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Liu L, Manley JL. Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3' ends. RNA (NEW YORK, N.Y.) 2024; 30:1122-1140. [PMID: 38986572 DOI: 10.1261/rna.080108.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
The cleavage and polyadenylation specificity factor (CPSF) complex plays a central role in the formation of mRNA 3' ends, being responsible for the recognition of the poly(A) signal sequence, the endonucleolytic cleavage step, and recruitment of poly(A) polymerase. CPSF has been extensively studied for over three decades, and its functions and those of its individual subunits are becoming increasingly well-defined, with much current research focusing on the impact of these proteins on the normal functioning or disease/stress states of cells. In this review, we provide an overview of the general functions of CPSF and its subunits, followed by a discussion of how they exert their functions in a surprisingly diverse variety of biological processes and cellular conditions. These include transcription termination, small RNA processing, and R-loop prevention/resolution, as well as more generally cancer, differentiation/development, and infection/immunity.
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Affiliation(s)
- Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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2
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Khadka P, Thapaliya J. New option: targeting RNase J and RNase HI in the fight against multi-drug-resistant tuberculosis. Ann Med Surg (Lond) 2024; 86:2376-2378. [PMID: 38694338 PMCID: PMC11060219 DOI: 10.1097/ms9.0000000000001859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/13/2024] [Indexed: 05/04/2024] Open
Affiliation(s)
- Priyatam Khadka
- Tribhuvan University, Trichandra Multiple Campus, Kirtipur, Nepal
- State University of New York, Upstate Medical University, Syracuse, NY
| | - Januka Thapaliya
- Tribhuvan University, Trichandra Multiple Campus, Kirtipur, Nepal
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3
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Yuan S, Xi S, Weng H, Guo MM, Zhang JH, Yu ZP, Zhang H, Yu Z, Xing Z, Liu MY, Ming DJ, Sah RK, Zhou Y, Li G, Zeng T, Hong X, Li Y, Zeng XT, Hu H. YTHDC1 as a tumor progression suppressor through modulating FSP1-dependent ferroptosis suppression in lung cancer. Cell Death Differ 2023; 30:2477-2490. [PMID: 37903990 PMCID: PMC10733405 DOI: 10.1038/s41418-023-01234-w] [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: 01/09/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Ferroptosis is a regulated cell death process initiated by iron-dependent phospholipid peroxidation and is mainly suppressed by GPX4-dependent and FSP1-dependent surveillance mechanisms. However, how the ferroptosis surveillance system is regulated during cancer development remains largely unknown. Here, we report that the YTHDC1-mediated m6A epigenetic regulation of FSP1 alleviates the FSP1-dependent ferroptosis suppression that partially contributes to the tumor suppressive role of YTHDC1 in lung cancer progression. YTHDC1 knockdown promoted the lung tumor progression and upregulated FSP1 protein level that resulted in ferroptosis resistance of lung cancer cells. Silencing FSP1 abrogated YTHDC1 knockdown-induced proliferation increase and ferroptosis resistance. Mechanistically, YTHDC1 binding to the m6A sites in the FSP1 3'-UTR recruited the alternative polyadenylation regulator CSTF3 to generate a less stable shorter 3'-UTR contained FSP1 mRNA, whereas YTHDC1 downregulation generated the longer 3'-UTR contained FSP1 mRNA that is stabilized by RNA binding protein HuR and thus led to the enhanced FSP1 protein level. Therefore, our findings identify YTHDC1 as a tumor progression suppressor in lung cancer and a ferroptosis regulator through modulating the FSP1 mRNA stability and thus suggest a ferroptosis-related therapeutic option for YTHDC1high lung cancer.
