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Song Y, Cui J, Zhu J, Kim B, Kuo ML, Potts PR. RNATACs: Multispecific small molecules targeting RNA by induced proximity. Cell Chem Biol 2024; 31:1101-1117. [PMID: 38876100 DOI: 10.1016/j.chembiol.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
RNA-targeting small molecules (rSMs) have become an attractive modality to tackle traditionally undruggable proteins and expand the druggable space. Among many innovative concepts, RNA-targeting chimeras (RNATACs) represent a new class of multispecific, induced proximity small molecules that act by chemically bringing RNA targets into proximity with an endogenous RNA effector, such as a ribonuclease (RNase). Depending on the RNA effector, RNATACs can alter the stability, localization, translation, or splicing of the target RNA. Although still in its infancy, this new modality has the potential for broad applications in the future to treat diseases with high unmet need. In this review, we discuss potential advantages of RNATACs, recent progress in the field, and challenges to this cutting-edge technology.
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Affiliation(s)
- Yan Song
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
| | - Jia Cui
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Jiaqiang Zhu
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Boseon Kim
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Mei-Ling Kuo
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
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2
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Aranega AE, Franco D. Posttranscriptional Regulation by Proteins and Noncoding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:313-339. [PMID: 38884719 DOI: 10.1007/978-3-031-44087-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Posttranscriptional regulation comprises those mechanisms occurring after the initial copy of the DNA sequence is transcribed into an intermediate RNA molecule (i.e., messenger RNA) until such a molecule is used as a template to generate a protein. A subset of these posttranscriptional regulatory mechanisms essentially are destined to process the immature mRNA toward its mature form, conferring the adequate mRNA stability, providing the means for pertinent introns excision, and controlling mRNA turnover rate and quality control check. An additional layer of complexity is added in certain cases, since discrete nucleotide modifications in the mature RNA molecule are added by RNA editing, a process that provides large mature mRNA diversity. Moreover, a number of posttranscriptional regulatory mechanisms occur in a cell- and tissue-specific manner, such as alternative splicing and noncoding RNA-mediated regulation. In this chapter, we will briefly summarize current state-of-the-art knowledge of general posttranscriptional mechanisms, while major emphases will be devoted to those tissue-specific posttranscriptional modifications that impact on cardiac development and congenital heart disease.
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Affiliation(s)
- Amelia E Aranega
- Cardiovascular Research Group, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Diego Franco
- Cardiovascular Research Group, Department of Experimental Biology, University of Jaén, Jaén, Spain.
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3
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Kataoka N. The Nuclear Cap-Binding Complex, a multitasking binding partner of RNA polymerase II transcripts. J Biochem 2023; 175:9-15. [PMID: 37830942 PMCID: PMC10771035 DOI: 10.1093/jb/mvad081] [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: 07/24/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
In eukaryotic cells, RNAs transcribed by RNA polymerase-II receive the modification at the 5' end. This structure is called the cap structure. The cap structure has a fundamental role for translation initiation by recruiting eukaryotic translation initiation factor 4F (eIF4F). The other important mediator of the cap structure is a nuclear cap-binding protein complex (CBC). CBC consists of two proteins, which are renamed as NCBP1 and NCBP2 (previously called as CBP80/NCBP and CBP20/NIP1, respectively). This review article discusses the multiple roles CBC mediates and co-ordinates in several gene expression steps in eukaryotes.
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Affiliation(s)
- Naoyuki Kataoka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Agriculture Bldg. 7A, Room 703, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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4
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Katahira J, Ohmae T, Yasugi M, Sasaki R, Itoh Y, Kohda T, Hieda M, Yokota Hirai M, Okamoto T, Miyamoto Y. Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex. Nucleic Acids Res 2023; 51:7602-7618. [PMID: 37260089 PMCID: PMC10415132 DOI: 10.1093/nar/gkad483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
To facilitate selfish replication, viruses halt host gene expression in various ways. The nuclear export of mRNA is one such process targeted by many viruses. SARS-CoV-2, the etiological agent of severe acute respiratory syndrome, also prevents mRNA nuclear export. In this study, Nsp14, a bifunctional viral replicase subunit, was identified as a novel inhibitor of mRNA nuclear export. Nsp14 induces poly(A)+ RNA nuclear accumulation and the dissolution/coalescence of nuclear speckles. Genome-wide gene expression analysis revealed the global dysregulation of splicing and 3'-end processing defects of replication-dependent histone mRNAs by Nsp14. These abnormalities were also observed in SARS-CoV-2-infected cells. A mutation introduced at the guanine-N7-methyltransferase active site of Nsp14 diminished these inhibitory activities. Targeted capillary electrophoresis-mass spectrometry analysis (CE-MS) unveiled the production of N7-methyl-GTP in Nsp14-expressing cells. Association of the nuclear cap-binding complex (NCBC) with the mRNA cap and subsequent recruitment of U1 snRNP and the stem-loop binding protein (SLBP) were impaired by Nsp14. These data suggest that the defects in mRNA processing and export arise from the compromise of NCBC function by N7-methyl-GTP, thus exemplifying a novel viral strategy to block host gene expression.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Tatsuya Ohmae
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Mayo Yasugi
- Laboratory of Veterinary Public Health, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoko Kohda
- Laboratory of Veterinary Epidemiology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Miki Hieda
- Department of Medical Technology, Ehime Prefectural University of Health Sciences, 543 Tobe-Cho Takaoda, Iyo, Ehime791-2102, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085, Japan
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5
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Meng S, Xia Y, Li M, Wu Y, Wang D, Zhou Y, Ma D, Ye J, Sun T, Ji C. NCBP1 enhanced proliferation of DLBCL cells via METTL3-mediated m6A modification of c-Myc. Sci Rep 2023; 13:8606. [PMID: 37244946 DOI: 10.1038/s41598-023-35777-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is malignant hyperplasia of B lymphocytes and standard care cannot satisfactorily meet clinical needs. Potential diagnostic and prognostic DLBCL biomarkers are needed. NCBP1 could bind to the 5'-end cap of pre-mRNAs to participate in RNA processing, transcript nuclear export and translation. Aberrant NCBP1 expression is involved in the pathogenesis of cancers, but little is known about NCBP1 in DLBCL. We proved that NCBP1 is significantly elevated in DLBCL patients and is associated with their poor prognosis. Then, we found that NCBP1 is important for the proliferation of DLBCL cells. Moreover, we verified that NCBP1 enhances the proliferation of DLBCL cells in a METTL3-dependent manner and found that NCBP1 enhances the m6A catalytic function of METTL3 by maintaining METTL3 mRNA stabilization. Mechanistically, the expression of c-MYC is regulated by NCBP1-enhanced METTL3, and the NCBP1/METTL3/m6A/c-MYC axis is important for DLBCL progression. We identified a new pathway for DLBCL progression and suggest innovative ideas for molecular targeted therapy of DLBCL.
