyi Zhou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chuanjian Lu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Shaochun Yuan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Anlong Xu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
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55
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Bryce-Smith S, Brown AL, Mehta PR, Mattedi F, Mikheenko A, Barattucci S, Zanovello M, Dattilo D, Yome M, Hill SE, Qi YA, Wilkins OG, Sun K, Ryadnov E, Wan Y, Vargas JNS, Birsa N, Raj T, Humphrey J, Keuss M, Ward M, Secrier M, Fratta P. TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576625. [PMID: 38313254 PMCID: PMC10836071 DOI: 10.1101/2024.01.22.576625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3' end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3'UTR extensions (3'Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3'Exts occur in multiple transcription factors, such as ELK1, SIX3, and TLX1, and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.
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Affiliation(s)
- Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Francesca Mattedi
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dario Dattilo
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Yome
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah E. Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yue A. Qi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Kai Sun
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Yixuan Wan
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | | | - Jose Norberto S. Vargas
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicol Birsa
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
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56
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Zeng Y, Lovchykova A, Akiyama T, Liu C, Guo C, Jawahar VM, Sianto O, Calliari A, Prudencio M, Dickson DW, Petrucelli L, Gitler AD. TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.575730. [PMID: 38328059 PMCID: PMC10849503 DOI: 10.1101/2024.01.22.575730] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B) and providing evidence that alternative polyadenylation is a new facet of TDP-43 pathology.
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Affiliation(s)
- Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tetsuya Akiyama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chang Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Caiwei Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vidhya Maheswari Jawahar
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Odilia Sianto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Calliari
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
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57
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Flores CC, Pasetto NA, Wang H, Dimitrov A, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders. RESEARCH SQUARE 2024:rs.3.rs-3867797. [PMID: 38313253 PMCID: PMC10836116 DOI: 10.21203/rs.3.rs-3867797/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Sleep and circadian rhythm disruptions are comorbid features of many pathologies and can negatively influence numerous health conditions, including degenerative diseases, metabolic illnesses, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. Thus, associations between sleep and/or circadian rhythm and alternative polyadenylation (APA), particularly in the context of other health challenges, are largely undescribed. APA is a process that generates various transcript isoforms from the same gene, resulting in effects on mRNA translation, stability, localization, and subsequent function. Here, we have identified unique APAs in rat brain that exhibit time-of-day-dependent oscillations in expression as well as APAs that are altered by sleep deprivation and the subsequent recovery period. Genes affected by APA usage include Mapt/Tau, Ntrk2, Homer1A, Sin3band Sorl. Sorl1 has two APAs which cycle with a 24 h period, one additional APA cycles with a 12 h period and one more that is reduced during recovery sleep. Finally, we compared sleep- or circadian-associated APAs with recently described APA-linked brain disorder susceptibility genes and found 46 genes in common.
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58
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Liu L, Seimiya T, Manley JL. WDR33 alternative polyadenylation is dependent on stochastic poly(a) site usage and splicing efficiencies. RNA Biol 2024; 21:25-35. [PMID: 39327832 PMCID: PMC11445923 DOI: 10.1080/15476286.2024.2408708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/03/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
Transcripts from the human WDR33 gene, which encodes a central component of the mRNA polyadenylation (PA) machinery, are subject to alternative polyadenylation (APA) within promoter-proximal introns/exons. This APA, which itself involves usage of multiple PA sites, results in the production of two non-canonical protein isoforms, V2 and V3, that are functionally completely unrelated to the full-length protein, with roles in innate immunity. The mechanism and regulation of WDR33 APA are unclear. Here, we report that levels of the PA factor CFIm25 modulate V2 and V3 expression, and that PA site usage of both V2 and V3 varies in distinct immune responses. Using newly developed assays to measure splicing and PA site strength, we show that splicing of V2-associated intron 6 is inefficient, allowing V2 to be produced using weak PA sites. Usage of V3's strong PA sites, on the other hand, is relatively low, reflecting the high efficiency of intron 7 splicing coupled with dependency on usage of an alternative 3' splice site within the intron. Overall, our findings demonstrate that usage of WDR33 alternative PA sites is stochastic, dependent on a complex interplay between splicing and PA, and thus provide new insights into mechanisms underlying APA.
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Affiliation(s)
- Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Takahiro Seimiya
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - James L. Manley
- Department of Biological Sciences, Columbia University, New York, NY, USA
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59
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Neumann DP, Pillman KA, Dredge BK, Bert AG, Phillips CA, Lumb R, Ramani Y, Bracken CP, Hollier BG, Selth LA, Beilharz TH, Goodall GJ, Gregory PA. The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking. RNA Biol 2024; 21:1-11. [PMID: 38112323 PMCID: PMC10732628 DOI: 10.1080/15476286.2023.2294222] [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] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3' end anchored RNA sequencing, we mapped the alternative polyadenylation (APA) landscape following Transforming Growth Factor (TGF)-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3'UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a subset of events including the length of its own transcript. Analysis of QKI crosslinked immunoprecipitation (CLIP)-sequencing data identified the binding of QKI within 3' untranslated regions (UTRs) was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts is altered to produce predominantly shorter 3'UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.
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Affiliation(s)
- Daniel P. Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Katherine A. Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - B. Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Andrew G. Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Caroline A. Phillips
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Yesha Ramani
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Cameron P. Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Brett G. Hollier
- Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Luke A. Selth
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Traude H. Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Gregory J. Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Philip A. Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
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60
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Liu L, Yu AM, Wang X, Soles LV, Teng X, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, England W, Spitale R, Yu Z, Marazzi I, Qiao F, Li W, Seelig G, Shi Y. The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. Nat Struct Mol Biol 2023; 30:1947-1957. [PMID: 38087090 DOI: 10.1038/s41594-023-01161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
JTE-607 is an anticancer and anti-inflammatory compound and its active form, compound 2, directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-messenger RNA (pre-mRNA) 3' processing. Surprisingly, compound 2-mediated inhibition of pre-mRNA cleavage is sequence specific and the drug sensitivity is predominantly determined by sequences flanking the cleavage site (CS). Using massively parallel in vitro assays, we identified key sequence features that determine drug sensitivity. We trained a machine learning model that can predict poly(A) site (PAS) relative sensitivity to compound 2 and provide the molecular basis for understanding the impact of JTE-607 on PAS selection and transcription termination genome wide. We propose that CPSF73 and associated factors bind to the CS region in a sequence-dependent manner and the interaction affinity determines compound 2 sensitivity. These results have not only elucidated the mechanism of action of JTE-607, but also unveiled an evolutionarily conserved sequence specificity of the mRNA 3' processing machinery.
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Affiliation(s)
- Liang Liu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Center for Virus Research, University of California, Irvine, Irvine, CA, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Seattle, WA, USA
| | - Xiuye Wang
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Guangzhou Laboratory, Guangdong, China
| | - Lindsey V Soles
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Xueyi Teng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yiling Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yoseop Yoon
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kristianna S K Sarkan
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Marielle Cárdenas Valdez
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Johannes Linder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Robert Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, Irvine, CA, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Seattle, WA, USA.
- Paul G Allen School of Computer Science and Engineering, University of Washington, Seattle, Seattle, WA, USA.
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA.
- Center for Virus Research, University of California, Irvine, Irvine, CA, USA.
