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Bokros M, Balukoff NC, Grunfeld A, Sebastiao M, Beurel E, Bourgault S, Lee S. RNA tailing machinery drives amyloidogenic phase transition. Proc Natl Acad Sci U S A 2024; 121:e2316734121. [PMID: 38805292 PMCID: PMC11161805 DOI: 10.1073/pnas.2316734121] [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: 09/26/2023] [Accepted: 04/18/2024] [Indexed: 05/30/2024] Open
Abstract
The RNA tailing machinery adds nucleotides to the 3'-end of RNA molecules that are implicated in various biochemical functions, including protein synthesis and RNA stability. Here, we report a role for the RNA tailing machinery as enzymatic modifiers of intracellular amyloidogenesis. A targeted RNA interference screen identified Terminal Nucleotidyl-transferase 4b (TENT4b/Papd5) as an essential participant in the amyloidogenic phase transition of nucleoli into solid-like Amyloid bodies. Full-length-and-mRNA sequencing uncovered starRNA, a class of unusually long untemplated RNA molecules synthesized by TENT4b. StarRNA consists of short rRNA fragments linked to long, linear mixed tails that operate as polyanionic stimulators of amyloidogenesis in cells and in vitro. Ribosomal intergenic spacer noncoding RNA (rIGSRNA) recruit TENT4b in intranucleolar foci to coordinate starRNA synthesis driving their amyloidogenic phase transition. The exoribonuclease RNA Exosome degrades starRNA and functions as a general suppressor of cellular amyloidogenesis. We propose that amyloidogenic phase transition is under tight enzymatic control by the RNA tailing and exosome axis.
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Affiliation(s)
- Michael Bokros
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
| | - Nathan C. Balukoff
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
| | - Alex Grunfeld
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
| | - Mathew Sebastiao
- Department of Chemistry, Université du Québec à Montréal, MontrealQCH3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Montreal, QCH3C 3P8, Canada
| | - Eléonore Beurel
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL33136
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, MontrealQCH3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Montreal, QCH3C 3P8, Canada
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
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Zhang S, Huang J, Lan Z, Xiao Y, Liao Y, Basnet S, Huang P, Li Y, Yan J, Sheng Y, Zhou W, Liu Q, Tan H, Tan Y, Yuan L, Wang L, Dai L, Zhang W, Du C. CPEB1 Controls NRF2 Proteostasis and Ferroptosis Susceptibility in Pancreatic Cancer. Int J Biol Sci 2024; 20:3156-3172. [PMID: 38904009 PMCID: PMC11186365 DOI: 10.7150/ijbs.95962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024] Open
Abstract
Pancreatic cancer is the deadliest malignancy with a poor response to chemotherapy but is potentially indicated for ferroptosis therapy. Here we identified that cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates NRF2 proteostasis and susceptibility to ferroptosis in pancreatic ductal adenocarcinoma (PDAC). We found that CPEB1 deficiency in cancer cells promotes the translation of p62/SQSTM1 by facilitating mRNA polyadenylation. Consequently, upregulated p62 enhances NRF2 stability by sequestering KEAP1, an E3 ligase for proteasomal degradation of NRF2, leading to the transcriptional activation of anti-ferroptosis genes. In support of the critical role of this signaling cascade in cancer therapy, CPEB1-deficient pancreatic cancer cells display higher resistance to ferroptosis-inducing agents than their CPEB1-normal counterparts in vitro and in vivo. Furthermore, based on the pathological evaluation of tissue specimens from 90 PDAC patients, we established that CPEB1 is an independent prognosticator whose expression level is closely associated with clinical therapeutic outcomes in PDAC. These findings identify the role of CPEB1 as a key ferroptosis regulator and a potential prognosticator in pancreatic cancer.
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Affiliation(s)
- Shuxia Zhang
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
- Department of Gastroenterology, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Shenzhen, Guangdong 518020, P.R. China
| | - Jingnan Huang
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Shenzhen, Guangdong 518020, P.R. China
| | - Zhangzhang Lan
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Yanlin Xiao
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Youyou Liao
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Shiva Basnet
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Piying Huang
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Shenzhen, Guangdong 518020, P.R. China
| | - Yunze Li
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Jingyu Yan
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Yuling Sheng
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Wenwen Zhou
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Qi Liu
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Haoyuan Tan
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Yi Tan
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Leyong Yuan
- Clinical laboratory, Southern University of Science and Technology Hospital, 6019 Liuxian Street, Xili Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Lisheng Wang
- Department of Gastroenterology, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Shenzhen, Guangdong 518020, P.R. China
| | - Lingyun Dai
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Shenzhen, Guangdong 518020, P.R. China
| | - Wenyong Zhang
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
| | - Changzheng Du
- Key University Laboratory of Metabolism and Health of Guangdong, Biochemistry Department, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, P.R. China
- Beijing Tsinghua Changgung Hospital & Tsinghua University School of Medicine, 168 Litang Road, Changping District, Beijing 102218, P.R. China
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3
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Singh M, Kim JH. Measurement of Poly A Tail Length from Drosophila Larva Brain and Cell Line. J Vis Exp 2024:10.3791/66116. [PMID: 38284531 PMCID: PMC10954090 DOI: 10.3791/66116] [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] [Indexed: 01/30/2024] Open
Abstract
Polyadenylation is a crucial posttranscriptional modification that adds poly(A) tails to the 3' end of mRNA molecules. The length of the poly(A) tail is tightly regulated by cellular processes. Dysregulation of mRNA polyadenylation has been associated with abnormal gene expression and various diseases, including cancer, neurological disorders, and developmental abnormalities. Therefore, comprehending the dynamics of polyadenylation is vital for unraveling the complexities of mRNA processing and posttranscriptional gene regulation. This paper presents a method for measuring poly(A) tail lengths in RNA samples isolated from Drosophila larval brains and Drosophila Schneider S2 cells. We employed the guanosine/inosine (G/I) tailing approach, which involves the enzymatic addition of G/I residues at the 3' end of mRNA using yeast poly(A) polymerase. This modification protects the RNA's 3' end from enzymatic degradation. The protected full-length poly(A) tails are then reverse-transcribed using a universal antisense primer. Subsequently, PCR amplification is performed using a gene-specific oligo that targets the gene of interest, along with a universal sequence oligo used for reverse transcription. This generates PCR products encompassing the poly(A) tails of the gene of interest. Since polyadenylation is not a uniform modification and results in tails of varying lengths, the PCR products display a range of sizes, leading to a smear pattern on agarose gel. Finally, the PCR products are subjected to high-resolution capillary gel electrophoresis, followed by quantification using the sizes of the poly(A) PCR products and the gene-specific PCR product. This technique offers a straightforward and reliable tool for analyzing poly(A) tail lengths, enabling us to gain deeper insights into the intricate mechanisms governing mRNA regulation.
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Affiliation(s)
- Monika Singh
- Department of Biology, University of Nevada, Reno
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4
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Mauxion F, Séraphin B. An RNA-Ligation-Based RACE-PAT Assay to Monitor Poly(A) Tail Length of mRNAs of Interest. Methods Mol Biol 2024; 2723:113-123. [PMID: 37824067 DOI: 10.1007/978-1-0716-3481-3_7] [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] [Indexed: 10/13/2023]
Abstract
In eukaryotes, a non-templated poly-adenosine (poly(A)) tail is added co-transcriptionally to almost every messenger RNA (mRNA). The length of this poly(A) tail changes during the lifetime of mRNAs and has been shown in many circumstances to be an important factor controlling transcript fates. Yet, the measure of the length of this homogenous nucleotide sequence is technically challenging, making it difficult to assess its dynamic variation. In this chapter, we describe an RNA-ligation-based RACE-PAT (Rapid Amplification of cDNA End-Poly(A) Tail) assay to monitor the poly(A) tail length of mRNAs. In the first step, an RNA oligonucleotide is ligated to mRNA 3' ends providing an anchoring site to prime cDNA synthesis, avoiding the bias introduced by oligo(dT)-derived primers. Afterward, reverse transcription is performed with an anchor primer with a unique 5' extension. The choice of the oligonucleotide 3' end at this step allows further flexibility to amplify modified tails, for example, by uridylation. Next, short DNA fragments encompassing the poly(A) tails are amplified by Polymerase Chain Reaction (PCR) using as forward primer, a transcript-specific primer hybridizing close to the transcript polyadenylation signal, and as reverse primer, an oligonucleotide corresponding to the 5' extension of the primer used for cDNA synthesis, ensuring that only cDNAs are amplified. The resulting DNA fragments are then visualized after size fractionation by electrophoresis. This method does not provide exact nucleotide count and composition but has the advantage of allowing the processing of many samples in parallel at a low cost.
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Affiliation(s)
- Fabienne Mauxion
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104 - Institut National de Santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, Illkirch, France.