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Affiliation(s)
- Shuai Yuan
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shu Xi
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hong Weng
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Meng-Meng Guo
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jin-Hui Zhang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhi-Ping Yu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Haozhe Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhaojun Yu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zengzhen Xing
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Meng-Yang Liu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dao-Jing Ming
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rajiv Kumar Sah
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yi Zhou
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Gang Li
- Cancer Center, Faculty of Health Sciences, MoE Frontier Science Center for Precision Oncology, University of Macau, Taipa, Macau, SAR, China
| | - Tao Zeng
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Army Medical University, Chongqing, China.
| | - Xian-Tao Zeng
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Hailiang Hu
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
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4
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Yang XC, Desotell A, Lin MH, Paige AS, Malinowska A, Sun Y, Aik WS, Dadlez M, Tong L, Dominski Z. In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome. RNA (NEW YORK, N.Y.) 2023; 29:1673-1690. [PMID: 37562960 PMCID: PMC10578488 DOI: 10.1261/rna.079709.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/08/2023] [Indexed: 08/12/2023]
Abstract
U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B, and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50, and pICln known to methylate arginines in the carboxy-terminal regions of the Sm proteins B, D1, and D3 during the spliceosomal Sm ring assembly. Both biochemical and cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the amino-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an amino-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.
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Affiliation(s)
- Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Anthony Desotell
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Andrew S Paige
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Agata Malinowska
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Yadong Sun
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Wei Shen Aik
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Michał Dadlez
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Warsaw University, 02-106 Warsaw, Poland
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Hao S, Zhang L, Zhao D, Zhou J, Ye C, Qu H, Li QQ. Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73. PLANT PHYSIOLOGY 2023; 193:537-554. [PMID: 37335917 DOI: 10.1093/plphys/kiad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/09/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023]
Abstract
Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.
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Affiliation(s)
- Saiqi Hao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Lidan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Danhui Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Haidong Qu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
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6
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Huang Y, Ji H, Dong J, Wang X, He Z, Cheng Z, Zhu Q. CPSF3 Promotes Pre-mRNA Splicing and Prevents CircRNA Cyclization in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:4057. [PMID: 37627085 PMCID: PMC10452738 DOI: 10.3390/cancers15164057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
CircRNAs are crucial in tumorigenesis and metastasis, and are comprehensively downregulated in hepatocellular carcinoma (HCC). Previous studies demonstrated that the back-splicing of circRNAs was closely related to 3'-end splicing. As a core executor of 3'-end cleavage, we hypothesized that CPSF3 modulated circRNA circularization. Clinical data were analyzed to establish the prognostic correlations. Cytological experiments were performed to determine the role of CPSF3 in HCC. A fluorescent reporter was employed to explore the back-splicing mechanism. The circRNAs regulated by CPSF3 were screened by RNA-seq and validated by PCR, and changes in downstream pathways were explored by molecular experiments. Finally, the safety and efficacy of the CPSF3 inhibitor JTE-607 were verified both in vitro and in vivo. The results showed that CPSF3 was highly expressed in HCC cells, promoting their proliferation and migration, and that a high CPSF3 level was predictive of a poor prognosis. A mechanistic study revealed that CPSF3 enhanced RNA cleavage, thereby reducing circRNAs, and increasing linear mRNAs. Furthermore, inhibition of CPSF3 by JET-607 suppressed the proliferation of HCC cells. Our findings indicate that the increase of CPSF3 in HCC promotes the shift of pre-mRNA from circRNA to linear mRNA, leading to uncontrolled cell proliferation. JTE-607 exerted a therapeutic effect on HCC by blocking CPSF3.
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Affiliation(s)
- Ying Huang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Haofei Ji
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Jiani Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Xueying Wang
- China National Intellectual Property Administration, Beijing 100088, China;
| | - Zhilin He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
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Abstract
Formation of the 3' end of a eukaryotic mRNA is a key step in the production of a mature transcript. This process is mediated by a number of protein factors that cleave the pre-mRNA, add a poly(A) tail, and regulate transcription by protein dephosphorylation. Cleavage and polyadenylation specificity factor (CPSF) in humans, or cleavage and polyadenylation factor (CPF) in yeast, coordinates these enzymatic activities with each other, with RNA recognition, and with transcription. The site of pre-mRNA cleavage can strongly influence the translation, stability, and localization of the mRNA. Hence, cleavage site selection is highly regulated. The length of the poly(A) tail is also controlled to ensure that every transcript has a similar tail when it is exported from the nucleus. In this review, we summarize new mechanistic insights into mRNA 3'-end processing obtained through structural studies and biochemical reconstitution and outline outstanding questions in the field.