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61
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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62
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Murphy MR, Ramadei A, Doymaz A, Varriano S, Natelson D, Yu A, Aktas S, Mazzeo M, Mazzeo M, Zakusilo G, Kleiman F. Long non-coding RNA generated from CDKN1A gene by alternative polyadenylation regulates p21 expression during DNA damage response. Nucleic Acids Res 2023; 51:11911-11926. [PMID: 37870464 PMCID: PMC10681730 DOI: 10.1093/nar/gkad899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/21/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DDR-activated APA event occurs in the first intron of CDKN1A, inducing an alternate last exon-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon DNA Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high-throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform under non-stress conditions, and SPUD is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53. The RNA binding protein HuR binds to and promotes the stability of SPUD precursor RNA. SPUD induction increases p21 protein, but not mRNA levels, affecting p21 functions in cell-cycle, CDK2 expression and cell growth. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD alters their association with CDKN1A full-length in a DDR-dependent manner, promoting CDKN1A translation. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cell-cycle.
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Affiliation(s)
- Michael R Murphy
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Anthony Ramadei
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Ahmet Doymaz
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Sophia Varriano
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Devorah M Natelson
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Amy Yu
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Sera Aktas
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Marie Mazzeo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Michael Mazzeo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - George Zakusilo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Frida E Kleiman
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
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63
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Chemparathy A, Guen YL, Zeng Y, Gorzynski J, Jensen T, Yang C, Kasireddy N, Talozzi L, Belloy ME, Stewart I, Gitler AD, Wagner AD, Mormino E, Henderson VW, Wyss-Coray T, Ashley E, Cruchaga C, Greicius MD. A 3'UTR Insertion Is a Candidate Causal Variant at the TMEM106B Locus Associated with Increased Risk for FTLD-TDP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.06.23292312. [PMID: 37461476 PMCID: PMC10350161 DOI: 10.1101/2023.07.06.23292312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Background and Objectives Single nucleotide variants near TMEM106B associate with risk of frontotemporal lobar dementia with TDP-43 inclusions (FTLD-TDP) and Alzheimer's disease (AD) in genome-wide association studies (GWAS), but the causal variant at this locus remains unclear. Here we asked whether a novel structural variant on TMEM106B is the causal variant. Methods An exploratory analysis identified structural variants on neurodegeneration-related genes. Subsequent analyses focused on an Alu element insertion on the 3'UTR of TMEM106B. This study included data from longitudinal aging and neurogenerative disease cohorts at Stanford University, case-control cohorts in the Alzheimer's Disease Sequencing Project (ADSP), and expression and proteomics data from Washington University in St. Louis (WUSTL). 432 individuals from two Stanford aging cohorts were whole-genome long-read and short-read sequenced. 16,906 samples from ADSP were short-read sequenced. Genotypes, transcriptomics, and proteomics data were available in 1,979 participants from an aging and dementia cohort at WUSTL. Selection criteria were specific to each cohort. In primary analyses, the linkage disequilibrium between the TMEM106B locus variants in the FTLD-TDP GWAS and the 3'UTR insertion was estimated. We then estimated linkage by ancestry in the ADSP and evaluated the effect of the TMEM106B lead variant on mRNA and protein levels. Results The primary analysis included 432 participants (52.5% females, age range 45-92 years old). We identified a 316 bp Alu insertion overlapping the TMEM106B 3'UTR tightly linked with top GWAS variants rs3173615(C) and rs1990622(A). In ADSP European-ancestry participants, this insertion is in equivalent linkage with rs1990622(A) (R2=0.962, D'=0.998) and rs3173615(C) (R2=0.960, D'=0.996). In African-ancestry participants, the insertion is in stronger linkage with rs1990622(A) (R2=0.992, D'=0.998) than with rs3173615(C) (R2=0.811, D'=0.994). In public datasets, rs1990622 was consistently associated with TMEM106B protein levels but not with mRNA expression. In the WUSTL dataset, rs1990622 is associated with TMEM106B protein levels in plasma and cerebrospinal fluid, but not with TMEM106B mRNA expression. Discussion We identified a novel Alu element insertion in the 3'UTR of TMEM106B in tight linkage with the lead FTLD-TDP risk variant. The lead variant is associated with TMEM106B protein levels, but not expression. The 3'UTR insertion is a lead candidate for the causal variant at this complex locus, pending confirmation with functional studies.
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Affiliation(s)
- Augustine Chemparathy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - John Gorzynski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Tanner Jensen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Chengran Yang
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO
| | - Nandita Kasireddy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Lia Talozzi
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Michael E. Belloy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Ilaria Stewart
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Anthony D. Wagner
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Elizabeth Mormino
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Victor W. Henderson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Euan Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Carlos Cruchaga
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO
| | - Michael D. Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
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64
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Stroup EK, Ji Z. Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease. Nat Commun 2023; 14:7378. [PMID: 37968271 PMCID: PMC10651852 DOI: 10.1038/s41467-023-43266-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023] Open
Abstract
The genomic distribution of cleavage and polyadenylation (polyA) sites should be co-evolutionally optimized with the local gene structure. Otherwise, spurious polyadenylation can cause premature transcription termination and generate aberrant proteins. To obtain mechanistic insights into polyA site optimization across the human genome, we develop deep/machine learning models to identify genome-wide putative polyA sites at unprecedented nucleotide-level resolution and calculate their strength and usage in the genomic context. Our models quantitatively measure position-specific motif importance and their crosstalk in polyA site formation and cleavage heterogeneity. The intronic site expression is governed by the surrounding splicing landscape. The usage of alternative polyA sites in terminal exons is modulated by their relative locations and distance to downstream genes. Finally, we apply our models to reveal thousands of disease- and trait-associated genetic variants altering polyadenylation activity. Altogether, our models represent a valuable resource to dissect molecular mechanisms mediating genome-wide polyA site expression and characterize their functional roles in human diseases.
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Affiliation(s)
- Emily Kunce Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA.
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65
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Liu S, Wu R, Chen L, Deng K, Ou X, Lu X, Li M, Liu C, Chen S, Fu Y, Xu A. CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation. Cell Rep 2023; 42:113197. [PMID: 37777964 DOI: 10.1016/j.celrep.2023.113197] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
Cancer cells usually exhibit shortened 3' untranslated regions (UTRs) due to alternative polyadenylation (APA) to promote cell proliferation and migration. Upregulated CPSF6 leads to a systematic prolongation of 3' UTRs, but CPSF6 expression in tumors is typically higher than that in healthy tissues. This contradictory observation suggests that it is necessary to investigate the underlying mechanism by which CPSF6 regulates APA switching in cancer. Here, we find that CPSF6 can undergo liquid-liquid phase separation (LLPS), and elevated LLPS is associated with the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs CPSF6 LLPS by phosphorylating its arginine/serine-like domain. The reduction of CPSF6 LLPS can lead to a shortened 3' UTR of cell-cycle-related genes and accelerate cell proliferation. These results suggest that CPSF6 LLPS, rather than its expression level, may be responsible for APA regulation in cancer cells.
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Affiliation(s)
- Susu Liu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Runze Wu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Liutao Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Ke Deng
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xin Ou
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xin Lu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Mengxia Li
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Chao Liu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Shangwu Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yonggui Fu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China.
| | - Anlong Xu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China; School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, P.R. China.