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104 - Institut National de Santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, Illkirch, France
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5
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Arvola RM, Goldstrohm AC. Measuring Poly-Adenosine Tail Length of RNAs by High-Resolution Northern Blotting Coupled with RNase H Cleavage. Methods Mol Biol 2024; 2723:93-111. [PMID: 37824066 DOI: 10.1007/978-1-0716-3481-3_6] [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] [Indexed: 10/13/2023]
Abstract
The poly-adenosine, or poly(A) tail, plays key roles in controlling the stability and translation of messenger RNAs in all eukaryotes, and, as such, facile assays that can measure poly(A) length are needed. This chapter describes an approach that couples RNase H-mediated cleavage of an RNA of interest with high-resolution denaturing gel electrophoresis and northern blot-based detection. Major advantages of this method include the ability to directly measure the abundance of any RNA and the length of its poly(A) tail without amplification steps. The assay provides high specificity, sensitivity, and reproducibility for accurate quantitation using standard molecular biology equipment and reagents. Overall, the high-resolution northern blotting approach offers a cost-effective means of poly(A) RNA analysis that is especially useful for small numbers of transcripts and comparisons between experimental conditions or time points.
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Affiliation(s)
- René M Arvola
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
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6
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Li C, Zhu L, Liu JX, Guo J, Xie J, Shi CM, Sun QY, Huang GN, Li JY. Cordycepin delays postovulatory aging of oocytes through inhibition of maternal mRNAs degradation via DCP1A polyadenylation suppression. Cell Mol Life Sci 2023; 80:372. [PMID: 38001238 PMCID: PMC10674002 DOI: 10.1007/s00018-023-05030-0] [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: 08/06/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023]
Abstract
Postovulatory aging leads to the decline in oocyte quality and subsequent impairment of embryonic development, thereby reducing the success rate of assisted reproductive technology (ART). Potential preventative strategies preventing oocytes from aging and the associated underlying mechanisms warrant investigation. In this study, we identified that cordycepin, a natural nucleoside analogue, promoted the quality of oocytes aging in vitro, as indicated by reduced oocyte fragmentation, improved spindle/chromosomes morphology and mitochondrial function, as well as increased embryonic developmental competence. Proteomic and RNA sequencing analyses revealed that cordycepin inhibited the degradation of several crucial maternal proteins and mRNAs caused by aging. Strikingly, cordycepin was found to suppress the elevation of DCP1A protein by inhibiting polyadenylation during postovulatory aging, consequently impeding the decapping of maternal mRNAs. In humans, the increased degradation of DCP1A and total mRNA during postovulatory aging was also inhibited by cordycepin. Collectively, our findings demonstrate that cordycepin prevents postovulatory aging of mammalian oocytes by inhibition of maternal mRNAs degradation via suppressing polyadenylation of DCP1A mRNA, thereby promoting oocyte developmental competence.
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Affiliation(s)
- Chong Li
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jun-Xia Liu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jing Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Juan Xie
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Chun-Meng Shi
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing, China.
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Guo-Ning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
| | - Jing-Yu Li
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
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7
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Brothers WR, Ali F, Kajjo S, Fabian MR. The EDC4-XRN1 interaction controls P-body dynamics to link mRNA decapping with decay. EMBO J 2023; 42:e113933. [PMID: 37621215 PMCID: PMC10620763 DOI: 10.15252/embj.2023113933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
Deadenylation-dependent mRNA decapping and decay is the major cytoplasmic mRNA turnover pathway in eukaryotes. Many mRNA decapping and decay factors are associated with each other via protein-protein interaction motifs. For example, the decapping enzyme DCP2 and the 5'-3' exonuclease XRN1 interact with the enhancer of mRNA-decapping protein 4 (EDC4), a large scaffold that has been reported to stimulate mRNA decapping. mRNA decapping and decay factors are also found in processing bodies (P-bodies), evolutionarily conserved ribonucleoprotein granules that are often enriched with mRNAs targeted for decay, yet paradoxically are not required for mRNA decay to occur. Here, we show that disrupting the EDC4-XRN1 interaction or altering their stoichiometry inhibits mRNA decapping, with microRNA-targeted mRNAs being stabilized in a translationally repressed state. Importantly, we demonstrate that this concomitantly leads to larger P-bodies that are responsible for preventing mRNA decapping. Finally, we demonstrate that P-bodies support cell viability and prevent stress granule formation when XRN1 is limiting. Taken together, these data demonstrate that the interaction between XRN1 and EDC4 regulates P-body dynamics to properly coordinate mRNA decapping with 5'-3' decay in human cells.
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Affiliation(s)
- William R Brothers
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Farah Ali
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Sam Kajjo
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Marc R Fabian
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
- Department of BiochemistryMcGill UniversityMontrealQCCanada
- Department of OncologyMcGill UniversityMontrealQCCanada
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8
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Kattan FG, Koukouraki P, Anagnostopoulos AK, Tsangaris GT, Doxakis E. RNA binding protein AUF1/HNRNPD regulates nuclear export, stability and translation of SNCA transcripts. Open Biol 2023; 13:230158. [PMID: 37989221 PMCID: PMC10688287 DOI: 10.1098/rsob.230158] [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: 05/25/2023] [Accepted: 10/11/2023] [Indexed: 11/23/2023] Open
Abstract
Alpha-synuclein (SNCA) accumulation plays a central role in the pathogenesis of Parkinson's disease. Determining and interfering with the mechanisms that control SNCA expression is one approach to limiting disease progression. Currently, most of our understanding of SNCA regulation is protein-based. Post-transcriptional mechanisms directly regulating SNCA mRNA expression via its 3' untranslated region (3'UTR) were investigated here. Mass spectrometry of proteins pulled down from murine brain lysates using a biotinylated SNCA 3'UTR revealed multiple RNA-binding proteins, of which HNRNPD/AUF1 was chosen for further analysis. AUF1 bound both proximal and distal regions of the SNCA 3'UTR, but not the 5'UTR or CDS. In the nucleus, AUF1 attenuated SNCA pre-mRNA maturation and was indispensable for the export of SNCA transcripts. AUF1 destabilized SNCA transcripts in the cytosol, primarily those with shorter 3'UTRs, independently of microRNAs by recruiting the CNOT1-CNOT7 deadenylase complex to trim the polyA tail. Furthermore, AUF1 inhibited SNCA mRNA binding to ribosomes. These data identify AUF1 as a multi-tasking protein regulating maturation, nucleocytoplasmic shuttling, stability and translation of SNCA transcripts.
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Affiliation(s)
- Fedon-Giasin Kattan
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
- Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Pelagia Koukouraki
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - Athanasios K. Anagnostopoulos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - George T. Tsangaris
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
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9
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Kases K, Schubert E, Hajikhezri Z, Larsson M, Devi P, Darweesh M, Andersson L, Akusjärvi G, Punga T, Younis S. The RNA-binding protein ZC3H11A interacts with the nuclear poly(A)-binding protein PABPN1 and alters polyadenylation of viral transcripts. J Biol Chem 2023; 299:104959. [PMID: 37356722 PMCID: PMC10371797 DOI: 10.1016/j.jbc.2023.104959] [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: 03/09/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.
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Affiliation(s)
- Katharina Kases
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Priya Devi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Microbiology and Immunology, Al-Azhr University, Assiut, Egypt
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Division of Immunology and Rheumatology, Stanford University, Stanford, California, USA.
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10
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Jiang X, Cheng Y, Zhu Y, Xu C, Li Q, Xing X, Li W, Zou J, Meng L, Azhar M, Cao Y, Tong X, Qin W, Zhu X, Bao J. Maternal NAT10 orchestrates oocyte meiotic cell-cycle progression and maturation in mice. Nat Commun 2023; 14:3729. [PMID: 37349316 PMCID: PMC10287700 DOI: 10.1038/s41467-023-39256-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
In mammals, the production of mature oocytes necessitates rigorous regulation of the discontinuous meiotic cell-cycle progression at both the transcriptional and post-transcriptional levels. However, the factors underlying this sophisticated but explicit process remain largely unclear. Here we characterize the function of N-acetyltransferase 10 (Nat10), a writer for N4-acetylcytidine (ac4C) on RNA molecules, in mouse oocyte development. We provide genetic evidence that Nat10 is essential for oocyte meiotic prophase I progression, oocyte growth and maturation by sculpting the maternal transcriptome through timely degradation of poly(A) tail mRNAs. This is achieved through the ac4C deposition on the key CCR4-NOT complex transcripts. Importantly, we devise a method for examining the poly(A) tail length (PAT), termed Hairpin Adaptor-poly(A) tail length (HA-PAT), which outperforms conventional methods in terms of cost, sensitivity, and efficiency. In summary, these findings provide genetic evidence that unveils the indispensable role of maternal Nat10 in oocyte development.
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Affiliation(s)
- Xue Jiang
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Yu Cheng
- School of Information Science and Technology, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Yuzhang Zhu
- Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Caoling Xu
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Qiaodan Li
- Laboratory animal center, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Xuemei Xing
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Wenqing Li
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Jiaqi Zou
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Lan Meng
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Muhammad Azhar
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Yuzhu Cao
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Xianhong Tong
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), 510600, Guangzhou, China.
| | - Xiaoli Zhu
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China.
| | - Jianqiang Bao
- Reproductive and Genetic Hospital, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China.
- Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), 230001, Hefei, Anhui, China.
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11
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Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
Abstract
The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). This epitranscriptomic regulation of mRNA recently became one of the most interesting aspects in the field. Advances in RNA sequencing technologies and software development have allowed the precise measurement of poly(A) tails, identification of new ncPAPs, expansion of the function of known enzymes, discovery and a better understanding of the physiological role of tail heterogeneity, and recognition of a correlation between tail length and RNA translatability. Here, we summarize the development of polyadenylation research methods, including classic low-throughput approaches, Illumina-based genome-wide analysis, and advanced state-of-art techniques that utilize long-read third-generation sequencing with Pacific Biosciences and Oxford Nanopore Technologies platforms. A boost in technical opportunities over recent decades has allowed a better understanding of the regulation of gene expression at the mRNA level. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Aleksandra Brouze
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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12
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Wu L, Zhong Y, Yu X, Wu D, Xu P, Lv L, Ruan X, Liu Q, Feng Y, Liu J, Li X. Selective poly adenylation predicts the efficacy of immunotherapy in patients with lung adenocarcinoma by multiple omics research. Anticancer Drugs 2022; 33:943-959. [PMID: 35946526 PMCID: PMC9481295 DOI: 10.1097/cad.0000000000001319] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/14/2022] [Indexed: 02/05/2023]
Abstract
The aim of this study was to find the application value of selective polyadenylation in immune cell infiltration, biological transcription function and risk assessment of survival and prognosis in lung adenocarcinoma (LUAD). The processed original mRNA expression data of LUAD were downloaded, and the expression profiles of 594 patient samples were collected. The (APA) events in TCGA-NA-SEQ data were evaluated by polyadenylation site use Index (PDUI) values, and the invasion of stromal cells and immune cells and tumor purity were calculated to group and select the differential genes. Lasso regression and stratified analysis were used to examine the role of risk scores in predicting patient outcomes. The study also used the GDSC database to predict the chemotherapeutic sensitivity of each tumor sample and used a regression method to obtain an IC50 estimate for each specific chemotherapeutic drug treatment. Then CIBERSORT algorithm was used to conduct Spearman correlation analysis, immune regulatory factor analysis and TIDE immune system function analysis for gene expression level and immune cell content. Finally, the Kaplan-Meier curve was used to analyze the correlation between stromal score and the immune score of LUAD. In this study, APA's LUAD risk score prognostic model was constructed. KM survival analysis showed that immune score affected the prognosis of LUAD patients ( P = 0.027) but the matrix score was not statistically significant ( P = 0.1). We extracted 108 genes with APA events from 827 different genes and based on PUDI clustering and heat map, the survival rate of patients in the four groups was significantly different ( P = 0.05). Multiple omics studies showed that risk score was significantly positively correlated with Macrophages M0, T cells Follicular helper, B cells naive and NK cells resting. It is significantly negatively correlated with dendritic cells resting, mast cells resting, monocyte, T cells CD4 memory resting and B cells memory. We further explored the relationship between the expression of immunosuppressor genes and risk score and found that ADORA2A, BTLA, CD160, CD244, CD274, CD96, CSF1R and CTLA4 genes were highly correlated with the risk score. Selective poly adenylation plays an important role in the development and progression of LUAD, immune invasion, tumor cell invasion and metastasis and biological transcription, and affects the survival and prognosis of LUAD patients.
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Affiliation(s)
- Liusheng Wu
- Peking University Shenzhen Hospital, Clinical College of Anhui Medical University
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Yanfeng Zhong
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Xiaoya Yu
- First Clinical Medical College, Southern Medical University, Guangzhou
| | - Dingwang Wu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Pengcheng Xu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Le Lv
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Xin Ruan
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
- Shantou University Medical College, Shantou, Guangdong, China
| | - Qi Liu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Yu Feng
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Jixian Liu
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
| | - Xiaoqiang Li
- Peking University Shenzhen Hospital, Clinical College of Anhui Medical University
- Peking University Shenzhen Hospital, Thoracic surgery, Shenzhen
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13
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Cuerda-Gil D, Hung YH, Panda K, Slotkin RK. A plant tethering system for the functional study of protein-RNA interactions in vivo. PLANT METHODS 2022; 18:75. [PMID: 35658900 PMCID: PMC9166424 DOI: 10.1186/s13007-022-00907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The sorting of RNA transcripts dictates their ultimate post-transcriptional fates, such as translation, decay or degradation by RNA interference (RNAi). This sorting of RNAs into distinct fates is mediated by their interaction with RNA-binding proteins. While hundreds of RNA binding proteins have been identified, which act to sort RNAs into different pathways is largely unknown. Particularly in plants, this is due to the lack of reliable protein-RNA artificial tethering tools necessary to determine the mechanism of protein action on an RNA in vivo. Here we generated a protein-RNA tethering system which functions on an endogenous Arabidopsis RNA that is tracked by the quantitative flowering time phenotype. Unlike other protein-RNA tethering systems that have been attempted in plants, our system circumvents the inadvertent triggering of RNAi. We successfully in vivo tethered a protein epitope, deadenylase protein and translation factor to the target RNA, which function to tag, decay and boost protein production, respectively. We demonstrated that our tethering system (1) is sufficient to engineer the downstream fate of an RNA, (2) enables the determination of any protein's function upon recruitment to an RNA, and (3) can be used to discover new interactions with RNA-binding proteins.
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Affiliation(s)
- Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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14
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Guénolé A, Velilla F, Chartier A, Rich A, Carvunis AR, Sardet C, Simonelig M, Sobhian B. RNF219 regulates CCR4-NOT function in mRNA translation and deadenylation. Sci Rep 2022; 12:9288. [PMID: 35660762 PMCID: PMC9166816 DOI: 10.1038/s41598-022-13309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional regulatory mechanisms play a role in many biological contexts through the control of mRNA degradation, translation and localization. Here, we show that the RING finger protein RNF219 co-purifies with the CCR4-NOT complex, the major mRNA deadenylase in eukaryotes, which mediates translational repression in both a deadenylase activity-dependent and -independent manner. Strikingly, RNF219 both inhibits the deadenylase activity of CCR4-NOT and enhances its capacity to repress translation of a target mRNA. We propose that the interaction of RNF219 with the CCR4-NOT complex directs the translational repressive activity of CCR4-NOT to a deadenylation-independent mechanism.
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Affiliation(s)
- Aude Guénolé
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), 34298, Montpellier, France.
| | - Fabien Velilla
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), 34298, Montpellier, France
| | - Aymeric Chartier
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396, Montpellier, France
| | - April Rich
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), 34298, Montpellier, France
| | - Martine Simonelig
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396, Montpellier, France
| | - Bijan Sobhian
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), 34298, Montpellier, France. .,Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396, Montpellier, France.
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15
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Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA (NEW YORK, N.Y.) 2022; 28:878-894. [PMID: 35351812 PMCID: PMC9074902 DOI: 10.1261/rna.079104.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/12/2022] [Indexed: 05/22/2023]
Abstract
Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.
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Affiliation(s)
- Eliza S Lee
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Harrison W Smith
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Eric J Wolf
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Aysegul Guvenek
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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16
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Kajjo S, Sharma S, Chen S, Brothers WR, Cott M, Hasaj B, Jovanovic P, Larsson O, Fabian MR. PABP prevents the untimely decay of select mRNA populations in human cells. EMBO J 2022; 41:e108650. [PMID: 35156721 PMCID: PMC8922270 DOI: 10.15252/embj.2021108650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Gene expression is tightly regulated at the levels of both mRNA translation and stability. The poly(A)-binding protein (PABP) is thought to play a role in regulating these processes by binding the mRNA 3' poly(A) tail and interacting with both the translation and mRNA deadenylation machineries. In this study, we directly investigate the impact of PABP on translation and stability of endogenous mRNAs in human cells. Remarkably, our transcriptome-wide analysis only detects marginal mRNA translation changes in PABP-depleted cells. In contrast, rapidly depleting PABP alters mRNA abundance and stability, albeit non-uniformly. Otherwise stable transcripts, including those encoding proteins with constitutive functions, are destabilized in PABP-depleted cells. In contrast, many unstable mRNAs, including those encoding proteins with regulatory functions, decay at similar rates in presence or absence of PABP. Moreover, PABP depletion-induced cell death can partially be suppressed by disrupting the mRNA decapping and 5'-3' decay machinery. Finally, we provide evidence that the LSM1-7 complex promotes decay of "stable" mRNAs in PABP-depleted cells. Taken together, these findings suggest that PABP plays an important role in preventing the untimely decay of select mRNA populations.