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Affiliation(s)
- Vytautė Boreikaitė
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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8
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Yang XC, Desotell A, Lin MH, Paige AS, Malinowska A, Sun Y, Aik WS, Dadlez M, Tong L, Dominski Z. In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540203. [PMID: 37215023 PMCID: PMC10197641 DOI: 10.1101/2023.05.10.540203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
U7 snRNP is a multi-subunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50 and pICln known to methylate arginines in the C-terminal regions of the Sm proteins B, D1 and D3 during the spliceosomal Sm ring assembly. Both biochemical and Cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the N-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an N-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.
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9
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Bao L, Hu J, Zhan B, Chi M, Li Z, Wang S, Shan C, Zhao Z, Guo Y, Ding X, Ji C, Tao S, Ni T, Zhang X, Zhao G, Li J. Structural insights into RNase J that plays an essential role in Mycobacterium tuberculosis RNA metabolism. Nat Commun 2023; 14:2280. [PMID: 37080992 PMCID: PMC10119312 DOI: 10.1038/s41467-023-38045-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/13/2023] [Indexed: 04/22/2023] Open
Abstract
Ribonucleases (RNases) are responsible for RNA metabolism. RNase J, the core enzyme of the RNA degradosome, plays an essential role in global mRNA decay. Emerging evidence showed that the RNase J of Mycobacterium tuberculosis (Mtb-RNase J) could be an excellent target for treating Mtb infection. Here, crystal structures of Mtb-RNase J in apo-state and complex with the single-strand RNA reveal the conformational change upon RNA binding and hydrolysis. Mtb-RNase J forms an active homodimer through the interactions between the β-CASP and the β-lactamase domain. Knockout of RNase J slows the growth rate and changes the colony morphologies and cell length in Mycobacterium smegmatis, which is restored by RNase J complementation. Finally, RNA-seq analysis shows that the knockout strain significantly changes the expression levels of 49 genes in metabolic pathways. Thus, our current study explores the structural basis of Mtb-RNase J and might provide a promising candidate in pharmacological treatment for tuberculosis.
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Affiliation(s)
- Luyao Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Juan Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Bowen Zhan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Mingzhe Chi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Sen Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Chan Shan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Yanchao Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Xiaoming Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China
| | - Shengce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Xuelian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China.
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China.
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Engineering Research Center of Gene Technology of MOE, Fudan University, 200438, Shanghai, China.
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, 200040, Shanghai, China.
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UBE3D Regulates mRNA 3'-End Processing and Maintains Adipogenic Potential in 3T3-L1 Cells. Mol Cell Biol 2022; 42:e0017422. [PMID: 36519931 PMCID: PMC9753722 DOI: 10.1128/mcb.00174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have previously described the role of an essential Saccharomyces cerevisiae gene, important for cleavage and polyadenylation 1 (IPA1), in the regulation of gene expression through its interaction with Ysh1, the endonuclease subunit of the mRNA 3'-end processing complex. Through a similar mechanism, the mammalian homolog ubiquitin protein ligase E3D (UBE3D) promotes the migratory and invasive potential of breast cancer cells, but its role in the regulation of gene expression during normal cellular differentiation has not previously been described. In this study, we show that CRISPR/Cas9-mediated knockout of Ube3d in 3T3-L1 cells blocks their ability to differentiate into mature adipocytes. Consistent with previous studies in other cell types, Ube3d knockout leads to decreased levels of CPSF73 and global changes in cellular mRNAs indicative of a loss of 3'-end processing capacity. Ube3d knockout cells also display decreased expression of known preadipogenic markers. Overexpression of either UBE3D or CPSF73 rescues the differentiation defect and partially restores protein levels of these markers. These results support a model in which UBE3D is necessary for the maintenance of the adipocyte-committed state via its regulation of the mRNA 3'-end processing machinery.