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Yu P, Song S, Zhang X, Cui S, Wei G, Huang Z, Zeng L, Ni T, Sun A. Downregulation of apoptotic repressor AVEN exacerbates cardiac injury after myocardial infarction. Proc Natl Acad Sci U S A 2023; 120:e2302482120. [PMID: 37816050 PMCID: PMC10589712 DOI: 10.1073/pnas.2302482120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023] Open
Abstract
Myocardial infarction (MI) is a leading cause of heart failure (HF), associated with morbidity and mortality worldwide. As an essential part of gene expression regulation, the role of alternative polyadenylation (APA) in post-MI HF remains elusive. Here, we revealed a global, APA-mediated, 3' untranslated region (3' UTR)-lengthening pattern in both human and murine post-MI HF samples. Furthermore, the 3' UTR of apoptotic repressor gene, AVEN, is lengthened after MI, contributing to its downregulation. AVEN knockdown increased cardiomyocyte apoptosis, whereas restoration of AVEN expression substantially improved cardiac function. Mechanistically, AVEN 3' UTR lengthening provides additional binding sites for miR-30b-5p and miR-30c-5p, thus reducing AVEN expression. Additionally, PABPN1 (poly(A)-binding protein 1) was identified as a potential regulator of AVEN 3' UTR lengthening after MI. Altogether, our findings revealed APA as a unique mechanism regulating cardiac injury in response to MI and also indicated that the APA-regulated gene, AVEN, holds great potential as a critical therapeutic target for treating post-MI HF.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Shujun Cui
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
| | - Zihang Huang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Linqi Zeng
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai200040, China
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot010021, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai201203, China
| | - Aijun Sun
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai201203, China
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Stroup EK, Ji Z. Delineating yeast cleavage and polyadenylation signals using deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561764. [PMID: 37873420 PMCID: PMC10592759 DOI: 10.1101/2023.10.10.561764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
3'-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared to well-defined regulatory elements in mammals. Especially, recent deep sequencing experiments showed extensive cleavage heterogeneity for some mRNAs in Saccharomyces cerevisiae and uncovered the polyA motif differences between S. cerevisiae vs. Schizosaccharomyces pombe . The findings raised the fundamental question of how polyadenylation signals are formed in yeast. Here we addressed this question by developing deep learning models to deconvolute degenerate cis -regulatory elements and quantify their positional importance in mediating yeast polyA site formation, cleavage heterogeneity, and strength. In S. cerevisiae , cleavage heterogeneity is promoted by the depletion of U-rich elements around polyA sites as well as multiple occurrences of upstream UA-rich elements. Sites with high cleavage heterogeneity show overall lower strength. The site strength and tandem site distances modulate alternative polyadenylation (APA) under the diauxic stress. Finally, we developed a deep learning model to reveal the distinct motif configuration of S. pombe polyA sites which show more precise cleavage than S. cerevisiae . Altogether, our deep learning models provide unprecedented insights into polyA site formation across yeast species.
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68
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Zhang L, More KR, Ojha A, Jackson CB, Quinlan BD, Li H, He W, Farzan M, Pardi N, Choe H. Effect of mRNA-LNP components of two globally-marketed COVID-19 vaccines on efficacy and stability. NPJ Vaccines 2023; 8:156. [PMID: 37821446 PMCID: PMC10567765 DOI: 10.1038/s41541-023-00751-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
During the COVID-19 pandemic, Pfizer-BioNTech and Moderna successfully developed nucleoside-modified mRNA lipid nanoparticle (LNP) vaccines. SARS-CoV-2 spike protein expressed by those vaccines are identical in amino acid sequence, but several key components are distinct. Here, we compared the effect of ionizable lipids, untranslated regions (UTRs), and nucleotide composition of the two vaccines, focusing on mRNA delivery, antibody generation, and long-term stability. We found that the ionizable lipid, SM-102, in Moderna's vaccine performs better than ALC-0315 in Pfizer-BioNTech's vaccine for intramuscular delivery of mRNA and antibody production in mice and long-term stability at 4 °C. Moreover, Pfizer-BioNTech's 5' UTR and Moderna's 3' UTR outperform their counterparts in their contribution to transgene expression in mice. We further found that varying N1-methylpseudouridine content at the wobble position of mRNA has little effect on vaccine efficacy. These findings may contribute to the further improvement of nucleoside-modified mRNA-LNP vaccines and therapeutics.
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Affiliation(s)
- Lizhou Zhang
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
| | - Kunal R More
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Amrita Ojha
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Cody B Jackson
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Brian D Quinlan
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Hao Li
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
- Skaggs Graduate School, The Scripps Research Institute, La Jolla, CA, USA
| | - Wenhui He
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
- Center For Integrated Solutions for Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Farzan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
- Skaggs Graduate School, The Scripps Research Institute, La Jolla, CA, USA
- Center For Integrated Solutions for Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyeryun Choe
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Department of Immunology and Microbiology, UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
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69
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Kang B, Yang Y, Hu K, Ruan X, Liu YL, Lee P, Lee J, Wang J, Zhang X. Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain. Genome Res 2023; 33:1774-1787. [PMID: 37907328 PMCID: PMC10691540 DOI: 10.1101/gr.277864.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/12/2023] [Indexed: 11/02/2023]
Abstract
Differential polyadenylation sites (PAs) critically regulate gene expression, but their cell type-specific usage and spatial distribution in the brain have not been systematically characterized. Here, we present Infernape, which infers and quantifies PA usage from single-cell and spatial transcriptomic data and show its application in the mouse brain. Infernape uncovers alternative intronic PAs and 3'-UTR lengthening during cortical neurogenesis. Progenitor-neuron comparisons in the excitatory and inhibitory neuron lineages show overlapping PA changes in embryonic brains, suggesting that the neural proliferation-differentiation axis plays a prominent role. In the adult mouse brain, we uncover cell type-specific PAs and visualize such events using spatial transcriptomic data. Over two dozen neurodevelopmental disorder-associated genes such as Csnk2a1 and Mecp2 show differential PAs during brain development. This study presents Infernape to identify PAs from scRNA-seq and spatial data, and highlights the role of alternative PAs in neuronal gene regulation.
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Affiliation(s)
- Bowei Kang
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yalan Yang
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kaining Hu
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Xiangbin Ruan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yi-Lin Liu
- Department of Statistics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Pinky Lee
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jasper Lee
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jingshu Wang
- Department of Statistics, The University of Chicago, Chicago, Illinois 60637, USA;
| | - Xiaochang Zhang
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA;
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, USA
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70
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Erdem M, Cicek M, Erson-Bensan AE. Versatile RNA: overlooked gems of the transcriptome. FEBS J 2023; 290:4843-4851. [PMID: 36719259 DOI: 10.1111/febs.16742] [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: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/01/2023]
Abstract
The critical role of RNA, its use and targetability concerning different aspects of human health are gaining more attention because our understanding of the versatility of RNA has dramatically evolved over the last decades. We now appreciate that RNA is far more critical than a messenger molecule and possesses many complicated functions. As a multifunctional molecule with its sequence, flexible structures and enzymatic abilities, RNA is genuinely powerful. Mammalian transcriptomes consist of a dynamically regulated plethora of coding and noncoding RNA types. However, some aspects of RNA metabolism remain to be explored. In this Viewpoint, we focus on the transcriptome's unconventional and possibly overlooked aspects to emphasize the importance of RNA in mammalian systems.
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Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mustafa Cicek
- Department of Biology, Kamil Ozdag Faculty of Science, Karamanoglu Mehmetbey University, Karaman, Turkey
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71
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Angst P, Pombert JF, Ebert D, Fields PD. Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis. G3 (BETHESDA, MD.) 2023; 13:jkad185. [PMID: 37565496 PMCID: PMC10542269 DOI: 10.1093/g3journal/jkad185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/05/2023] [Indexed: 08/12/2023]
Abstract
Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences (PacBio), and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56% interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | | | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
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72
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Zhou J, Li QQ. Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation. MOLECULAR HORTICULTURE 2023; 3:19. [PMID: 37789388 PMCID: PMC10536700 DOI: 10.1186/s43897-023-00066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The sessile nature of plants confines their responsiveness to changing environmental conditions. Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors. Alternative polyadenylation (APA) is known for its capacity to augment transcriptome diversity and plasticity, thereby furnishing an additional set of tools for modulating gene expression. APA has also been demonstrated to exhibit intimate associations with plant stress responses. In this study, we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses. These stresses include adverse environmental stresses, and pathogenic attacks, such as cadmium toxicity, high salt, hypoxia, oxidative stress, cold, heat shock, along with bacterial, fungal, and viral infections. We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition. We also proposed a general APA model where transacting factors, including poly(A) factors, epigenetic regulators, RNA m6A modification factors, and phase separation proteins, assume pivotal roles in APA related transcriptome plasticity during stress response in plants.