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Affiliation(s)
- Sam Kajjo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Sahil Sharma
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Shan Chen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - William R Brothers
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Megan Cott
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Benedeta Hasaj
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Predrag Jovanovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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17
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Moderate Folic Acid Supplementation in Pregnant Mice Results in Altered Sex-Specific Gene Expression in Brain of Young Mice and Embryos. Nutrients 2022; 14:nu14051051. [PMID: 35268026 PMCID: PMC8912750 DOI: 10.3390/nu14051051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/07/2023] Open
Abstract
Food fortification and increased vitamin intake have led to higher folic acid (FA) consumption by many pregnant women. We showed that FA-supplemented diet in pregnant mice (fivefold higher FA than the recommended level (5xFASD)) led to hyperactivity-like behavior and memory impairment in pups. Disturbed choline/methyl metabolism and altered placental gene expression were identified. The aim of this study was to examine the impact of 5xFASD on the brain at two developmental stages, postnatal day (P) 30 and embryonic day (E) 17.5. Female C57BL/6 mice were fed a control diet or 5xFASD for 1 month before mating. Diets were maintained throughout the pregnancy and lactation until P30 or during pregnancy until E17.5. The 5xFASD led to sex-specific transcription changes in P30 cerebral cortex and E17.5 cerebrum, with microarrays showing a total of 1003 and 623 changes, respectively. Enhanced mRNA degradation was observed in E17.5 cerebrum. Expression changes of genes involved in neurotransmission, neuronal growth and development, and angiogenesis were verified by qRT-PCR; 12 and 15 genes were verified at P30 and E17.5, respectively. Hippocampal collagen staining suggested decreased vessel density in FASD male embryos. This study provides insight into the mechanisms of neurobehavioral alterations and highlights potential deleterious consequences of moderate folate oversupplementation during pregnancy.
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18
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Implications of Poly(A) Tail Processing in Repeat Expansion Diseases. Cells 2022; 11:cells11040677. [PMID: 35203324 PMCID: PMC8870147 DOI: 10.3390/cells11040677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/21/2022] Open
Abstract
Repeat expansion diseases are a group of more than 40 disorders that affect mainly the nervous and/or muscular system and include myotonic dystrophies, Huntington’s disease, and fragile X syndrome. The mutation-driven expanded repeat tract occurs in specific genes and is composed of tri- to dodeca-nucleotide-long units. Mutant mRNA is a pathogenic factor or important contributor to the disease and has great potential as a therapeutic target. Although repeat expansion diseases are quite well known, there are limited studies concerning polyadenylation events for implicated transcripts that could have profound effects on transcript stability, localization, and translation efficiency. In this review, we briefly present polyadenylation and alternative polyadenylation (APA) mechanisms and discuss their role in the pathogenesis of selected diseases. We also discuss several methods for poly(A) tail measurement (both transcript-specific and transcriptome-wide analyses) and APA site identification—the further development and use of which may contribute to a better understanding of the correlation between APA events and repeat expansion diseases. Finally, we point out some future perspectives on the research into repeat expansion diseases, as well as APA studies.
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19
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Turner RE, Harrison PF, Swaminathan A, Kraupner-Taylor CA, Goldie BJ, See M, Peterson AL, Schittenhelm RB, Powell DR, Creek DJ, Dichtl B, Beilharz TH. Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast. eLife 2021; 10:65331. [PMID: 34232857 PMCID: PMC8263057 DOI: 10.7554/elife.65331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/22/2021] [Indexed: 01/23/2023] Open
Abstract
Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3’ untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3’ end formation factors, which revealed 3’UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3’UTRs. We show that the anti-cancer drug cordycepin, 3’ deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3’ end processing and controlled by the availability of 3’ end factors, nucleotide levels and chromatin landscape.
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Affiliation(s)
- Rachael Emily Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Calvin A Kraupner-Taylor
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Belinda J Goldie
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Michael See
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Amanda L Peterson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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20
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TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer. Int J Mol Sci 2021; 22:ijms22136957. [PMID: 34203408 PMCID: PMC8267958 DOI: 10.3390/ijms22136957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA polymerases bypass unrepaired DNA lesions. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η and RAD18 E3 ligase, which guides the polymerase to replication stalling sites and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD and via the long non-coding antisense RNA PAXIP1-AS2, which had no known function. Knocking down the expression of TENT4A or CYLD, or overexpression of PAXIP1-AS2 led each to reduced amounts of the RAD18 protein and DNA polymerase η, leading to reduced TLS, highlighting PAXIP1-AS2 as a new TLS regulator. Bioinformatics analysis revealed that TLS error-prone DNA polymerase genes and their TENT4A-related regulators are frequently mutated in endometrial cancer genomes, suggesting that TLS is dysregulated in this cancer.
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21
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Komini C, Theohari I, Lambrianidou A, Nakopoulou L, Trangas T. PAPOLA contributes to cyclin D1 mRNA alternative polyadenylation and promotes breast cancer cell proliferation. J Cell Sci 2021; 134:237820. [PMID: 33712453 DOI: 10.1242/jcs.252304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Poly(A) polymerases add the poly(A) tail at the 3' end of nearly all eukaryotic mRNA, and are associated with proliferation and cancer. To elucidate the role of the most-studied mammalian poly(A) polymerase, poly(A) polymerase α (PAPOLA), in cancer, we assessed its expression in 221 breast cancer samples and found it to correlate strongly with the aggressive triple-negative subtype. Silencing PAPOLA in MCF-7 and MDA-MB-231 breast cancer cells reduced proliferation and anchorage-independent growth by decreasing steady-state cyclin D1 (CCND1) mRNA and protein levels. Whereas the length of the CCND1 mRNA poly(A) tail was not affected, its 3' untranslated region (3'UTR) lengthened. Overexpressing PAPOLA caused CCND1 mRNA 3'UTR shortening with a concomitant increase in the amount of corresponding transcript and protein, resulting in growth arrest in MCF-7 cells and DNA damage in HEK-293 cells. Such overexpression of PAPOLA promoted proliferation in the p53 mutant MDA-MB-231 cells. Our data suggest that PAPOLA is a possible candidate target for the control of tumor growth that is mostly relevant to triple-negative tumors, a group characterized by PAPOLA overexpression and lack of alternative targeted therapies.
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Affiliation(s)
- Chrysoula Komini
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, 45110, Greece
| | - Irini Theohari
- First Department of Pathology, Medical School, University of Athens, Athens, 11517, Greece
| | - Andromachi Lambrianidou
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, 45110, Greece
| | - Lydia Nakopoulou
- First Department of Pathology, Medical School, University of Athens, Athens, 11517, Greece
| | - Theoni Trangas
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, 45110, Greece
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22
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Winata CL, Łapiński M, Ismail H, Mathavan S, Sampath P. Exploring Translational Control of Maternal mRNAs in Zebrafish. Methods Mol Biol 2021; 2218:367-380. [PMID: 33606246 DOI: 10.1007/978-1-0716-0970-5_29] [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] [Indexed: 06/12/2023]
Abstract
The study of translational regulation requires reliable measurement of both mRNA levels and protein synthesis. Cytoplasmic polyadenylation is a prevalent mode of translational regulation during oogenesis and early embryogenesis. Here the length of the poly(A) tail of an mRNA is coupled to its translatability. We describe a protocol to identify translationally regulated genes and measure their translation rate in the early zebrafish embryo using genome-wide polysome profiling. This protocol relies on the isolation of mRNA by means of an rRNA depletion strategy, which avoids capture bias due to short poly(A) tail that can occur when using conventional oligo(dT)-based methods. We also present a simple PCR-based method to measure the poly(A) tail length of selected mRNAs.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
- Max Planck Institute for Heart and Lung Research, Bad-Nauheim, Germany.
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Hisyam Ismail
- Skin Research Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | | | - Prabha Sampath
- Skin Research Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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23
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Cassart C, Yague-Sanz C, Bauer F, Ponsard P, Stubbe FX, Migeot V, Wery M, Morillon A, Palladino F, Robert V, Hermand D. RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans. SCIENCE ADVANCES 2020; 6:6/50/eabc1450. [PMID: 33298437 PMCID: PMC7725455 DOI: 10.1126/sciadv.abc1450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
Serine 2 phosphorylation (S2P) within the CTD of RNA polymerase II is considered a Cdk9/Cdk12-dependent mark required for 3'-end processing. However, the relevance of CTD S2P in metazoan development is unknown. We show that cdk-12 lesions or a full-length CTD S2A substitution results in an identical phenotype in Caenorhabditis elegans Embryogenesis occurs in the complete absence of S2P, but the hatched larvae arrest development, mimicking the diapause induced when hatching occurs in the absence of food. Genome-wide analyses indicate that when CTD S2P is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of cleavage stimulatory factor necessary for SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of the C. elegans developmental program.
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Affiliation(s)
- C Cassart
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - C Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - F Bauer
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - P Ponsard
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - F X Stubbe
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - V Migeot
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - M Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - A Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - F Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - V Robert
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - D Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium.