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Affiliation(s)
- Sibo Meng
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
- Department of Medical Oncology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Heifei Road, Qingdao, 266035, Shandong, People's Republic of China
| | - Yuan Xia
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Mingying Li
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yuyan Wu
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Dongmei Wang
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Ying Zhou
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Jingjing Ye
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Tao Sun
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
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6
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Sun H, Zhang Y, Wang G, Yang W, Xu Y. mRNA-Based Therapeutics in Cancer Treatment. Pharmaceutics 2023; 15:pharmaceutics15020622. [PMID: 36839944 PMCID: PMC9964383 DOI: 10.3390/pharmaceutics15020622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 02/15/2023] Open
Abstract
Over the past two decades, significant technological innovations have led to messenger RNA (mRNA) becoming a promising option for developing prophylactic and therapeutic vaccines, protein replacement therapies, and genome engineering. The success of the two COVID-19 mRNA vaccines has sparked new enthusiasm for other medical applications, particularly in cancer treatment. In vitro-transcribed (IVT) mRNAs are structurally designed to resemble naturally occurring mature mRNA. Delivery of IVT mRNA via delivery platforms such as lipid nanoparticles allows host cells to produce many copies of encoded proteins, which can serve as antigens to stimulate immune responses or as additional beneficial proteins for supplements. mRNA-based cancer therapeutics include mRNA cancer vaccines, mRNA encoding cytokines, chimeric antigen receptors, tumor suppressors, and other combination therapies. To better understand the current development and research status of mRNA therapies for cancer treatment, this review focused on the molecular design, delivery systems, and clinical indications of mRNA therapies in cancer.
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Affiliation(s)
- Han Sun
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ge Wang
- Department of Oral Maxillofacial & Head and Neck Oncology, National Center of Stomatology, National Clinical Research Center for Oral Disease, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Wen Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence:
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7
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Wyrzykowska A, Bielewicz D, Plewka P, Sołtys‐Kalina D, Wasilewicz‐Flis I, Marczewski W, Jarmolowski A, Szweykowska‐Kulinska Z. The MYB33, MYB65, and MYB101 transcription factors affect Arabidopsis and potato responses to drought by regulating the ABA signaling pathway. PHYSIOLOGIA PLANTARUM 2022; 174:e13775. [PMID: 36050907 PMCID: PMC9828139 DOI: 10.1111/ppl.13775] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the main climate threats limiting crop production. Potato is one of the four most important food crop species worldwide and is sensitive to water shortage. The CBP80 gene was shown to affect Arabidopsis and potato responses to drought by regulating the level of microRNA159 and, consequently, the levels of the MYB33 and MYB101 transcription factors (TFs). Here, we show that three MYB TFs, MYB33, MYB65, and MYB101, are involved in plant responses to water shortage. Their downregulation in Arabidopsis causes stomatal hyposensitivity to abscisic acid (ABA), leading to reduced tolerance to drought. Transgenic Arabidopsis and potato plants overexpressing these genes, with a mutated recognition site in miR159, show hypersensitivity to ABA and relatively high tolerance to drought conditions. Thus, the MYB33, MYB65, and MYB101 genes may be potential targets for innovative breeding to obtain crops with relatively high tolerance to drought.