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Affiliation(s)
- Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA.
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73
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Herron RS, Kunisky AK, Madden JR, Anyaeche VI, Maung MZ, Hwang HW. A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway. eLife 2023; 12:e85036. [PMID: 37665675 PMCID: PMC10476966 DOI: 10.7554/elife.85036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/16/2023] [Indexed: 09/06/2023] Open
Abstract
Alternative polyadenylation (APA) generates mRNA isoforms and diversifies gene expression. Here we report the discovery that the mTORC1 signaling pathway balances the expression of two Trim9/TRIM9 isoforms through APA regulation in human and mouse. We showed that CFIm components, CPSF6 and NUDT21, promote the short Trim9/TRIM9 isoform (Trim9-S/TRIM9-S) expression. In addition, we identified an evolutionarily conserved twin UGUA motif, UGUAYUGUA, in TRIM9-S polyadenylation site (PAS) that is critical for its regulation by CPSF6. We found additional CPSF6-regulated PASs with similar twin UGUA motifs in human and experimentally validated the twin UGUA motif functionality in BMPR1B, MOB4, and BRD4-L. Importantly, we showed that inserting a twin UGUA motif into a heterologous PAS was sufficient to confer regulation by CPSF6 and mTORC1. Our study reveals an evolutionarily conserved mechanism to regulate gene isoform expression by mTORC1 and implicates possible gene isoform imbalance in cancer and neurological disorders with mTORC1 pathway dysregulation.
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Affiliation(s)
- R Samuel Herron
- Department of Pathology, University of PittsburghPittsburghUnited States
| | | | - Jessica R Madden
- Department of Pathology, University of PittsburghPittsburghUnited States
| | - Vivian I Anyaeche
- Department of Pathology, University of PittsburghPittsburghUnited States
| | - May Z Maung
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Hun-Way Hwang
- Department of Pathology, University of PittsburghPittsburghUnited States
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74
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Moon Y, Burri D, Zavolan M. Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR Genom Bioinform 2023; 5:lqad079. [PMID: 37705828 PMCID: PMC10495540 DOI: 10.1093/nargab/lqad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative polyadenylation is a main driver of transcriptome diversity in mammals, generating transcript isoforms with different 3' ends via cleavage and polyadenylation at distinct polyadenylation (poly(A)) sites. The regulation of cell type-specific poly(A) site choice is not completely resolved, and requires quantitative poly(A) site usage data across cell types. 3' end-based single-cell RNA-seq can now be broadly used to obtain such data, enabling the identification and quantification of poly(A) sites with direct experimental support. We propose SCINPAS, a computational method to identify poly(A) sites from scRNA-seq datasets. SCINPAS modifies the read deduplication step to favor the selection of distal reads and extract those with non-templated poly(A) tails. This approach improves the resolution of poly(A) site recovery relative to standard software. SCINPAS identifies poly(A) sites in genic and non-genic regions, providing complementary information relative to other tools. The workflow is modular, and the key read deduplication step is general, enabling the use of SCINPAS in other typical analyses of single cell gene expression. Taken together, we show that SCINPAS is able to identify experimentally-supported, known and novel poly(A) sites from 3' end-based single-cell RNA sequencing data.
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Affiliation(s)
- Youngbin Moon
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dominik Burri
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
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75
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Luisier R, Andreassi C, Fournier L, Riccio A. The predicted RNA-binding protein regulome of axonal mRNAs. Genome Res 2023; 33:1497-1512. [PMID: 37582635 PMCID: PMC10620043 DOI: 10.1101/gr.277804.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023]
Abstract
Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their cytoarchitecture. The targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3' Untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting with specific RNA-binding proteins (RBPs). However, how 3' UTRs contribute to mRNA metabolism and the nature of RBP complexes responsible for these functions remains elusive. We performed 3' end sequencing of RNA isolated from cell bodies and axons of sympathetic neurons exposed to either nerve growth factor (NGF) or neurotrophin 3 (NTF3, also known as NT-3). NGF and NTF3 are growth factors essential for sympathetic neuron development through distinct signaling mechanisms. Whereas NTF3 acts mostly locally, NGF signal is retrogradely transported from axons to cell bodies. We discovered that both NGF and NTF3 affect transcription and alternative polyadenylation in the nucleus and induce the localization of specific 3' UTR isoforms to axons, including short 3' UTR isoforms found exclusively in axons. The integration of our data with CLIP sequencing data supports a model whereby long 3' UTR isoforms associate with RBP complexes in the nucleus and, upon reaching the axons, are remodeled locally into shorter isoforms. Our findings shed new light into the complex relationship between nuclear polyadenylation, mRNA localization, and local 3' UTR remodeling in developing neurons.
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Affiliation(s)
- Raphaëlle Luisier
- Idiap Research Institute, Martigny 1920, Switzerland;
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Catia Andreassi
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Lisa Fournier
- Idiap Research Institute, Martigny 1920, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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76
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Hong H, Dill-McFarland KA, Simmons JD, Peterson GJ, Benchek P, Mayanja-Kizza H, Boom WH, Stein CM, Hawn TR. Mycobacterium tuberculosis-dependent Monocyte Expression Quantitative Trait Loci and Tuberculosis Pathogenesis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.28.23294698. [PMID: 37693490 PMCID: PMC10491362 DOI: 10.1101/2023.08.28.23294698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The heterogeneity of outcomes after Mycobacterium tuberculosis (Mtb) exposure is a conundrum associated with millennia of host-pathogen co-evolution. We hypothesized that human myeloid cells contain genetically encoded, Mtb-specific responses that regulate critical steps in tuberculosis (TB) pathogenesis. We mapped genome-wide expression quantitative trait loci (eQTLs) in Mtb-infected monocytes with RNAseq from 80 Ugandan household contacts of pulmonary TB cases to identify monocyte-specific, Mtb-dependent eQTLs and their association with cytokine expression and clinical resistance to tuberculin skin test (TST) and interferon-γ release assay (IGRA) conversion. cis-eQTLs (n=1,567) were identified in Mtb-infected monocytes (FDR<0.01), including 29 eQTLs in 16 genes which were Mtb-dependent (significant for Mtb:genotype interaction [FDR<0.1], but not classified as eQTL in media condition [FDR≥0.01]). A subset of eQTLs were associated with Mtb-induced cytokine expression (n=8) and/or clinical resistance to TST/IGRA conversion (n=1). Expression of BMP6, an Mtb-dependent eQTL gene, was associated with IFNB1 induction in Mtb-infected and DNA ligand-induced cells. Network and enrichment analyses identified fatty acid metabolism as a pathway associated with eQTL genes. These findings suggest that monocyte genes contain Mtb-dependent eQTLs, including a subset associated with cytokine expression and/or clinical resistance to TST/IGRA conversion, providing insight into immunogenetic pathways regulating susceptibility to Mtb infection and TB pathogenesis.