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24
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Wu X, Wang J, Wu X, Hong Y, Li QQ. Heat Shock Responsive Gene Expression Modulated by mRNA Poly(A) Tail Length. FRONTIERS IN PLANT SCIENCE 2020; 11:1255. [PMID: 32922425 PMCID: PMC7456977 DOI: 10.3389/fpls.2020.01255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/30/2020] [Indexed: 05/31/2023]
Abstract
Poly(A) tail length (PAL) has been implicated in the regulation of mRNA translation activities. However, the extent of such regulation at the transcriptome level is less understood in plants. Herein, we report the development and optimization of a large-scale sequencing technique called the Assay for PAL-sequencing (APAL-seq). To explore the role of PAL on post-transcriptional modification and translation, we performed PAL profiling of Arabidopsis transcriptome in response to heat shock. Transcripts of 2,477 genes were found to have variable PAL upon heat treatments. Further study of the transcripts of 14 potential heat-responsive genes identified two distinct groups of genes. In one group, PAL was heat stress-independent, and in the other, PAL was heat stress-sensitive. Meanwhile, the protein expression of HSP70 and HSP17.6C was determined to test the impact of PAL on translational activity. In the absence of heat stress, neither gene demonstrated protein expression; however, under gradual or abrupt heat stress, both transcripts showed enhanced protein expression with elongated PAL. Interestingly, HSP17.6C protein levels were positively correlated with the severity of heat treatment and peaked when treated with abrupt heat. Our results suggest that plant genes have a high variability of PALs and that PAL contributes to swift posttranslational stress responses.
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Affiliation(s)
- Xuan Wu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Jie Wang
- Department of Biology, Miami University, Oxford, OH, United States
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, China
| | - Yiling Hong
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
- Department of Biology, Miami University, Oxford, OH, United States
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25
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Turner RE, Henneken LM, Liem-Weits M, Harrison PF, Swaminathan A, Vary R, Nikolic I, Simpson KJ, Powell DR, Beilharz TH, Dichtl B. Requirement for cleavage factor II m in the control of alternative polyadenylation in breast cancer cells. RNA (NEW YORK, N.Y.) 2020; 26:969-981. [PMID: 32295865 PMCID: PMC7373993 DOI: 10.1261/rna.075226.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Alternative polyadenylation (APA) determines stability, localization and translation potential of the majority of mRNA in eukaryotic cells. The heterodimeric mammalian cleavage factor II (CF IIm) is required for pre-mRNA 3' end cleavage and is composed of the RNA kinase hClp1 and the termination factor hPcf11; the latter protein binds to RNA and the RNA polymerase II carboxy-terminal domain. Here, we used siRNA mediated knockdown and poly(A) targeted RNA sequencing to analyze the role of CF IIm in gene expression and APA in estrogen receptor positive MCF7 breast cancer cells. Identified gene ontology terms link CF IIm function to regulation of growth factor activity, protein heterodimerization and the cell cycle. An overlapping requirement for hClp1 and hPcf11 suggested that CF IIm protein complex was involved in the selection of proximal poly(A) sites. In addition to APA shifts within 3' untranslated regions (3'-UTRs), we observed shifts from promoter proximal regions to the 3'-UTR facilitating synthesis of full-length mRNAs. Moreover, we show that several truncated mRNAs that resulted from APA within introns in MCF7 cells cosedimented with ribosomal components in an EDTA sensitive manner suggesting that those are translated into protein. We propose that CF IIm contributes to the regulation of mRNA function in breast cancer.
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Affiliation(s)
- Rachael E Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Lee M Henneken
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Marije Liem-Weits
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
- Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Robert Vary
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
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26
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Swaminathan A, Harrison PF, Preiss T, Beilharz TH. PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes. Methods Mol Biol 2020; 2049:141-164. [PMID: 31602610 DOI: 10.1007/978-1-4939-9736-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing (NGS) and its application to RNA (RNA-seq) has opened up multiple aspects of RNA processing to deep transcriptome-wide analysis at nucleotide resolution. This has been useful in delineating the transcribed areas of the genome, and in quantitation of RNA isoforms. Such isoforms can diversify the regulatory repertoire of mRNAs. For example, the 3'-end of mRNA can vary in two important ways, in the position chosen for cleavage and polyadenylation, and in the length of the poly(A)-tail. Accordingly, the step-up in resolution made possible by NGS has revealed an unexpectedly high level of alternative polyadenylation (APA). Moreover, it has massively simplified the transcriptome-wide detection of poly(A)-tail length changes. Here we present our approach to the study of 3'-end dynamics using a 3'-focused RNA-seq method called PAT-seq (for poly(A)-test sequencing). The approach records gene expression, APA, and poly(A)-tail changes between transcriptomes to reveal complex interplay between transcriptional and posttranscriptional control mechanisms.
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Affiliation(s)
- Angavai Swaminathan
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
| | - Thomas Preiss
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.
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27
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Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, Yu H, Wei Y, Wu Q, Zhang Y. Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS One 2020; 15:e0234696. [PMID: 32544193 PMCID: PMC7297374 DOI: 10.1371/journal.pone.0234696] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly(A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development- and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.
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Affiliation(s)
- Fengyun Yu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
- ABLife BioBigData Instibute, Wuhan, PR China
| | - Yu Zhang
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Chao Cheng
- ABLife BioBigData Instibute, Wuhan, PR China
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Wenqing Wang
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Zisong Zhou
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Wenliang Rang
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Han Yu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Yaxun Wei
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Qijia Wu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Yi Zhang
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
- ABLife BioBigData Instibute, Wuhan, PR China
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
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28
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Slobodin B, Bahat A, Sehrawat U, Becker-Herman S, Zuckerman B, Weiss AN, Han R, Elkon R, Agami R, Ulitsky I, Shachar I, Dikstein R. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol Cell 2020; 78:434-444.e5. [PMID: 32294471 DOI: 10.1016/j.molcel.2020.03.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 02/02/2023]
Abstract
Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show that reduced transcription dynamics of specific genes leads to enhanced m6A deposition, preferential activity of the CCR4-Not complex, shortened poly(A) tails, and reduced stability of the respective mRNAs. These effects are also exerted by internal ribosome entry site (IRES) elements, which we found to be transcriptional pause sites. However, when transcription dynamics, and subsequently poly(A) tails, are globally altered, cells buffer mRNA levels by adjusting the expression of mRNA degradation machinery. Stress-provoked global impediment of transcription elongation leads to a dramatic inhibition of the mRNA degradation machinery and massive mRNA stabilization. Accordingly, globally enhanced transcription, such as following B cell activation or glucose stimulation, has the opposite effects. This study uncovers two molecular pathways that maintain balanced gene expression in mammalian cells by linking transcription to mRNA stability.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirly Becker-Herman
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amanda N Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idit Shachar
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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29
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Brocard M, Khasnis S, Wood CD, Shannon-Lowe C, West MJ. Pumilio directs deadenylation-associated translational repression of the cyclin-dependent kinase 1 activator RGC-32. Nucleic Acids Res 2019; 46:3707-3725. [PMID: 29385536 PMCID: PMC5909466 DOI: 10.1093/nar/gky038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/22/2018] [Indexed: 12/11/2022] Open
Abstract
Response gene to complement-32 (RGC-32) activates cyclin-dependent kinase 1, regulates the cell cycle and is deregulated in many human tumours. We previously showed that RGC-32 expression is upregulated by the cancer-associated Epstein-Barr virus (EBV) in latently infected B cells through the relief of translational repression. We now show that EBV infection of naïve primary B cells also induces RGC-32 protein translation. In EBV-immortalised cell lines, we found that RGC-32 depletion resulted in cell death, indicating a key role in B cell survival. Studying RGC-32 translational control in EBV-infected cells, we found that the RGC-32 3′untranslated region (3′UTR) mediates translational repression. Repression was dependent on a single Pumilio binding element (PBE) adjacent to the polyadenylation signal. Mutation of this PBE did not affect mRNA cleavage, but resulted in increased polyA tail length. Consistent with Pumilio-dependent recruitment of deadenylases, we found that depletion of Pumilio in EBV-infected cells increased RGC-32 protein expression and polyA tail length. The extent of Pumilio binding to the endogenous RGC-32 mRNA in EBV-infected cell lines also correlated with RGC-32 protein expression. Our data demonstrate the importance of RGC-32 for the survival of EBV-immortalised B cells and identify Pumilio as a key regulator of RGC-32 translation.