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Affiliation(s)
- Anna Wyrzykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Dorota Sołtys‐Kalina
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Iwona Wasilewicz‐Flis
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Zofia Szweykowska‐Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
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8
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The Role of RNA-Binding Proteins in Hematological Malignancies. Int J Mol Sci 2022; 23:ijms23179552. [PMID: 36076951 PMCID: PMC9455611 DOI: 10.3390/ijms23179552] [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: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Hematological malignancies comprise a plethora of different neoplasms, such as leukemia, lymphoma, and myeloma, plus a myriad of dysplasia, such as myelodysplastic syndromes or anemias. Despite all the advances in patient care and the development of new therapies, some of these malignancies remain incurable, mainly due to resistance and refractoriness to treatment. Therefore, there is an unmet clinical need to identify new biomarkers and potential therapeutic targets that play a role in treatment resistance and contribute to the poor outcomes of these tumors. RNA-binding proteins (RBPs) are a diverse class of proteins that interact with transcripts and noncoding RNAs and are involved in every step of the post-transcriptional processing of transcripts. Dysregulation of RBPs has been associated with the development of hematological malignancies, making them potential valuable biomarkers and potential therapeutic targets. Although a number of dysregulated RBPs have been identified in hematological malignancies, there is a critical need to understand the biology underlying their contribution to pathology, such as the spatiotemporal context and molecular mechanisms involved. In this review, we emphasize the importance of deciphering the regulatory mechanisms of RBPs to pinpoint novel therapeutic targets that could drive or contribute to hematological malignancy biology.
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9
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Boris-Lawrie K, Singh G, Osmer PS, Zucko D, Staller S, Heng X. Anomalous HIV-1 RNA, How Cap-Methylation Segregates Viral Transcripts by Form and Function. Viruses 2022; 14:935. [PMID: 35632676 PMCID: PMC9145092 DOI: 10.3390/v14050935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022] Open
Abstract
The acquisition of m7G-cap-binding proteins is now recognized as a major variable driving the form and function of host RNAs. This manuscript compares the 5'-cap-RNA binding proteins that engage HIV-1 precursor RNAs, host mRNAs, small nuclear (sn)- and small nucleolar (sno) RNAs and sort into disparate RNA-fate pathways. Before completion of the transcription cycle, the transcription start site of nascent class II RNAs is appended to a non-templated guanosine that is methylated (m7G-cap) and bound by hetero-dimeric CBP80-CBP20 cap binding complex (CBC). The CBC is a nexus for the co-transcriptional processing of precursor RNAs to mRNAs and the snRNA and snoRNA of spliceosomal and ribosomal ribonucleoproteins (RNPs). Just as sn/sno-RNAs experience hyper-methylation of m7G-cap to trimethylguanosine (TMG)-cap, so do select HIV RNAs and an emerging cohort of mRNAs. TMG-cap is blocked from Watson:Crick base pairing and disqualified from participating in secondary structure. The HIV TMG-cap has been shown to license select viral transcripts for specialized cap-dependent translation initiation without eIF4E that is dependent upon CBP80/NCBP3. The exceptional activity of HIV precursor RNAs secures their access to maturation pathways of sn/snoRNAs, canonical and non-canonical host mRNAs in proper stoichiometry to execute the retroviral replication cycle.
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Affiliation(s)
- Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Seth Staller
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
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10
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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11
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Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Res 2020; 48:10413-10427. [PMID: 32960271 PMCID: PMC7544205 DOI: 10.1093/nar/gkaa744] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear Cap-Binding Complex (CBC), consisting of Nuclear Cap-Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5′cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein–protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association in vitro and in vivo requires EJC core integrity and the in vivo RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting mRNA expression.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Isabelle Barbosa
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Claudia Iasillo
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wiebke Manuela Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
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12
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Esencan E, Kallen A, Zhang M, Seli E. Translational activation of maternally derived mRNAs in oocytes and early embryos and the role of embryonic poly(A) binding protein (EPAB). Biol Reprod 2020; 100:1147-1157. [PMID: 30806655 DOI: 10.1093/biolre/ioz034] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/23/2019] [Accepted: 02/23/2019] [Indexed: 12/20/2022] Open
Abstract
Transcription ceases upon stimulation of oocyte maturation and gene expression during oocyte maturation, fertilization, and early cleavage relies on translational activation of maternally derived mRNAs. Two key mechanisms that mediate translation of mRNAs in oocytes have been described in detail: cytoplasmic polyadenylation-dependent and -independent. Both of these mechanisms utilize specific protein complexes that interact with cis-acting sequences located on 3'-untranslated region (3'-UTR), and both involve embryonic poly(A) binding protein (EPAB), the predominant poly(A) binding protein during early development. While mechanistic details of these pathways have primarily been elucidated using the Xenopus model, their roles are conserved in mammals and targeted disruption of key regulators in mouse results in female infertility. Here, we provide a detailed account of the molecular mechanisms involved in translational activation during oocyte and early embryo development, and the role of EPAB in this process.
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Affiliation(s)
- Ecem Esencan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | - Amanda Kallen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | - Man Zhang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | - Emre Seli
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
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13
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Wang B, Chai H, Zhong Y, Shen Y, Yang W, Chen J, Xin Z, Shi H. The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1598-1613. [PMID: 31745559 PMCID: PMC7242002 DOI: 10.1093/jxb/erz523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/19/2019] [Indexed: 05/29/2023]
Abstract
Gene regulation is central for growth, development, and adaptation to environmental changes in all living organisms. Many genes are induced by environmental cues, and the expression of these inducible genes is often repressed under normal conditions. Here, we show that the SHINY2 (SHI2) gene is important for repressing salt-inducible genes and also plays a role in cold response. The shi2 mutant displayed hypersensitivity to cold, abscisic acid (ABA), and LiCl. Map-based cloning demonstrates that SHI2 encodes a DEAD- (Asp-Glu-Ala-Asp) box RNA helicase with similarity to a yeast splicing factor. Transcriptomic analysis of the shi2 mutant in response to cold revealed that the shi2 mutation decreased the number of cold-responsive genes and the magnitude of their response, and resulted in the mis-splicing of some cold-responsive genes. Under salt stress, however, the shi2 mutation increased the number of salt-responsive genes but had a negligible effect on mRNA splicing. Our results suggest that SHI2 is a component in a ready-for-transcription repressor complex important for gene repression under normal conditions, and for gene activation and transcription under stress conditions. In addition, SHI2 also serves as a splicing factor required for proper splicing of cold-responsive genes and affects 5' capping and polyadenylation site selection.