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Affiliation(s)
- Hyejeong Hong
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jason D. Simmons
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - W. Henry Boom
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Catherine M. Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Thomas R. Hawn
- Department of Medicine, University of Washington, Seattle, WA, USA
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77
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Bergant V, Schnepf D, de Andrade Krätzig N, Hubel P, Urban C, Engleitner T, Dijkman R, Ryffel B, Steiger K, Knolle PA, Kochs G, Rad R, Staeheli P, Pichlmair A. mRNA 3'UTR lengthening by alternative polyadenylation attenuates inflammatory responses and correlates with virulence of Influenza A virus. Nat Commun 2023; 14:4906. [PMID: 37582777 PMCID: PMC10427651 DOI: 10.1038/s41467-023-40469-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/27/2023] [Indexed: 08/17/2023] Open
Abstract
Changes of mRNA 3'UTRs by alternative polyadenylation (APA) have been associated to numerous pathologies, but the mechanisms and consequences often remain enigmatic. By combining transcriptomics, proteomics and recombinant viruses we show that all tested strains of IAV, including A/PR/8/34(H1N1) (PR8) and A/Cal/07/2009 (H1N1) (Cal09), cause APA. We mapped the effect to the highly conserved glycine residue at position 184 (G184) of the viral non-structural protein 1 (NS1). Unbiased mass spectrometry-based analyses indicate that NS1 causes APA by perturbing the function of CPSF4 and that this function is unrelated to virus-induced transcriptional shutoff. Accordingly, IAV strain PR8, expressing an NS1 variant with weak CPSF binding, does not induce host shutoff but only APA. However, recombinant IAV (PR8) expressing NS1(G184R) lacks binding to CPSF4 and thereby also the ability to cause APA. Functionally, the impaired ability to induce APA leads to an increased inflammatory cytokine production and an attenuated phenotype in a mouse infection model. Investigating diverse viral infection models showed that APA induction is a frequent ability of many pathogens. Collectively, we propose that targeting of the CPSF complex, leading to widespread alternative polyadenylation of host transcripts, constitutes a general immunevasion mechanism employed by a variety of pathogenic viruses.
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Affiliation(s)
- Valter Bergant
- Institute of Virology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Max Planck Institute of Biochemistry, Munich, Germany
| | - Daniel Schnepf
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Immunoregulation Laboratory, The Francis Crick Institute, London, UK
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Philipp Hubel
- Max Planck Institute of Biochemistry, Munich, Germany
| | - Christian Urban
- Institute of Virology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Max Planck Institute of Biochemistry, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Ronald Dijkman
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Bernhard Ryffel
- CNRS, UMR7355, Orleans, France
- Experimental and Molecular Immunology and Neurogenetics, University of Orléans, Orléans, France
| | - Katja Steiger
- Institut für allgemeine Pathologie und Pathologische Anatomie, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, Munich, Germany
- Department of Medicine II, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Peter Staeheli
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
| | - Andreas Pichlmair
- Institute of Virology, TUM School of Medicine, Technical University of Munich, Munich, Germany.
- Max Planck Institute of Biochemistry, Munich, Germany.
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.
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78
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Bergfort A, Neugebauer KM. The promoter as a trip navigator: Guiding alternative polyadenylation site destinations. Mol Cell 2023; 83:2395-2397. [PMID: 37478824 DOI: 10.1016/j.molcel.2023.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
Alfonso-Gonzalez et al.1 present an innovative combination of long-read-sequencing approaches that reveal coupling of alternative transcription start sites and alternative polyadenylation site usage on a global level.
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Affiliation(s)
- Alexandra Bergfort
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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79
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Rodríguez‐Molina JB, Turtola M. Birth of a poly(A) tail: mechanisms and control of mRNA polyadenylation. FEBS Open Bio 2023; 13:1140-1153. [PMID: 36416579 PMCID: PMC10315857 DOI: 10.1002/2211-5463.13528] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
During their synthesis in the cell nucleus, most eukaryotic mRNAs undergo a two-step 3'-end processing reaction in which the pre-mRNA is cleaved and released from the transcribing RNA polymerase II and a polyadenosine (poly(A)) tail is added to the newly formed 3'-end. These biochemical reactions might appear simple at first sight (endonucleolytic RNA cleavage and synthesis of a homopolymeric tail), but their catalysis requires a multi-faceted enzymatic machinery, the cleavage and polyadenylation complex (CPAC), which is composed of more than 20 individual protein subunits. The activity of CPAC is further orchestrated by Poly(A) Binding Proteins (PABPs), which decorate the poly(A) tail during its synthesis and guide the mRNA through subsequent gene expression steps. Here, we review the structure, molecular mechanism, and regulation of eukaryotic mRNA 3'-end processing machineries with a focus on the polyadenylation step. We concentrate on the CPAC and PABPs from mammals and the budding yeast, Saccharomyces cerevisiae, because these systems are the best-characterized at present. Comparison of their functions provides valuable insights into the principles of mRNA 3'-end processing.
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Affiliation(s)
| | - Matti Turtola
- Department of Life TechnologiesUniversity of TurkuFinland
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80
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Cacioppo R, Akman HB, Tuncer T, Erson-Bensan AE, Lindon C. Differential translation of mRNA isoforms underlies oncogenic activation of cell cycle kinase Aurora A. eLife 2023; 12:RP87253. [PMID: 37384380 DOI: 10.7554/elife.87253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
Aurora Kinase A (AURKA) is an oncogenic kinase with major roles in mitosis, but also exerts cell cycle- and kinase-independent functions linked to cancer. Therefore, control of its expression, as well as its activity, is crucial. A short and a long 3'UTR isoform exist for AURKA mRNA, resulting from alternative polyadenylation (APA). We initially observed that in triple-negative breast cancer, where AURKA is typically overexpressed, the short isoform is predominant and this correlates with faster relapse times of patients. The short isoform is characterized by higher translational efficiency since translation and decay rate of the long isoform are targeted by hsa-let-7a tumor-suppressor miRNA. Additionally, hsa-let-7a regulates the cell cycle periodicity of translation of the long isoform, whereas the short isoform is translated highly and constantly throughout interphase. Finally, disrupted production of the long isoform led to an increase in proliferation and migration rates of cells. In summary, we uncovered a new mechanism dependent on the cooperation between APA and miRNA targeting likely to be a route of oncogenic activation of human AURKA.
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Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Hesna Begum Akman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Taner Tuncer
- Department of Biology, Ondokuz Mayis Universitesi, Samsun, Turkey
| | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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81
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Zhang Q, Tian B. The emerging theme of 3'UTR mRNA isoform regulation in reprogramming of cell metabolism. Biochem Soc Trans 2023; 51:1111-1119. [PMID: 37171086 PMCID: PMC10771799 DOI: 10.1042/bst20221128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/26/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
The 3' untranslated region (3'UTR) of mRNA plays a key role in the post-transcriptional regulation of gene expression. Most eukaryotic protein-coding genes express 3'UTR isoforms owing to alternative cleavage and polyadenylation (APA). The 3'UTR isoform expression profile of a cell changes in cell proliferation, differentiation, and stress conditions. Here, we review the emerging theme of regulation of 3'UTR isoforms in cell metabolic reprogramming, focusing on cell growth and autophagy responses through the mTOR pathway. We discuss regulatory events that converge on the Cleavage Factor I complex, a master regulator of APA in 3'UTRs, and recent understandings of isoform-specific m6A modification and endomembrane association in determining differential metabolic fates of 3'UTR isoforms.