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Affiliation(s)
- Michèle Brocard
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Sarika Khasnis
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - C David Wood
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Claire Shannon-Lowe
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Michelle J West
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
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30
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Liao SE, Kandasamy SK, Zhu L, Fukunaga R. DEAD-box RNA helicase Belle posttranscriptionally promotes gene expression in an ATPase activity-dependent manner. RNA (NEW YORK, N.Y.) 2019; 25:825-839. [PMID: 30979781 PMCID: PMC6573787 DOI: 10.1261/rna.070268.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Drosophila Belle (human ortholog DDX3) is a conserved DEAD-box RNA helicase implicated in regulating gene expression. However, the molecular mechanisms by which Belle/DDX3 regulates gene expression are poorly understood. Here we performed systematic mutational analysis to determine the contributions of conserved motifs within Belle to its in vivo function. We found that Belle RNA-binding and RNA-unwinding activities and intrinsically disordered regions (IDRs) are required for Belle in vivo function. Expression of Belle ATPase mutants that cannot bind, hydrolyze, or release ATP resulted in dominant toxic phenotypes. Mechanistically, we discovered that Belle up-regulates reporter protein level when tethered to reporter mRNA, without corresponding changes at the mRNA level, indicating that Belle promotes translation of mRNA that it binds. Belle ATPase activity and amino-terminal IDR were required for this translational promotion activity. We also found that ectopic ovary expression of dominant Belle ATPase mutants decreases levels of cyclin proteins, including Cyclin B, without corresponding changes in their mRNA levels. Finally, we found that Belle binds endogenous cyclin B mRNA. We propose that Belle promotes translation of specific target mRNAs, including cyclin B mRNA, in an ATPase activity-dependent manner.
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Affiliation(s)
- Susan E Liao
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Suresh K Kandasamy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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31
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PA-X antagonises MAVS-dependent accumulation of early type I interferon messenger RNAs during influenza A virus infection. Sci Rep 2019; 9:7216. [PMID: 31076606 PMCID: PMC6510759 DOI: 10.1038/s41598-019-43632-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
The sensing of viral nucleic acids by the innate immune system activates a potent antiviral response in the infected cell, a key component of which is the expression of genes encoding type I interferons (IFNs). Many viruses counteract this response by blocking the activation of host nucleic acid sensors. The evolutionarily conserved influenza A virus (IAV) protein PA-X has been implicated in suppressing the host response to infection, including the expression of type I IFNs. Here, we characterise this further using a PA-X-deficient virus of the mouse-adapted PR8 strain to study activation of the innate immune response in a mouse model of the early response to viral infection. We show that levels of Ifna4 and Ifnb1 mRNAs in the lungs of infected mice were elevated in the absence of PA-X and that this was completely dependent on MAVS. This therefore suggests a role for PA-X in preventing the accumulation of early type I IFN mRNAs in the lung during IAV infection.
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32
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Rodríguez-Romero J, Marconi M, Ortega-Campayo V, Demuez M, Wilkinson MD, Sesma A. Virulence- and signaling-associated genes display a preference for long 3'UTRs during rice infection and metabolic stress in the rice blast fungus. THE NEW PHYTOLOGIST 2019; 221:399-414. [PMID: 30169888 DOI: 10.1111/nph.15405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Generation of mRNA isoforms by alternative polyadenylation (APA) and their involvement in regulation of fungal cellular processes, including virulence, remains elusive. Here, we investigated genome-wide polyadenylation site (PAS) selection in the rice blast fungus to understand how APA regulates pathogenicity. More than half of Magnaporthe oryzae transcripts undergo APA and show novel motifs in their PAS region. Transcripts with shorter 3'UTRs are more stable and abundant in polysomal fractions, suggesting they are being translated more efficiently. Importantly, rice colonization increases the use of distal PASs of pathogenicity genes, especially those participating in signalling pathways like 14-3-3B, whose long 3'UTR is required for infection. Cleavage factor I (CFI) Rbp35 regulates expression and distal PAS selection of virulence and signalling-associated genes, tRNAs and transposable elements, pointing its potential to drive genomic rearrangements and pathogen evolution. We propose a noncanonical PAS selection mechanism for Rbp35 that recognizes UGUAH, unlike humans, without CFI25. Our results showed that APA controls turnover and translation of transcripts involved in fungal growth and environmental adaptation. Furthermore, these data provide useful information for enhancing genome annotations and for cross-species comparisons of PASs and PAS usage within the fungal kingdom and the tree of life.
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Affiliation(s)
- Julio Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marco Marconi
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Víctor Ortega-Campayo
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marie Demuez
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Mark D Wilkinson
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Ane Sesma
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
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3′-UTRs and the Control of Protein Expression in Space and Time. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:133-148. [DOI: 10.1007/978-3-030-31434-7_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes. Nat Commun 2018; 9:4031. [PMID: 30279526 PMCID: PMC6168497 DOI: 10.1038/s41467-018-06404-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/01/2018] [Indexed: 12/30/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays an essential role during oocyte maturation. Here we report that Drosophila MARF1 (Meiosis Regulator And mRNA Stability Factor 1), which consists of one RNA-recognition motif and six tandem LOTUS domains with unknown molecular function, is essential for oocyte maturation. When tethered to a reporter mRNA, MARF1 post-transcriptionally silences reporter expression by shortening reporter mRNA poly-A tail length and thereby reducing reporter protein level. This activity is mediated by the MARF1 LOTUS domain, which binds the CCR4-NOT deadenylase complex. MARF1 binds cyclin A mRNA and shortens its poly-A tail to reduce Cyclin A protein level during oocyte maturation. This study identifies MARF1 as a regulator in oocyte maturation and defines the conserved LOTUS domain as a post-transcriptional effector domain that recruits CCR4-NOT deadenylase complex to shorten target mRNA poly-A tails and suppress their translation. The RNA-binding protein MARF1 is required for post-transcriptional regulation of mRNAs during mouse oogenesis. Here, by analyzing a Drosophila MARF1 mutant, the authors show that MARF1 recruits CCR4-NOT deadenylase to shorten the poly-A tails of target mRNAs such as cyclin A and suppress their translation during Drosophila oogenesis.
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35
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Translation termination-dependent deadenylation of MYC mRNA in human cells. Oncotarget 2018; 9:26171-26182. [PMID: 29899850 PMCID: PMC5995228 DOI: 10.18632/oncotarget.25459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 05/08/2018] [Indexed: 11/25/2022] Open
Abstract
The earliest step in the mRNA degradation process is deadenylation, a progressive shortening of the mRNA poly(A) tail by deadenylases. The question of when deadenylation takes place remains open. MYC mRNA is one of the rare examples for which it was proposed a shortening of the poly(A) tail during ongoing translation. In this study, we analyzed the poly(A) tail length distribution of various mRNAs, including MYC mRNA. The mRNAs were isolated from the polysomal fractions of polysome profiling experiments and analyzed using ligase-mediated poly(A) test analysis. We show that, for all the mRNAs tested with the only exception of MYC, the poly(A) tail length distribution does not change in accordance with the number of ribosomes carried by the mRNA. Conversely, for MYC mRNA, we observed a poly(A) tail length decrease in the fractions containing the largest polysomes. Because the fractions with the highest number of ribosomes are also those for which translation termination is more frequent, we analyzed the poly(A) tail length distribution in polysomal fractions of cells depleted in translation termination factor eRF3. Our results show that the shortening of MYC mRNA poly(A) tail is alleviated by the silencing of translation termination factor eRF3. These findings suggest that MYC mRNA is co-translationally deadenylated and that the deadenylation process requires translation termination to proceed.
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36
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Coll O, Guitart T, Villalba A, Papin C, Simonelig M, Gebauer F. Dicer-2 promotes mRNA activation through cytoplasmic polyadenylation. RNA (NEW YORK, N.Y.) 2018; 24:529-539. [PMID: 29317541 PMCID: PMC5855953 DOI: 10.1261/rna.065417.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Cytoplasmic polyadenylation is a widespread mechanism to regulate mRNA translation. In vertebrates, this process requires two sequence elements in target 3' UTRs: the U-rich cytoplasmic polyadenylation element and the AAUAAA hexanucleotide. In Drosophila melanogaster, cytoplasmic polyadenylation of Toll mRNA occurs independently of these canonical elements and requires a machinery that remains to be characterized. Here we identify Dicer-2 as a component of this machinery. Dicer-2, a factor previously involved in RNA interference (RNAi), interacts with the cytoplasmic poly(A) polymerase Wispy. Depletion of Dicer-2 from polyadenylation-competent embryo extracts and analysis of wispy mutants indicate that both factors are necessary for polyadenylation and translation of Toll mRNA. We further identify r2d2 mRNA, encoding a Dicer-2 partner in RNAi, as a Dicer-2 polyadenylation target. Our results uncover a novel function of Dicer-2 in activation of mRNA translation through cytoplasmic polyadenylation.
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Affiliation(s)
- Olga Coll
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
| | - Ana Villalba
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
| | - Catherine Papin
- Institute of Human Genetics, CNRS UMR9002-University of Montpellier, mRNA Regulation and Development, 34396-Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, CNRS UMR9002-University of Montpellier, mRNA Regulation and Development, 34396-Montpellier, France
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
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37
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Chartier A, Joly W, Simonelig M. Measurement of mRNA Poly(A) Tail Lengths in Drosophila Female Germ Cells and Germ-Line Stem Cells. Methods Mol Biol 2018; 1463:93-102. [PMID: 27734350 DOI: 10.1007/978-1-4939-4017-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
mRNA regulation by poly(A) tail length variations plays an important role in many developmental processes. Recent advances have shown that, in particular, deadenylation (the shortening of mRNA poly(A) tails) is essential for germ-line stem cell biology in the Drosophila ovary. Therefore, a rapid and accurate method to analyze poly(A) tail lengths of specific mRNAs in this tissue is valuable. Several methods of poly(A) test (PAT) assays have been reported to measure mRNA poly(A) tail lengths in vivo. Here, we describe two of these methods (PAT and ePAT) that we have adapted for Drosophila ovarian germ cells and germ-line stem cells.