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Affiliation(s)
- Bangshing Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Haoxi Chai
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yingli Zhong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Yun Shen
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Wannian Yang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, USA
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
- School of Life Sciences, Central China Normal University, Wuhan, China
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14
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Ferreira PA. The coming-of-age of nucleocytoplasmic transport in motor neuron disease and neurodegeneration. Cell Mol Life Sci 2019; 76:2247-2273. [PMID: 30742233 PMCID: PMC6531325 DOI: 10.1007/s00018-019-03029-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022]
Abstract
The nuclear pore is the gatekeeper of nucleocytoplasmic transport and signaling through which a vast flux of information is continuously exchanged between the nuclear and cytoplasmic compartments to maintain cellular homeostasis. A unifying and organizing principle has recently emerged that cements the notion that several forms of amyotrophic lateral sclerosis (ALS), and growing number of other neurodegenerative diseases, co-opt the dysregulation of nucleocytoplasmic transport and that this impairment is a pathogenic driver of neurodegeneration. The understanding of shared pathomechanisms that underpin neurodegenerative diseases with impairments in nucleocytoplasmic transport and how these interface with current concepts of nucleocytoplasmic transport is bound to illuminate this fundamental biological process in a yet more physiological context. Here, I summarize unresolved questions and evidence and extend basic and critical concepts and challenges of nucleocytoplasmic transport and its role in the pathogenesis of neurodegenerative diseases, such as ALS. These principles will help to appreciate the roles of nucleocytoplasmic transport in the pathogenesis of ALS and other neurodegenerative diseases, and generate a framework for new ideas of the susceptibility of motoneurons, and possibly other neurons, to degeneration by dysregulation of nucleocytoplasmic transport.
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Affiliation(s)
- Paulo A Ferreira
- Duke University Medical Center, DUEC 3802, 2351 Erwin Road, Durham, NC, 27710, USA.
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15
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Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export. Mol Cell Biol 2019; 39:MCB.00540-18. [PMID: 30745412 DOI: 10.1128/mcb.00540-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
Cap-binding complex (CBC) associates cotranscriptionally with the cap structure at the 5' end of nascent mRNA to protect it from exonucleolytic degradation. Here, we show that CBC promotes the targeting of an mRNA export adaptor, Yra1 (forming transcription export [TREX] complex with THO and Sub2), to the active genes and enhances mRNA export in Saccharomyces cerevisiae Likewise, recruitment of Npl3 (an hnRNP involved in mRNA export via formation of export-competent ribonuclear protein complex [RNP]) to the active genes is facilitated by CBC. Thus, CBC enhances targeting of the export factors and promotes mRNA export. Such function of CBC is not mediated via THO and Sub2 of TREX, cleavage and polyadenylation factors, or Sus1 (that regulates mRNA export via transcription export 2 [TREX-2]). However, CBC promotes splicing of SUS1 mRNA and, consequently, Sus1 protein level and mRNA export via TREX-2. Collectively, our results support the hypothesis that CBC promotes recruitment of Yra1 and Npl3 to the active genes, independently of THO, Sub2, or cleavage and polyadenylation factors, and enhances mRNA export via TREX and RNP, respectively, in addition to its role in facilitating SUS1 mRNA splicing to increase mRNA export through TREX-2, revealing distinct stimulatory functions of CBC in mRNA export.
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16
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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17
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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18
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Trotman JB, Schoenberg *DR. A recap of RNA recapping. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1504. [PMID: 30252202 PMCID: PMC6294674 DOI: 10.1002/wrna.1504] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/13/2018] [Accepted: 08/01/2018] [Indexed: 12/12/2022]
Abstract
The N7-methylguanosine cap is a hallmark of the 5' end of eukaryotic mRNAs and is required for gene expression. Loss of the cap was believed to lead irreversibly to decay. However, nearly a decade ago, it was discovered that mammalian cells contain enzymes in the cytoplasm that are capable of restoring caps onto uncapped RNAs. In this review, we summarize recent advances in our understanding of cytoplasmic RNA recapping and discuss the biochemistry of this process and its impact on regulating and diversifying the transcriptome. Although most studies focus on mammalian RNA recapping, we also highlight new observations for recapping in disparate eukaryotic organisms, with the trypanosome recapping system appearing to be a fascinating example of convergent evolution. We conclude with emerging insights into the biological significance of RNA recapping and prospects for the future of this evolving area of study. This article is categorized under: RNA Processing > RNA Editing and Modification Translation > Translation Regulation RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Jackson B. Trotman
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210,
| | - *Daniel R. Schoenberg
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, schoenberg,
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19
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The RNA binding protein Ars2 supports hematopoiesis at multiple levels. Exp Hematol 2018; 64:45-58.e9. [PMID: 29775646 DOI: 10.1016/j.exphem.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 12/22/2022]
Abstract
Recent biochemical characterization of arsenic resistance protein 2 (Ars2) has established it as central in determining the fate of nascent ribonucleic acid (RNA) polymerase II (RNAPII) transcripts. Through interactions with the nuclear 5'-7-methylguanosine cap-binding complex, Ars2 promotes cotranscriptional processing coupled with nuclear export or degradation of several classes of RNAPII transcripts, allowing for gene expression programs that facilitate rapid and sustained proliferation of immortalized cells in culture. However, rapidly dividing cells in culture do not represent the physiological condition of the vast majority of cells in an adult mammal. To examine functions of Ars2 in a physiological setting, we generated inducible Ars2 knockout mice and found that deletion of Ars2 from adult mice resulted in defective hematopoiesis in bone marrow and thymus. Importantly, only some of this defect could be explained by the requirement of Ars2 for rapid proliferation, which we found to be cell-type specific in vivo. Rather, Ars2 was required for survival of developing thymocytes and for limiting differentiation of bone marrow resident long-term hematopoietic stem cells. As a result, Ars2 knockout led to rapid thymic involution and loss of the ability of mice to regenerate peripheral blood after myeloablation. These in vivo data demonstrate that Ars2 expression is important at several steps of hematopoiesis, likely because Ars2 acts on gene expression programs underlying essential cell fate decisions such as the decision to die,proliferate, or differentiate.