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Affiliation(s)
- Qiang Zhang
- Gene Expression and Regulation Program and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, U.S.A
| | - Bin Tian
- Gene Expression and Regulation Program and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, U.S.A
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82
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Abstract
Chemical modifications on mRNA represent a critical layer of gene expression regulation. Research in this area has continued to accelerate over the last decade, as more modifications are being characterized with increasing depth and breadth. mRNA modifications have been demonstrated to influence nearly every step from the early phases of transcript synthesis in the nucleus through to their decay in the cytoplasm, but in many cases, the molecular mechanisms involved in these processes remain mysterious. Here, we highlight recent work that has elucidated the roles of mRNA modifications throughout the mRNA life cycle, describe gaps in our understanding and remaining open questions, and offer some forward-looking perspective on future directions in the field.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA;
| | - Sigrid Nachtergaele
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA;
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83
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Cao J, Kuyumcu-Martinez MN. Alternative polyadenylation regulation in cardiac development and cardiovascular disease. Cardiovasc Res 2023; 119:1324-1335. [PMID: 36657944 PMCID: PMC10262186 DOI: 10.1093/cvr/cvad014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 01/21/2023] Open
Abstract
Cleavage and polyadenylation of pre-mRNAs is a necessary step for gene expression and function. Majority of human genes exhibit multiple polyadenylation sites, which can be alternatively used to generate different mRNA isoforms from a single gene. Alternative polyadenylation (APA) of pre-mRNAs is important for the proteome and transcriptome landscape. APA is tightly regulated during development and contributes to tissue-specific gene regulation. Mis-regulation of APA is linked to a wide range of pathological conditions. APA-mediated gene regulation in the heart is emerging as a new area of research. Here, we will discuss the impact of APA on gene regulation during heart development and in cardiovascular diseases. First, we will briefly review how APA impacts gene regulation and discuss molecular mechanisms that control APA. Then, we will address APA regulation during heart development and its dysregulation in cardiovascular diseases. Finally, we will discuss pre-mRNA targeting strategies to correct aberrant APA patterns of essential genes for the treatment or prevention of cardiovascular diseases. The RNA field is blooming due to advancements in RNA-based technologies. RNA-based vaccines and therapies are becoming the new line of effective and safe approaches for the treatment and prevention of human diseases. Overall, this review will be influential for understanding gene regulation at the RNA level via APA in the heart and will help design RNA-based tools for the treatment of cardiovascular diseases in the future.
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Affiliation(s)
- Jun Cao
- Faculty of Environment and Life, Beijing University of Technology, Xueyuan Road, Haidian District, Beijing 100124, PR China
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
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84
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Watt K, Postovit LM. Tailoring 3' UTRs alters metastatic potential. Nat Cell Biol 2023; 25:805-807. [PMID: 37156910 DOI: 10.1038/s41556-023-01127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Kathleen Watt
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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85
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Alfonso-Gonzalez C, Legnini I, Holec S, Arrigoni L, Ozbulut HC, Mateos F, Koppstein D, Rybak-Wolf A, Bönisch U, Rajewsky N, Hilgers V. Sites of transcription initiation drive mRNA isoform selection. Cell 2023; 186:2438-2455.e22. [PMID: 37178687 PMCID: PMC10228280 DOI: 10.1016/j.cell.2023.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 12/16/2022] [Accepted: 04/06/2023] [Indexed: 05/15/2023]
Abstract
The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Here, we assess the regulatory relationships between transcription initiation, alternative splicing, and 3' end site selection. Applying long-read sequencing to accurately represent even the longest transcripts from end to end, we quantify mRNA isoforms in Drosophila tissues, including the transcriptionally complex nervous system. We find that in Drosophila heads, as well as in human cerebral organoids, 3' end site choice is globally influenced by the site of transcription initiation (TSS). "Dominant promoters," characterized by specific epigenetic signatures including p300/CBP binding, impose a transcriptional constraint to define splice and polyadenylation variants. In vivo deletion or overexpression of dominant promoters as well as p300/CBP loss disrupted the 3' end expression landscape. Our study demonstrates the crucial impact of TSS choice on the regulation of transcript diversity and tissue identity.
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Affiliation(s)
- Carlos Alfonso-Gonzalez
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwig University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), 79108 Freiburg, Germany
| | - Ivano Legnini
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Sarah Holec
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Laura Arrigoni
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Hasan Can Ozbulut
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwig University, 79104 Freiburg, Germany
| | - Fernando Mateos
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - David Koppstein
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Agnieszka Rybak-Wolf
- Organoid Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Ulrike Bönisch
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Charité - Universitätsmedizin, Charitépl. 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany; NeuroCure Cluster of Excellence, Berlin, Germany; German Cancer Consortium (DKTK); National Center for Tumor Diseases (NCT), Site Berlin, Berlin, Germany
| | - Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Signalling Research Centre CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
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86
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Liu L, Yu AM, Wang X, Soles LV, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, Marazzi I, Yu Z, Qiao F, Li W, Seelig G, Shi Y. The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536453. [PMID: 37090613 PMCID: PMC10120630 DOI: 10.1101/2023.04.11.536453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3' processing. Although CPSF73 is universally required for mRNA 3' end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3' processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3' processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3' processing machinery.
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87
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Rivera-Rivas LA, Arroyo R. Iron restriction increases the expression of a cytotoxic cysteine proteinase TvCP2 by a novel mechanism of tvcp2 mRNA alternative polyadenylation in Trichomonas vaginalis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194935. [PMID: 37011833 DOI: 10.1016/j.bbagrm.2023.194935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023]
Abstract
Trichomonas vaginalis TvCP2 (TVAG_057000) is a cytotoxic cysteine proteinase (CP) expressed under iron-limited conditions. This work aimed to identify one of the mechanisms of tvcp2 gene expression regulation by iron at the posttranscriptional level. We checked tvcp2 mRNA stability under both iron-restricted (IR) and high iron (HI) conditions in the presence of actinomycin D. Greater stability of the tvcp2 mRNA under the IR than in HI conditions was observed, as expected. In silico analysis of the 3' regulatory region showed the presence of two putative polyadenylation signals in the tvcp2 transcript. By 3'-RACE assays, we demonstrated the existence of two isoforms of the tvcp2 mRNA with different 3'-UTR that resulted in more TvCP2 protein under IR than in HI conditions detected by WB assays. Additionally, we searched for homologs of the trichomonad polyadenylation machinery by an in silico analysis in the genome database, TrichDB. 16 genes that encode proteins that could be part of the trichomonad polyadenylation machinery were found. qRT-PCR assays showed that most of these genes were positively regulated by iron. Thus, our results show the presence of alternative polyadenylation as a novel iron posttranscriptional regulatory mechanism in T. vaginalis for the tvcp2 gene expression.
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Affiliation(s)
- Luis Alberto Rivera-Rivas
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico.
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88
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Yu L, Majerciak V, Jia R, Zheng ZM. Revisiting and corrections to the annotated SRSF3 (SRp20) gene structure and RefSeq sequences from the human and mouse genomes. CELL INSIGHT 2023; 2:100089. [PMID: 37193066 PMCID: PMC10134197 DOI: 10.1016/j.cellin.2023.100089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 05/18/2023]
Abstract
SRSF3 (SRp20) is the smallest member of the serine/arginine (SR)-rich protein family. We found the annotated human SRSF3 and mouse Srsf3 RefSeq sequences are much larger than the detected SRSF3/Srsf3 RNA size by Northern blot. Mapping of RNA-seq reads from various human and mouse cell lines to the annotated SRSF3/Srsf3 gene illustrated only a partial coverage of its terminal exon 7. By 5' RACE and 3' RACE, we determined that SRSF3 gene spanning over 8422 bases and Srsf3 gene spanning over 9423 bases. SRSF3/Srsf3 gene has seven exons with exon 7 bearing two alternative polyadenylation signals (PAS). Through alternative PAS selection and exon 4 exclusion/inclusion by alternative RNA splicing, SRSF3/Srsf3 gene expresses four RNA isoforms. The major SRSF3 mRNA isoform with exon 4 exclusion by using a favorable distal PAS to encode a full-length protein is 1411 nt long (not annotated 4228 nt) and the same major mouse Srsf3 mRNA isoform is only 1295 nt (not annotated 2585 nt). The difference from the redefined RNA size of SRSF3/Srsf3 to the corresponding RefSeq sequence is at the 3' UTR region. Collectively, the redefined SRSF3/Srsf3 gene structure and expression will allow better understanding of SRSF3 functions and its regulations in health and diseases.