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Affiliation(s)
- Aymeric Chartier
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR1142 and University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Willy Joly
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR1142 and University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Martine Simonelig
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR1142 and University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
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38
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Beverly M, Hagen C, Slack O. Poly A tail length analysis of in vitro transcribed mRNA by LC-MS. Anal Bioanal Chem 2018; 410:1667-1677. [PMID: 29313076 DOI: 10.1007/s00216-017-0840-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/03/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022]
Abstract
The 3'-polyadenosine (poly A) tail of in vitro transcribed (IVT) mRNA was studied using liquid chromatography coupled to mass spectrometry (LC-MS). Poly A tails were cleaved from the mRNA using ribonuclease T1 followed by isolation with dT magnetic beads. Extracted tails were then analyzed by LC-MS which provided tail length information at single-nucleotide resolution. A 2100-nt mRNA with plasmid-encoded poly A tail lengths of either 27, 64, 100, or 117 nucleotides was used for these studies as enzymatically added poly A tails showed significant length heterogeneity. The number of As observed in the tails closely matched Sanger sequencing results of the DNA template, and even minor plasmid populations with sequence variations were detected. When the plasmid sequence contained a discreet number of poly As in the tail, analysis revealed a distribution that included tails longer than the encoded tail lengths. These observations were consistent with transcriptional slippage of T7 RNAP taking place within a poly A sequence. The type of RNAP did not alter the observed tail distribution, and comparison of T3, T7, and SP6 showed all three RNAPs produced equivalent tail length distributions. The addition of a sequence at the 3' end of the poly A tail did, however, produce narrower tail length distributions which supports a previously described model of slippage where the 3' end can be locked in place by having a G or C after the poly nucleotide region. Graphical abstract Determination of mRNA poly A tail length using magnetic beads and LC-MS.
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Affiliation(s)
- Michael Beverly
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA.
| | - Caitlin Hagen
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
| | - Olga Slack
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
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39
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Dufourt J, Bontonou G, Chartier A, Jahan C, Meunier AC, Pierson S, Harrison PF, Papin C, Beilharz TH, Simonelig M. piRNAs and Aubergine cooperate with Wispy poly(A) polymerase to stabilize mRNAs in the germ plasm. Nat Commun 2017; 8:1305. [PMID: 29101389 PMCID: PMC5670238 DOI: 10.1038/s41467-017-01431-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/18/2017] [Indexed: 11/12/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) and PIWI proteins play a crucial role in germ cells by repressing transposable elements and regulating gene expression. In Drosophila, maternal piRNAs are loaded into the embryo mostly bound to the PIWI protein Aubergine (Aub). Aub targets maternal mRNAs through incomplete base-pairing with piRNAs and can induce their destabilization in the somatic part of the embryo. Paradoxically, these Aub-dependent unstable mRNAs encode germ cell determinants that are selectively stabilized in the germ plasm. Here we show that piRNAs and Aub actively protect germ cell mRNAs in the germ plasm. Aub directly interacts with the germline-specific poly(A) polymerase Wispy, thus leading to mRNA polyadenylation and stabilization in the germ plasm. These results reveal a role for piRNAs in mRNA stabilization and identify Aub as an interactor of Wispy for mRNA polyadenylation. They further highlight the role of Aub and piRNAs in embryonic patterning through two opposite functions.
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Affiliation(s)
- Jérémy Dufourt
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Gwénaëlle Bontonou
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Aymeric Chartier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Camille Jahan
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Anne-Cécile Meunier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Stéphanie Pierson
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, 3800, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Catherine Papin
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Martine Simonelig
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France.
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40
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Kargapolova Y, Levin M, Lackner K, Danckwardt S. sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs. Nucleic Acids Res 2017; 45:6074-6086. [PMID: 28334977 PMCID: PMC5449641 DOI: 10.1093/nar/gkx152] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally, it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RBP-protein interaction landscapes in health and disease.
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Affiliation(s)
- Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Germany
| | - Michal Levin
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Germany
| | - Karl Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Germany
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41
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Kristó I, Bajusz C, Borsos BN, Pankotai T, Dopie J, Jankovics F, Vartiainen MK, Erdélyi M, Vilmos P. The actin binding cytoskeletal protein Moesin is involved in nuclear mRNA export. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1589-1604. [PMID: 28554770 DOI: 10.1016/j.bbamcr.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/29/2022]
Abstract
Current models imply that the evolutionarily conserved, actin-binding Ezrin-Radixin-Moesin (ERM) proteins perform their activities at the plasma membrane by anchoring membrane proteins to the cortical actin network. Here we show that beside its cytoplasmic functions, the single ERM protein of Drosophila, Moesin, has a novel role in the nucleus. The activation of transcription by heat shock or hormonal treatment increases the amount of nuclear Moesin, indicating biological function for the protein in the nucleus. The distribution of Moesin in the nucleus suggests a function in transcription and the depletion of mRNA export factors Nup98 or its interacting partner, Rae1, leads to the nuclear accumulation of Moesin, suggesting that the nuclear function of the protein is linked to mRNA export. Moesin localizes to mRNP particles through the interaction with the mRNA export factor PCID2 and knock down of Moesin leads to the accumulation of mRNA in the nucleus. Based on our results we propose that, beyond its well-known, manifold functions in the cytoplasm, the ERM protein of Drosophila is a new, functional component of the nucleus where it participates in mRNA export.
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Affiliation(s)
- Ildikó Kristó
- Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Bajusz
- Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Barbara N Borsos
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Tibor Pankotai
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Joseph Dopie
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | - Ferenc Jankovics
- Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Miklós Erdélyi
- Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Péter Vilmos
- Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.
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42
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Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM. Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Res 2017; 27:1184-1194. [PMID: 28381614 PMCID: PMC5495070 DOI: 10.1101/gr.215954.116] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/24/2017] [Indexed: 12/21/2022]
Abstract
During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNA-bound proteome. This protein constellation consists of many conserved RBPs, some of which are potential stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of these RBPs in embryogenesis, we focused on Hnrnpa1. iCLIP and subsequent mRNA reporter assays revealed a function for Hnrnpa1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3' UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that Hnrnpa1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-mir-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of Hnrnpa1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that Hnrnpa1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.
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Affiliation(s)
- Vladimir Despic
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Mario Dejung
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Mengting Gu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Jayanth Krishnan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Jing Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Korinna Straube
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Falk Butter
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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43
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Geissler R, Simkin A, Floss D, Patel R, Fogarty EA, Scheller J, Grimson A. A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1. Genes Dev 2017; 30:1070-85. [PMID: 27151978 PMCID: PMC4863738 DOI: 10.1101/gad.277392.116] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/05/2016] [Indexed: 11/24/2022]
Abstract
Geissler et al. identified two related novel 3' UTR motifs in mammals that specify transcript degradation. Degradation occurred via mRNA deadenylation, mediated by the CCR4–NOT complex. They purified trans factors that recognize the motifs and identified hnRNPs A1 and A2/B1. 3′-untranslated regions (UTRs) specify post-transcriptional fates of mammalian messenger RNAs (mRNAs), yet knowledge of the underlying sequences and mechanisms is largely incomplete. Here, we identify two related novel 3′ UTR motifs in mammals that specify transcript degradation. These motifs are interchangeable and active only within 3′ UTRs, where they are often preferentially conserved; furthermore, they are found in hundreds of transcripts, many encoding regulatory proteins. We found that degradation occurs via mRNA deadenylation, mediated by the CCR4–NOT complex. We purified trans factors that recognize the motifs and identified heterogeneous nuclear ribonucleoproteins (hnRNPs) A1 and A2/B1, which are required for transcript degradation, acting in a previously unknown manner. We used RNA sequencing (RNA-seq) to confirm hnRNP A1 and A2/B1 motif-dependent roles genome-wide, profiling cells depleted of these factors singly and in combination. Interestingly, the motifs are most active within the distal portion of 3′ UTRs, suggesting that their role in gene regulation can be modulated by alternative processing, resulting in shorter 3′ UTRs.