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20
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Targeting the Polyadenylation Signal of Pre-mRNA: A New Gene Silencing Approach for Facioscapulohumeral Dystrophy. Int J Mol Sci 2018; 19:ijms19051347. [PMID: 29751519 PMCID: PMC5983732 DOI: 10.3390/ijms19051347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 02/07/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is characterized by the contraction of the D4Z4 array located in the sub-telomeric region of the chromosome 4, leading to the aberrant expression of the DUX4 transcription factor and the mis-regulation of hundreds of genes. Several therapeutic strategies have been proposed among which the possibility to target the polyadenylation signal to silence the causative gene of the disease. Indeed, defects in mRNA polyadenylation leads to an alteration of the transcription termination, a disruption of mRNA transport from the nucleus to the cytoplasm decreasing the mRNA stability and translation efficiency. This review discusses the polyadenylation mechanisms, why alternative polyadenylation impacts gene expression, and how targeting polyadenylation signal may be a potential therapeutic approach for FSHD.
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21
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Abstract
Ribonucleic acid (RNA) homeostasis is dynamically modulated in response to changing physiological conditions. Tight regulation of RNA abundance through both transcription and degradation determines the amount, timing, and location of protein translation. This balance is of particular importance in neurons, which are among the most metabolically active and morphologically complex cells in the body. As a result, any disruptions in RNA degradation can have dramatic consequences for neuronal health. In this chapter, we will first discuss mechanisms of RNA stabilization and decay. We will then explore how the disruption of these pathways can lead to neurodegenerative disease.
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22
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Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH. The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One 2017; 12:e0189788. [PMID: 29244865 PMCID: PMC5731758 DOI: 10.1371/journal.pone.0189788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/03/2017] [Indexed: 11/26/2022] Open
Abstract
In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.
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Affiliation(s)
- Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dasuni Jayaweera
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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23
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Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate. Cell Rep 2017; 18:2635-2650. [PMID: 28297668 PMCID: PMC5368414 DOI: 10.1016/j.celrep.2017.02.046] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/13/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3′-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3′-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport. Surprisingly, these proteins all bind capped RNAs without strong preferences for given transcripts, and their steady-state binding correlates poorly with their function. Despite this, PHAX and ZC3H18 compete for CBC binding and we demonstrate that this competitive binding is functionally relevant. We further show that CBC-containing complexes are short lived in vivo, and we therefore suggest that RNA fate involves the transient formation of mutually exclusive CBC complexes, which may only be consequential at particular checkpoints during RNA biogenesis. PHAX and ZC3H18 compete for binding to the nuclear CBC PHAX and ZC3H18 have opposite effects on the fate of snRNA precursors and other RNAs PHAX, ARS2, and ZC3H18 bind capped RNAs without strong preference for given transcripts CBC-containing complexes are short lived in vivo, with a lifetime of a few seconds
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24
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Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2. Nat Commun 2017; 8:1302. [PMID: 29101316 PMCID: PMC5670239 DOI: 10.1038/s41467-017-01402-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022] Open
Abstract
Pol II transcribes diverse classes of RNAs that need to be directed into the appropriate nuclear maturation pathway. All nascent Pol II transcripts are 5′-capped and the cap is immediately sequestered by the nuclear cap-binding complex (CBC). Mutually exclusive interactions of CBC with different partner proteins have been implicated in transcript fate determination. Here, we characterise the direct interactions between CBC and NELF-E, a subunit of the negative elongation factor complex, ARS2 and PHAX. Our biochemical and crystal structure results show that the homologous C-terminal peptides of NELF-E and ARS2 bind identically to CBC and in each case the affinity is enhanced when CBC is bound to a cap analogue. Furthermore, whereas PHAX forms a complex with CBC and ARS2, NELF-E binding to CBC is incompatible with PHAX binding. We thus define two mutually exclusive complexes CBC–NELF–E and CBC–ARS2–PHAX, which likely act in respectively earlier and later phases of transcription. The nuclear cap-binding complex (CBC) binds to the 5′-cap structure of Pol II transcripts. Here, the authors give structural insights into CBC-mediated transcript processing and show that CBC forms mutual exclusive complexes with NELF and ARS2, which might act in earlier and later phases of transcription, respectively.