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Affiliation(s)
- Lulu Yu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST), Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
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89
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Zhu X, Gao M, Yang Y, Li W, Bao J, Li Y. The CRISPR/Cas9 System Delivered by Extracellular Vesicles. Pharmaceutics 2023; 15:pharmaceutics15030984. [PMID: 36986843 PMCID: PMC10053467 DOI: 10.3390/pharmaceutics15030984] [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: 02/17/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems can precisely manipulate DNA sequences to change the characteristics of cells and organs, which has potential in the mechanistic research on genes and the treatment of diseases. However, clinical applications are restricted by the lack of safe, targeted and effective delivery vectors. Extracellular vesicles (EVs) are an attractive delivery platform for CRISPR/Cas9. Compared with viral and other vectors, EVs present several advantages, including safety, protection, capacity, penetrating ability, targeting ability and potential for modification. Consequently, EVs are profitably used to deliver the CRISPR/Cas9 in vivo. In this review, the advantages and disadvantages of the delivery form and vectors of the CRISPR/Cas9 are concluded. The favorable traits of EVs as vectors, such as the innate characteristics, physiological and pathological functions, safety and targeting ability of EVs, are summarized. Furthermore, in terms of the delivery of the CRISPR/Cas9 by EVs, EV sources and isolation strategies, the delivery form and loading methods of the CRISPR/Cas9 and applications have been concluded and discussed. Finally, this review provides future directions of EVs as vectors of the CRISPR/Cas9 system in clinical applications, such as the safety, capacity, consistent quality, yield and targeting ability of EVs.
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Affiliation(s)
- Xinglong Zhu
- Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mengyu Gao
- Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongfeng Yang
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, China
- Precision Medicine Key Laboratory, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weimin Li
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, China
- Precision Medicine Key Laboratory, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ji Bao
- Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yi Li
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, China
- Precision Medicine Key Laboratory, West China Hospital, Sichuan University, Chengdu 610041, China
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90
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Novel roles of RNA-binding proteins in drug resistance of breast cancer: from molecular biology to targeting therapeutics. Cell Death Discov 2023; 9:52. [PMID: 36759501 PMCID: PMC9911762 DOI: 10.1038/s41420-023-01352-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Therapy resistance remains a huge challenge for current breast cancer treatments. Exploring molecular mechanisms of therapy resistance might provide therapeutic targets for patients with advanced breast cancer and improve their prognosis. RNA-binding proteins (RBPs) play an important role in regulating therapy resistance. Here we summarize the functions of RBPs, highlight their tremendously important roles in regulating therapy sensitivity and resistance and we also reveal current therapeutic approaches reversing abnormal functions of RBPs in breast cancer.
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91
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Hao Y, Cai T, Liu C, Zhang X, Fu XD. Sequential Polyadenylation to Enable Alternative mRNA 3' End Formation. Mol Cells 2023; 46:57-64. [PMID: 36697238 PMCID: PMC9880608 DOI: 10.14348/molcells.2023.2176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 01/27/2023] Open
Abstract
In eukaryotic cells, a key RNA processing step to generate mature mRNA is the coupled reaction for cleavage and polyadenylation (CPA) at the 3' end of individual transcripts. Many transcripts are alternatively polyadenylated (APA) to produce mRNAs with different 3' ends that may either alter protein coding sequence (CDS-APA) or create different lengths of 3'UTR (tandem-APA). As the CPA reaction is intimately associated with transcriptional termination, it has been widely assumed that APA is regulated cotranscriptionally. Isoforms terminated at different regions may have distinct RNA stability under different conditions, thus altering the ratio of APA isoforms. Such differential impacts on different isoforms have been considered as post-transcriptional APA, but strictly speaking, this can only be considered "apparent" APA, as the choice is not made during the CPA reaction. Interestingly, a recent study reveals sequential APA as a new mechanism for post-transcriptional APA. This minireview will focus on this new mechanism to provide insights into various documented regulatory paradigms.
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Affiliation(s)
- Yajing Hao
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ting Cai
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Chang Liu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Xuan Zhang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Present address: Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, China
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92
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Hong D, Jeong S. 3'UTR Diversity: Expanding Repertoire of RNA Alterations in Human mRNAs. Mol Cells 2023; 46:48-56. [PMID: 36697237 PMCID: PMC9880603 DOI: 10.14348/molcells.2023.0003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/27/2023] Open
Abstract
Genomic information stored in the DNA is transcribed to the mRNA and translated to proteins. The 3' untranslated regions (3'UTRs) of the mRNA serve pivotal roles in posttranscriptional gene expression, regulating mRNA stability, translation, and localization. Similar to DNA mutations producing aberrant proteins, RNA alterations expand the transcriptome landscape and change the cellular proteome. Recent global analyses reveal that many genes express various forms of altered RNAs, including 3'UTR length variants. Alternative polyadenylation and alternative splicing are involved in diversifying 3'UTRs, which could act as a hidden layer of eukaryotic gene expression control. In this review, we summarize the functions and regulations of 3'UTRs and elaborate on the generation and functional consequences of 3'UTR diversity. Given that dynamic 3'UTR length control contributes to phenotypic complexity, dysregulated 3'UTR diversity might be relevant to disease development, including cancers. Thus, 3'UTR diversity in cancer could open exciting new research areas and provide avenues for novel cancer theragnostics.
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Affiliation(s)
- Dawon Hong
- Laboratory of RNA Cell Biology, Department of Bioconvergence Engineering, Dankook University Graduate School, Yongin 16892, Korea
| | - Sunjoo Jeong
- Laboratory of RNA Cell Biology, Department of Bioconvergence Engineering, Dankook University Graduate School, Yongin 16892, Korea
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93
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Wu GH, Lee KM, Kao CY, Shih SR. The internal ribosome entry site determines the neurotropic potential of enterovirus A71. Microbes Infect 2023; 25:105107. [PMID: 36708870 DOI: 10.1016/j.micinf.2023.105107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023]
Abstract
The mechanisms underlying tissue-specific replication of enteroviruses are currently unclear. Although enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) are both common pathogens that cause hand-foot-mouth disease, they display quite different neurotropic properties. Herein, we characterized the role of the internal ribosomal entry site (IRES) in determining neurovirulence using an oral inoculation model of EV-A71. The receptor transgenic (hSCARB2-Tg) mice developed neurological symptoms after being infected with a mouse-adapted EV-A71 strain (MP4) via different administrative routes. Intragastric administration of the MP4 strain caused pathological changes such as neuronal loss and neuropil vacuolation, whereas replacing EV-A71 IRES with CV-A16 abolished the neuropathological phenotypes. The attenuated neurotropic potential of IRES-swapped EV-A71 was observed even in mice that received intraperitoneal and intracerebral inoculations. Fewer chimeric MP4 viral RNAs and proteins were detected in the mouse tissues, regardless of the inoculation route. Tissue-specific replication can be reflected in cell-based characterization. While chimeric MP4 virus replicated poorly in human intestinal C2BBe1 and neuroblastoma SH-SY5Y cells, its replication in susceptible rhabdomyosarcoma cells was not affected. Overall, our results demonstrated that the IRES determined the neurotropic potential of EV-A71 and CV-A16, emphasizing the importance of the IRES in tissue tropism, along with the host receptors.