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11
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Mitschka S, Mayr C. Context-specific regulation and function of mRNA alternative polyadenylation. Nat Rev Mol Cell Biol 2022; 23:779-796. [PMID: 35798852 PMCID: PMC9261900 DOI: 10.1038/s41580-022-00507-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Alternative cleavage and polyadenylation (APA) is a widespread mechanism to generate mRNA isoforms with alternative 3' untranslated regions (UTRs). The expression of alternative 3' UTR isoforms is highly cell type specific and is further controlled in a gene-specific manner by environmental cues. In this Review, we discuss how the dynamic, fine-grained regulation of APA is accomplished by several mechanisms, including cis-regulatory elements in RNA and DNA and factors that control transcription, pre-mRNA cleavage and post-transcriptional processes. Furthermore, signalling pathways modulate the activity of these factors and integrate APA into gene regulatory programmes. Dysregulation of APA can reprogramme the outcome of signalling pathways and thus can control cellular responses to environmental changes. In addition to the regulation of protein abundance, APA has emerged as a major regulator of mRNA localization and the spatial organization of protein synthesis. This role enables the regulation of protein function through the addition of post-translational modifications or the formation of protein-protein interactions. We further discuss recent transformative advances in single-cell RNA sequencing and CRISPR-Cas technologies, which enable the mapping and functional characterization of alternative 3' UTRs in any biological context. Finally, we discuss new APA-based RNA therapeutics, including compounds that target APA in cancer and therapeutic genome editing of degenerative diseases.
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Affiliation(s)
- Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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Ielasi FS, Ternifi S, Fontaine E, Iuso D, Couté Y, Palencia A. Human histone pre-mRNA assembles histone or canonical mRNA-processing complexes by overlapping 3'-end sequence elements. Nucleic Acids Res 2022; 50:12425-12443. [PMID: 36447390 PMCID: PMC9756948 DOI: 10.1093/nar/gkac878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 12/05/2022] Open
Abstract
Human pre-mRNA processing relies on multi-subunit macromolecular complexes, which recognize specific RNA sequence elements essential for assembly and activity. Canonical pre-mRNA processing proceeds via the recognition of a polyadenylation signal (PAS) and a downstream sequence element (DSE), and produces polyadenylated mature mRNAs, while replication-dependent (RD) histone pre-mRNA processing requires association with a stem-loop (SL) motif and a histone downstream element (HDE), and produces cleaved but non-polyadenylated mature mRNAs. H2AC18 mRNA, a specific H2A RD histone pre-mRNA, can be processed to give either a non-polyadenylated mRNA, ending at the histone SL, or a polyadenylated mRNA. Here, we reveal how H2AC18 captures the two human pre-mRNA processing complexes in a mutually exclusive mode by overlapping a canonical PAS (AAUAAA) sequence element with a HDE. Disruption of the PAS sequence on H2AC18 pre-mRNA prevents recruitment of the canonical complex in vitro, without affecting the histone machinery. This shows how the relative position of cis-acting elements in histone pre-mRNAs allows the selective recruitment of distinct human pre-mRNA complexes, thereby expanding the capability to regulate 3' processing and polyadenylation.
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Affiliation(s)
- Francesco S Ielasi
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Sara Ternifi
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Emeline Fontaine
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Domenico Iuso
- Institute for Advanced Biosciences (IAB), Epigenetics and Cell Signaling, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Andrés Palencia
- To whom correspondence should be addressed. Tel: +33 476 54 95 75;
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Liu J, Lu X, Zhang S, Yuan L, Sun Y. Molecular Insights into mRNA Polyadenylation and Deadenylation. Int J Mol Sci 2022; 23:ijms231910985. [PMID: 36232288 PMCID: PMC9570436 DOI: 10.3390/ijms231910985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Poly(A) tails are present on almost all eukaryotic mRNAs, and play critical roles in mRNA stability, nuclear export, and translation efficiency. The biosynthesis and shortening of a poly(A) tail are regulated by large multiprotein complexes. However, the molecular mechanisms of these protein machineries still remain unclear. Recent studies regarding the structural and biochemical characteristics of those protein complexes have shed light on the potential mechanisms of polyadenylation and deadenylation. This review summarizes the recent structural studies on pre-mRNA 3′-end processing complexes that initiate the polyadenylation and discusses the similarities and differences between yeast and human machineries. Specifically, we highlight recent biochemical efforts in the reconstitution of the active human canonical pre-mRNA 3′-end processing systems, as well as the roles of RBBP6/Mpe1 in activating the entire machinery. We also describe how poly(A) tails are removed by the PAN2-PAN3 and CCR4-NOT deadenylation complexes and discuss the emerging role of the cytoplasmic poly(A)-binding protein (PABPC) in promoting deadenylation. Together, these recent discoveries show that the dynamic features of these machineries play important roles in regulating polyadenylation and deadenylation.