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25
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Shi M, Zhang H, Wu X, He Z, Wang L, Yin S, Tian B, Li G, Cheng H. ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo. Nucleic Acids Res 2017; 45:9640-9653. [PMID: 28934468 PMCID: PMC5766156 DOI: 10.1093/nar/gkx597] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/04/2017] [Indexed: 12/04/2022] Open
Abstract
The TREX complex (TREX) plays key roles in nuclear export of mRNAs. However, little is known about its transcriptome-wide binding targets. We used individual cross-linking and immunoprecipitation (iCLIP) to identify the binding sites of ALYREF, an mRNA export adaptor in TREX, in human cells. Consistent with previous in vitro studies, ALYREF binds to a region near the 5′ end of the mRNA in a CBP80-dependent manner. Unexpectedly, we identified PABPN1-dependent ALYREF binding near the 3′ end of the mRNA. Furthermore, the 3′ processing factor CstF64 directly interacts with ALYREF and is required for the overall binding of ALYREF on the mRNA. In addition, we found that numerous middle exons harbor ALYREF binding sites and identified ALYREF-binding motifs that promote nuclear export of intronless mRNAs. Together, our study defines enrichment of ALYREF binding sites at the 5′ and the 3′ regions of the mRNA in vivo, identifies export-promoting ALYREF-binding motifs, and reveals CstF64- and PABPN1-mediated coupling of mRNA nuclear export to 3′ processing.
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Affiliation(s)
- Min Shi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Heng Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xudong Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhisong He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lantian Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bin Tian
- Departartment of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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26
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Catania F. From intronization to intron loss: How the interplay between mRNA-associated processes can shape the architecture and the expression of eukaryotic genes. Int J Biochem Cell Biol 2017; 91:136-144. [PMID: 28673893 DOI: 10.1016/j.biocel.2017.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/25/2017] [Accepted: 06/30/2017] [Indexed: 12/29/2022]
Abstract
Transcription-coupled processes such as capping, splicing, and cleavage/polyadenylation participate in the journey from genes to proteins. Although they are traditionally thought to serve only as steps in the generation of mature mRNAs, a synthesis of available data indicates that these processes could also act as a driving force for the evolution of eukaryotic genes. A theoretical framework for how mRNA-associated processes may shape gene structure and expression has recently been proposed. Factors that promote splicing and cleavage/polyadenylation in this framework compete for access to overlapping or neighboring signals throughout the transcription cycle. These antagonistic interactions allow mechanisms for intron gain and splice site recognition as well as common trends in eukaryotic gene structure and expression to be coherently integrated. Here, I extend this framework further. Observations that largely (but not exclusively) revolve around the formation of DNA-RNA hybrid structures, called R loops, and promoter directionality are integrated. Additionally, the interplay between splicing factors and cleavage/polyadenylation factors is theorized to also affect the formation of intragenic DNA double-stranded breaks thereby contributing to intron loss. The most notable prediction in this proposition is that RNA molecules can mediate intron loss by serving as a template to repair DNA double-stranded breaks. The framework presented here leverages a vast body of empirical observations, logically extending previous suggestions, and generating verifiable predictions to further substantiate the view that the intracellular environment plays an active role in shaping the structure and the expression of eukaryotic genes.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, 48149 Münster, Germany.
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27
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Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol 2017; 14:865-890. [PMID: 28453393 PMCID: PMC5546720 DOI: 10.1080/15476286.2017.1306171] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/02/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022] Open
Abstract
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.
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Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Zhiqiao Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alastair Louey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Krogh N, Pietschmann M, Schmid M, Jensen TH, Nielsen H. Lariat capping as a tool to manipulate the 5' end of individual yeast mRNA species in vivo. RNA (NEW YORK, N.Y.) 2017; 23:683-695. [PMID: 28159804 PMCID: PMC5393178 DOI: 10.1261/rna.059337.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
The 5' cap structure of eukaryotic mRNA is critical for its processing, transport, translation, and stability. The many functions of the cap and the fact that most, if not all, mRNA carries the same type of cap makes it difficult to analyze cap function in vivo at individual steps of gene expression. We have used the lariat capping ribozyme (LCrz) from the myxomycete Didymium to replace the mRNA m7G cap of a single reporter mRNA species with a tiny lariat in which the first and the third nucleotide are joined by a 2', 5' phosphodiester bond. We show that the ribozyme functions in vivo in the budding yeast Saccharomyces cerevisiae presumably without cofactors and that lariat capping occurs cotranscriptionally. The lariat-capped reporter mRNA is efficiently exported to the cytoplasm where it is found to be oligoadenylated and evenly distributed. Both the oligoadenylated form and a lariat-capped mRNA with a templated poly(A) tail translates poorly, underlining the critical importance of the m7G cap in translation. Finally, the lariat-capped RNA exhibits a threefold longer half-life compared to its m7G-capped counterpart, consistent with a key role for the m7G cap in mRNA turnover. Our study emphasizes important activities of the m7G cap and suggests new utilities of lariat capping as a molecular tool in vivo.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Max Pietschmann
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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29
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The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol 2017; 18:263-273. [PMID: 28248323 DOI: 10.1038/nrm.2017.10] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II (Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the transcription process, the CTD is dynamically modified by post-translational modifications, many of which facilitate or hinder the recruitment of key regulatory factors of Pol II that collectively constitute the 'CTD code'. Recent studies have revealed how the physicochemical properties of the CTD promote phase separation in the presence of other low-complexity domains. Here, we discuss the intricacies of the CTD code and how the newly characterized physicochemical properties of the CTD expand the function of the CTD beyond the code.