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Affiliation(s)
- Guan-Hong Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan
| | - Kuo-Ming Lee
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Division of Pediatric Infectious Diseases, Chang Gung Memorial Hospital, Linkou, Taoyuan, 333 Taiwan
| | - Chia-Yu Kao
- Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan
| | - Shin-Ru Shih
- Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333 Taiwan; Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, 333 Taiwan.
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Jonnakuti VS, Wagner EJ, Maletić-Savatić M, Liu Z, Yalamanchili HK. PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.523471. [PMID: 36747700 PMCID: PMC9900750 DOI: 10.1101/2023.01.23.523471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
More than half of human genes exercise alternative polyadenylation (APA) and generate mRNA transcripts with varying 3' untranslated regions (UTR). However, current computational approaches for identifying cleavage and polyadenylation sites (C/PASs) and quantifying 3'UTR length changes from bulk RNA-seq data fail to unravel tissue- and disease-specific APA dynamics. Here, we developed a next-generation bioinformatics algorithm and application, PolyAMiner-Bulk, that utilizes an attention-based machine learning architecture and an improved vector projection-based engine to infer differential APA dynamics accurately. When applied to earlier studies, PolyAMiner-Bulk accurately identified more than twice the number of APA changes in an RBM17 knockdown bulk RNA-seq dataset compared to current generation tools. Moreover, on a separate dataset, PolyAMiner-Bulk revealed novel APA dynamics and pathways in scleroderma pathology and identified differential APA in a gene that was identified as being involved in scleroderma pathogenesis in an independent study. Lastly, we used PolyAMiner-Bulk to analyze the RNA-seq data of post-mortem prefrontal cortexes from the ROSMAP data consortium and unraveled novel APA dynamics in Alzheimer's Disease. Our method, PolyAMiner-Bulk, creates a paradigm for future alternative polyadenylation analysis from bulk RNA-seq data.
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Affiliation(s)
- Venkata Soumith Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Mirjana Maletić-Savatić
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
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95
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Murphy MR, Ramadei A, Doymaz A, Varriano S, Natelson D, Yu A, Aktas S, Mazzeo M, Mazzeo M, Zakusilo G, Kleiman FE. Long Non-Coding RNA Generated from CDKN1A Gene by Alternative Polyadenylation Regulates p21 Expression during DNA Damage Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523318. [PMID: 36711808 PMCID: PMC9882041 DOI: 10.1101/2023.01.10.523318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DNA damage activated APA event occurs in the first intron of CDKN1A , inducing an alternate last exon (ALE)-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform and is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53 transcriptional activation. RNA binding protein (RBP) HuR and the transcriptional repressor CTCF regulate SPUD levels. SPUD induction increases p21 protein, but not CDKN1A full-length levels, affecting p21 functions in cell-cycle, CDK2 expression, and cell viability. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD can change their association with CDKN1A full-length in a DDR-dependent manner. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cellcycle.
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96
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Gallicchio L, Olivares GH, Berry CW, Fuller MT. Regulation and function of alternative polyadenylation in development and differentiation. RNA Biol 2023; 20:908-925. [PMID: 37906624 PMCID: PMC10730144 DOI: 10.1080/15476286.2023.2275109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein-protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation.
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Affiliation(s)
- Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
| | - Gonzalo H. Olivares
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Center for Integrative Biology (CIB), Universidad Mayor, Chile and Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Margaret T. Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
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97
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Gao W, Chen D, Liu J, Zang L, Xiao T, Zhang X, Li Z, Zhu H, Yu X. Interplay of four types of RNA modification writers revealed distinct tumor microenvironment and biological characteristics in pancreatic cancer. Front Immunol 2022; 13:1031184. [PMID: 36601127 PMCID: PMC9806142 DOI: 10.3389/fimmu.2022.1031184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Background Pancreatic cancer (PC) is one of the most lethal malignancies and carries a dismal mortality and morbidity. Four types of RNA modification (namely m6A, m1A, APA and A-to-I) could be catalyzed by distinct enzymatic compounds ("writers"), mediating numerous epigenetic events in carcinogenesis and immunomodulation. We aim to investigate the interplay mechanism of these writers in immunogenomic features and molecular biological characteristics in PC. Methods We first accessed the specific expression pattern and transcriptional variation of 26 RNA modification writers in The Cancer Genome Atlas (TCGA) dataset. Unsupervised consensus clustering was performed to divide patients into two RNA modification clusters. Then, based on the differentially expressed genes (DEGs) among two clusters, RNA modification score (WM_Score) model was established to determine RNA modification-based subtypes and was validated in International Cancer Genome Consortium (ICGC) dataset. What's more, we manifested the unique status of WM_Score in transcriptional and post-transcriptional regulation, molecular biological characteristics, targeted therapies and immunogenomic patterns. Results We documented the tight-knit correlations between transcriptional expression and variation of RNA modification writers. We classified patients into two distinct RNA modification patterns (WM_Score_high and _low), The WM_Score_high subgroup was correlated with worse prognosis, Th2/Th17 cell polarization and oncogenic pathways (e.g. EMT, TGF-β, and mTORC1 signaling pathways), whereas the WM_Score_low subgroup associated with favorable survival rate and Th1 cell trend. WM_Score model also proved robust predictive power in interpreting transcriptional and post-transcriptional events. Additionally, the potential targeted compounds with related pathways for the WM_Score model were further identified. Conclusions Our research unfolds a novel horizon on the interplay network of four RNA modifications in PC. This WM_Score model demonstrated powerful predictive capacity in epigenetic, immunological and biological landscape, providing a theoretical basis for future clinical judgments of PC.
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Affiliation(s)
- Wenzhe Gao
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dongjie Chen
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jixing Liu
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Nephrology, Institute of Nephrology, 2nd Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Longjun Zang
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tijun Xiao
- Department of General Surgery, Shaoyang University Affiliated Second Hospital, Shaoyang University, Shaoyang, Hunan, China
| | - Xianlin Zhang
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang, Hubei, China
| | - Zheng Li
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang, Hubei, China
| | - Hongwei Zhu
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Hongwei Zhu, ; Xiao Yu,
| | - Xiao Yu
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Hongwei Zhu, ; Xiao Yu,
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98
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Exploring the uncharted landscape of truncated mRNAs. Nat Rev Mol Cell Biol 2022; 23:776. [PMID: 36333456 DOI: 10.1038/s41580-022-00561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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99
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
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100
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Lo Giudice C, Zambelli F, Chiara M, Pavesi G, Tangaro M, Picardi E, Pesole G. UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. Nucleic Acids Res 2022; 51:D337-D344. [PMID: 36399486 PMCID: PMC9825521 DOI: 10.1093/nar/gkac1016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Since 1996, we have developed and maintained UTRdb, a specialized database of UTR sequences. Here we present UTRdb 2.0, a major update of UTRdb featuring an extensive collection of eukaryotic 5' and 3' UTR sequences, including over 26 million entries from over 6 million genes and 573 species, enriched with a curated set of functional annotations. Annotations include CAGE tags and polyA signals to label the completeness of 5' and 3'UTRs, respectively. In addition, uORFs and IRES are annotated in 5'UTRs as well as experimentally validated miRNA targets in 3'UTRs. Further annotations include evolutionarily conserved blocks, Rfam motifs, ADAR-mediated RNA editing events, and m6A modifications. A web interface allowing a flexible selection and retrieval of specific subsets of UTRs, selected according to a combination of criteria, has been implemented which also provides comprehensive download facilities. UTRdb 2.0 is accessible at http://utrdb.cloud.ba.infn.it/utrdb/.
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Affiliation(s)
- Claudio Lo Giudice
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, 70126 Bari, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, 20133 Milan, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, 20133 Milan, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, 70126 Bari, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Graziano Pesole
- To whom correspondence should be addressed. Tel: +39 0805443588;
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