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Liu H, Heller-Trulli D, Moore CL. Targeting the mRNA endonuclease CPSF73 inhibits breast cancer cell migration, invasion, and self-renewal. iScience 2022; 25:104804. [PMID: 35992060 PMCID: PMC9385686 DOI: 10.1016/j.isci.2022.104804] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/26/2022] [Accepted: 07/15/2022] [Indexed: 12/02/2022] Open
Abstract
Cleavage by the endonuclease CPSF73 and polyadenylation of nascent RNA is an essential step in co-transcriptional mRNA maturation. Recent work has surprisingly identified CPSF73 as a promising drug target for inhibiting the growth of specific cancers, triggering further studies on understanding CPSF73 regulation and functions in cells. Here, we report that a HECT-like E3 ligase, UBE3D, participates in stabilizing CPFS73 protein by preventing its ubiquitin-mediated degradation by the proteasome. Depletion of UBE3D leads to CPSF73 downregulation, a pre-mRNA cleavage defect, and dysregulated gene expression in cells. UBE3D dysfunction or chemical inactivation of CPSF73 inhibited migration and invasion as well as stem cell renewal phenotypes in vitro in triple-negative breast cancer cells. In addition, genetic overexpression of CPSF73 promoted breast cancer stemness and knocking down CPSF73 inhibited stem cell renewal properties. Together, our findings indicate that targeting the pre-mRNA processing nuclease CPSF73 has potential for breast cancer therapy.
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Affiliation(s)
- Huiyun Liu
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Daniel Heller-Trulli
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Claire L. Moore
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
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RBBP6 activates the pre-mRNA 3' end processing machinery in humans. Genes Dev 2022; 36:210-224. [PMID: 35177536 PMCID: PMC8887125 DOI: 10.1101/gad.349223.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
Abstract
In this study, Boreikaite et al. reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. 3′ end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3′ end of the mature transcript, which is important for mRNA localization, translation, and stability. Cleavage must therefore be tightly regulated. Here, we reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. Unlike its yeast homolog Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to humans. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in mRNA processing.
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U7 deciphered: the mechanism that forms the unusual 3' end of metazoan replication-dependent histone mRNAs. Biochem Soc Trans 2021; 49:2229-2240. [PMID: 34351387 DOI: 10.1042/bst20210323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022]
Abstract
In animal cells, replication-dependent histone mRNAs end with a highly conserved stem-loop structure followed by a 4- to 5-nucleotide single-stranded tail. This unique 3' end distinguishes replication-dependent histone mRNAs from all other eukaryotic mRNAs, which end with a poly(A) tail produced by the canonical 3'-end processing mechanism of cleavage and polyadenylation. The pioneering studies of Max Birnstiel's group demonstrated nearly 40 years ago that the unique 3' end of animal replication-dependent histone mRNAs is generated by a distinct processing mechanism, whereby histone mRNA precursors are cleaved downstream of the stem-loop, but this cleavage is not followed by polyadenylation. The key role is played by the U7 snRNP, a complex of a ∼60 nucleotide U7 snRNA and many proteins. Some of these proteins, including the enzymatic component CPSF73, are shared with the canonical cleavage and polyadenylation machinery, justifying the view that the two metazoan pre-mRNA 3'-end processing mechanisms have a common evolutionary origin. The studies on U7 snRNP culminated in the recent breakthrough of reconstituting an entirely recombinant human machinery that is capable of accurately cleaving histone pre-mRNAs, and determining its structure in complex with a pre-mRNA substrate (with 13 proteins and two RNAs) that is poised for the cleavage reaction. The structure uncovered an unanticipated network of interactions within the U7 snRNP and a remarkable mechanism of activating catalytically dormant CPSF73 for the cleavage. This work provides a conceptual framework for understanding other eukaryotic 3'-end processing machineries.
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