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Harlen KM, Churchman LS. Subgenic Pol II interactomes identify region-specific transcription elongation regulators. Mol Syst Biol 2017; 13:900. [PMID: 28043953 PMCID: PMC5293154 DOI: 10.15252/msb.20167279] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcription, RNA processing, and chromatin‐related factors all interact with RNA polymerase II (Pol II) to ensure proper timing and coordination of transcription and co‐transcriptional processes. Many transcription elongation regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the complement of factors regulating specific stages of transcription. To this end, we developed a strategy to purify Pol II elongation complexes from subgenic regions of a single gene, namely the 5′ and 3′ regions, using sequences in the nascent RNA. Applying this strategy to Saccharomyces cerevisiae, we determined the specific set of factors that interact with Pol II at precise stages during transcription. We identify many known region‐specific factors as well as determine unappreciated associations of regulatory factors during early and late stages of transcription. These data reveal a role for the transcription termination factor, Rai1, in regulating the early stages of transcription genome‐wide and support the role of Bye1 as a negative regulator of early elongation. We also demonstrate a role for the ubiquitin ligase, Bre1, in regulating Pol II dynamics during the latter stages of transcription. These data and our approach to analyze subgenic transcription elongation complexes will shed new light on the myriad factors that regulate the different stages of transcription and coordinate co‐transcriptional processes.
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Affiliation(s)
- Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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31
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Maity A, Chaudhuri A, Das B. DRN and TRAMP degrade specific and overlapping aberrant mRNAs formed at various stages of mRNP biogenesis inSaccharomyces cerevisiae. FEMS Yeast Res 2016; 16:fow088. [DOI: 10.1093/femsyr/fow088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
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32
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 448] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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Sutherland JM, Siddall NA, Hime GR, McLaughlin EA. RNA binding proteins in spermatogenesis: an in depth focus on the Musashi family. Asian J Androl 2016; 17:529-36. [PMID: 25851660 PMCID: PMC4492041 DOI: 10.4103/1008-682x.151397] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Controlled gene regulation during gamete development is vital for maintaining reproductive potential. During the complex process of mammalian spermatogenesis, male germ cells experience extended periods of the inactive transcription despite heavy translational requirements for continued growth and differentiation. Hence, spermatogenesis is highly reliant on mechanisms of posttranscriptional regulation of gene expression, facilitated by RNA binding proteins (RBPs), which remain abundantly expressed throughout this process. One such group of proteins is the Musashi family, previously identified as critical regulators of testis germ cell development and meiosis in Drosophila, and also shown to be vital to sperm development and reproductive potential in the mouse. This review describes the role and function of RBPs within the scope of male germ cell development, focusing on our recent knowledge of the Musashi proteins in spermatogenesis. The functional mechanisms utilized by RBPs within the cell are outlined in depth, and the significance of sub-cellular localization and stage-specific expression in relation to the mode and impact of posttranscriptional regulation is also highlighted. We emphasize the historical role of the Musashi family of RBPs in stem cell function and cell fate determination, as originally characterized in Drosophila and Xenopus, and conclude with our current understanding of the differential roles and functions of the mammalian Musashi proteins, Musashi-1 and Musashi-2, with a primary focus on our findings in spermatogenesis. This review highlights both the essential contribution of RBPs to posttranscriptional regulation and the importance of the Musashi family as master regulators of male gamete development.
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Affiliation(s)
| | | | | | - Eileen A McLaughlin
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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The mRNA cap-binding protein Cbc1 is required for high and timely expression of genes by promoting the accumulation of gene-specific activators at promoters. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:405-19. [PMID: 26775127 DOI: 10.1016/j.bbagrm.2016.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/15/2022]
Abstract
The highly conserved Saccharomyces cerevisiae cap-binding protein Cbc1/Sto1 binds mRNA co-transcriptionally and acts as a key coordinator of mRNA fate. Recently, Cbc1 has also been implicated in transcription elongation and pre-initiation complex (PIC) formation. Previously, we described Cbc1 to be required for cell growth under osmotic stress and to mediate osmostress-induced translation reprogramming. Here, we observe delayed global transcription kinetics in cbc1Δ during osmotic stress that correlates with delayed recruitment of TBP and RNA polymerase II to osmo-induced promoters. Interestingly, we detect an interaction between Cbc1 and the MAPK Hog1, which controls most gene expression changes during osmostress, and observe that deletion of CBC1 delays the accumulation of the activator complex Hot1-Hog1 at osmostress promoters. Additionally, CBC1 deletion specifically reduces transcription rates of highly transcribed genes under non-stress conditions, such as ribosomal protein (RP) genes, while having low impact on transcription of weakly expressed genes. For RP genes, we show that recruitment of the specific activator Rap1, and subsequently TBP, to promoters is Cbc1-dependent. Altogether, our results indicate that binding of Cbc1 to the capped mRNAs is necessary for the accumulation of specific activators as well as PIC components at the promoters of genes whose expression requires high and rapid transcription.