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Affiliation(s)
- Rene Geissler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Alfred Simkin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Doreen Floss
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Ravi Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA; Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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44
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Circadian- and UPR-dependent control of CPEB4 mediates a translational response to counteract hepatic steatosis under ER stress. Nat Cell Biol 2017; 19:94-105. [PMID: 28092655 DOI: 10.1038/ncb3461] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/09/2016] [Indexed: 12/18/2022]
Abstract
The cytoplasmic polyadenylation element-binding (CPEB) proteins regulate pre-mRNA processing and translation of CPE-containing mRNAs in early embryonic development and synaptic activity. However, specific functions in adult organisms are poorly understood. Here we show that CPEB4 is required for adaptation to high-fat-diet- and ageing-induced endoplasmic reticulum (ER) stress, and subsequent hepatosteatosis. Stress-activated liver CPEB4 expression is dual-mode regulated. First, Cpeb4 mRNA transcription is controlled by the circadian clock, and then its translation is regulated by the unfolded protein response (UPR) through upstream open reading frames within the 5'UTR. Thus, the CPEB4 protein is synthesized only following ER stress but the induction amplitude is circadian. In turn, CPEB4 activates a second wave of UPR translation required to maintain ER and mitochondrial homeostasis. Our results suggest that combined transcriptional and translational Cpeb4 regulation generates a 'circadian mediator', which coordinates hepatic UPR activity with periods of high ER-protein-folding demand. Accordingly, CPEB4 deficiency results in non-alcoholic fatty liver disease.
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45
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Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae. Arch Virol 2016; 162:891-895. [PMID: 27858291 DOI: 10.1007/s00705-016-3144-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/30/2016] [Indexed: 10/20/2022]
Abstract
In this study we characterize a novel positive and single stranded RNA (ssRNA) mycovirus isolated from the rice field isolate of Magnaporthe oryzae Guy11. The ssRNA contains a single open reading frame (ORF) of 2,373 nucleotides in length and encodes an RNA-dependent RNA polymerase (RdRp) closely related to ourmiaviruses (plant viruses) and ourmia-like mycoviruses. Accordingly, we name this virus Magnaporthe oryzae ourmia-like virus 1 (MOLV1). Although phylogenetic analysis suggests that MOLV1 is closely related to ourmia and ourmia-like viruses, it has some features never reported before within the Ourmiavirus genus. 3' RLM-RACE (RNA ligase-mediated rapid amplification of cDNA ends) and extension poly(A) tests (ePAT) suggest that the MOLV1 genome contains a poly(A) tail whereas the three cytosine and the three guanine residues present in 5' and 3' untranslated regions (UTRs) of ourmia viruses are not observed in the MOLV1 sequence. The discovery of this novel viral genome supports the hypothesis that plant pathogenic fungi may have acquired this type of viruses from their host plants.
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46
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Dutta DJ, Raj H, Dev AH. Polyadenylated tail length variation pattern in ultra-rapid vitrified bovine oocytes. Vet World 2016; 9:1070-1074. [PMID: 27847415 PMCID: PMC5104714 DOI: 10.14202/vetworld.2016.1070-1074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/28/2016] [Indexed: 11/16/2022] Open
Abstract
Aim: Thecurrent study aims at investigating the polyadenylated (poly[A]) tail length of morphologically high and low competent oocytes at different developmental stages. Furthermore, effect of ultra-rapid vitrification on the poly(A) tail length was studied. Materials and Methods: Fresh bovine cumulus oocyte complexes from abattoir originated ovaries were graded based on morphological characters and matured in vitro. Cryopreservation was done by ultra-rapid vitrification method. mRNA was isolated from different categories of oocyte and subjected to ligation-mediated poly(A) test followed by polymerase chain reaction for determining the poly(A) tail length of β actin, gap junction protein alpha 1 (GJA1), poly(A) polymerase alpha (PAPOLA), and heat shock 70 kDa protein (HSP70) transcripts. Results: GJA1, PAPOLA, and HSP70 showed significantly higher poly(A) in immature oocytes of higher competence irrespective of vitrification effects as compared to mature oocytes of higher competence. Conclusion: mRNA poly(A) tail size increases in developmentally high competent immature bovine oocytes. There was limited effect of ultra-rapid vitrification of bovine oocytes on poly(A).
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Affiliation(s)
- D J Dutta
- Department of Veterinary Physiology, Faculty of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati - 781 022, Assam, India
| | - Himangshu Raj
- Department of Veterinary Physiology, Faculty of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati - 781 022, Assam, India
| | - And Hiramoni Dev
- Department of Veterinary Physiology, Faculty of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati - 781 022, Assam, India
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47
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Bangru S, Kalsotra A. Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens. F1000Res 2016; 5:2668. [PMID: 27909578 PMCID: PMC5112568 DOI: 10.12688/f1000research.9511.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants. We also highlight the ongoing developments and challenges associated with RNA variant detection and quantification, including sample heterogeneity and isolation, as well as 'Omics' big data handling.
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Affiliation(s)
- Sushant Bangru
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Illinois, USA; College of Medicine, University of Illinois at Urbana-Champaign, Illinois, USA
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48
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Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS. Genetics 2016; 205:185-199. [PMID: 28049706 DOI: 10.1534/genetics.116.194852] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4) by Set1 complex/COMPASS is a hallmark of eukaryotic chromatin, but it remains poorly understood how this post-translational modification contributes to the regulation of biological processes like the cell cycle. Here, we report a H3K4 methylation-dependent pathway in Saccharomyces cerevisiae that governs toxicity toward benomyl, a microtubule destabilizing drug. Benomyl-sensitive growth of wild-type cells required mono- and dimethylation of H3K4 and Pho23, a PHD-containing subunit of the Rpd3L complex. Δset1 and Δpho23 deletions suppressed defects associated with ipl1-2 aurora kinase mutant, an integral component of the spindle assembly checkpoint during mitosis. Benomyl resistance of Δset1 strains was accompanied by deregulation of all four tubulin genes and the phenotype was suppressed by tub2-423 and Δtub3 mutations, establishing a genetic link between H3K4 methylation and microtubule function. Most interestingly, sine wave fitting and clustering of transcript abundance time series in synchronized cells revealed a requirement for Set1 for proper cell-cycle-dependent gene expression and Δset1 cells displayed delayed entry into S phase. Disruption of G1/S regulation in Δmbp1 and Δswi4 transcription factor mutants duplicated both benomyl resistance and suppression of ipl1-2 as was observed with Δset1 Taken together our results support a role for H3K4 methylation in the coordination of cell-cycle progression and proper assembly of the mitotic spindle during mitosis.
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49
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Characterization of the Role of Hexamer AGUAAA and Poly(A) Tail in Coronavirus Polyadenylation. PLoS One 2016; 11:e0165077. [PMID: 27760233 PMCID: PMC5070815 DOI: 10.1371/journal.pone.0165077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/05/2016] [Indexed: 01/21/2023] Open
Abstract
Similar to eukaryotic mRNA, the positive-strand coronavirus genome of ~30 kilobases is 5’-capped and 3’-polyadenylated. It has been demonstrated that the length of the coronaviral poly(A) tail is not static but regulated during infection; however, little is known regarding the factors involved in coronaviral polyadenylation and its regulation. Here, we show that during infection, the level of coronavirus poly(A) tail lengthening depends on the initial length upon infection and that the minimum length to initiate lengthening may lie between 5 and 9 nucleotides. By mutagenesis analysis, it was found that (i) the hexamer AGUAAA and poly(A) tail are two important elements responsible for synthesis of the coronavirus poly(A) tail and may function in concert to accomplish polyadenylation and (ii) the function of the hexamer AGUAAA in coronaviral polyadenylation is position dependent. Based on these findings, we propose a process for how the coronaviral poly(A) tail is synthesized and undergoes variation. Our results provide the first genetic evidence to gain insight into coronaviral polyadenylation.
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50
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Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT. Accessory subunits are integral for assembly and function of human mitochondrial complex I. Nature 2016; 538:123-126. [PMID: 27626371 DOI: 10.1038/nature19754] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans, making it one of the largest known multi-subunit membrane protein complexes. Complex I exists in supercomplex forms with respiratory chain complexes III and IV, which are together required for the generation of a transmembrane proton gradient used for the synthesis of ATP. Complex I is also a major source of damaging reactive oxygen species and its dysfunction is associated with mitochondrial disease, Parkinson's disease and ageing. Bacterial and human complex I share 14 core subunits that are essential for enzymatic function; however, the role and necessity of the remaining 31 human accessory subunits is unclear. The incorporation of accessory subunits into the complex increases the cellular energetic cost and has necessitated the involvement of numerous assembly factors for complex I biogenesis. Here we use gene editing to generate human knockout cell lines for each accessory subunit. We show that 25 subunits are strictly required for assembly of a functional complex and 1 subunit is essential for cell viability. Quantitative proteomic analysis of cell lines revealed that loss of each subunit affects the stability of other subunits residing in the same structural module. Analysis of proteomic changes after the loss of specific modules revealed that ATP5SL and DMAC1 are required for assembly of the distal portion of the complex I membrane arm. Our results demonstrate the broad importance of accessory subunits in the structure and function of human complex I. Coupling gene-editing technology with proteomics represents a powerful tool for dissecting large multi-subunit complexes and enables the study of complex dysfunction at a cellular level.
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Affiliation(s)
- David A Stroud
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Elliot E Surgenor
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Boris Reljic
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Ann E Frazier
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Marris G Dibley
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Laura D Osellame
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Tegan Stait
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - David R Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital 3052, Melbourne, Australia
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University 3086, Melbourne Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
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