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35
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Fox MJ, Mosley AL. Rrp6: Integrated roles in nuclear RNA metabolism and transcription termination. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:91-104. [PMID: 26612606 DOI: 10.1002/wrna.1317] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 11/08/2022]
Abstract
The yeast RNA exosome is a eukaryotic ribonuclease complex essential for RNA processing, surveillance, and turnover. It is comprised of a barrel-shaped core and cap as well as a 3'-5' ribonuclease known as Dis3 that contains both endo- and exonuclease domains. A second exonuclease, Rrp6, is added in the nucleus. Dis3 and Rrp6 have both shared and distinct roles in RNA metabolism, and this review will focus primarily on Rrp6 and the roles of the RNA exosome in the nucleus. The functions of the nuclear exosome are modulated by cofactors and interacting partners specific to each type of substrate. Generally, the cofactor TRAMP (Trf4/5-Air2/1-Mtr4 polyadenylation) complex helps unwind unstable RNAs, RNAs requiring processing such as rRNAs, tRNAs, or snRNAs or improperly processed RNAs and direct it toward the exosome. In yeast, Rrp6 interacts with Nrd1, the cap-binding complex, and RNA polymerase II to aid in nascent RNA processing, termination, and polyA tail length regulation. Recent studies have shown that proper termination and processing of short, noncoding RNAs by Rrp6 is particularly important for transcription regulation across the genome and has important implications for regulation of diverse processes at the cellular level. Loss of proper Rrp6 and exosome activity may contribute to various pathologies such as autoimmune disease, neurological disorders, and cancer. WIREs RNA 2016, 7:91-104. doi: 10.1002/wrna.1317 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Melanie J Fox
- Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - Amber L Mosley
- Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
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36
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Mutagenesis of ARS2 Domains To Assess Possible Roles in Cell Cycle Progression and MicroRNA and Replication-Dependent Histone mRNA Biogenesis. Mol Cell Biol 2015; 35:3753-67. [PMID: 26303529 DOI: 10.1128/mcb.00272-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
ARS2 is a regulator of RNA polymerase II transcript processing through its role in the maturation of distinct nuclear cap-binding complex (CBC)-controlled RNA families. In this study, we examined ARS2 domain function in transcript processing. Structural modeling based on the plant ARS2 orthologue, SERRATE, revealed 2 previously uncharacterized domains in mammalian ARS2: an N-terminal domain of unknown function (DUF3546), which is also present in SERRATE, and an RNA recognition motif (RRM) that is present in metazoan ARS2 but not in plants. Both the DUF3546 and zinc finger domain (ZnF) were required for association with microRNA and replication-dependent histone mRNA. Mutations in the ZnF disrupted interaction with FLASH, a key component in histone pre-mRNA processing. Mutations targeting the Mid domain implicated it in DROSHA interaction and microRNA biogenesis. The unstructured C terminus was required for interaction with the CBC protein CBP20, while the RRM was required for cell cycle progression and for binding to FLASH. Together, our results support a bridging model in which ARS2 plays a central role in RNA recognition and processing through multiple protein and RNA interactions.
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37
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Shi Y, Manley JL. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev 2015; 29:889-97. [PMID: 25934501 PMCID: PMC4421977 DOI: 10.1101/gad.261974.115] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Recent studies have significantly reshaped current models for the protein–RNA interactions involved in poly(A) site recognition. Here, Shi and Manley review the recent advances in this area and provide a perspective for future studies. The key RNA sequence elements and protein factors necessary for 3′ processing of polyadenylated mRNA precursors are well known. Recent studies, however, have significantly reshaped current models for the protein–RNA interactions involved in poly(A) site recognition, painting a picture more complex than previously envisioned and also providing new insights into regulation of this important step in gene expression. Here we review the recent advances in this area and provide a perspective for future studies.
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Affiliation(s)
- Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California at Irvine, Irvine, California 92697, USA;
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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38
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Gunawardana D, Domashevskiy AV, Gayler KR, Goss DJ. Efficient preparation and properties of mRNAs containing a fluorescent cap analog: Anthraniloyl-m(7)GpppG. ACTA ACUST UNITED AC 2015; 3:e988538. [PMID: 26779415 DOI: 10.4161/21690731.2014.988538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/30/2014] [Accepted: 11/12/2014] [Indexed: 11/19/2022]
Abstract
A method has been developed for synthesising fluorescently labeled capped mRNA. The method incorporates a single fluorescent molecule as part of the 5'-mRNA or oligonucleotide cap site. The fluorescent molecule, Ant-m(7)GTP is specifically incorporated into the cap site to yield Ant-m(7)GpppG-capped mRNA or oligonucleotide. Efficient capping was observed with 60-100% of the RNA transcripts capped with the fluorescent molecule. The Ant-m(7)G derivative, which has been previously shown to interact with the eukaryotic cap binding protein eIF4E, is shown in this paper to be a substrate for the Vaccinia capping enzyme and the DCP2 decapping enzyme from Arabidopsis. Further, the Ant-m(7)GTP-capped RNA is readily translated. This Ant-m(7)GTP-capped RNA provides an important tool for monitoring capping reactions, translation, and biophysical studies.
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Affiliation(s)
- Dilantha Gunawardana
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne, Parkville; Victoria, Australia; Present address: Department of Botany; University of Sri Jayewardenepura; Soratha Mawatha, Nugegoda, Sri Lanka
| | - Artem V Domashevskiy
- Department of Sciences; John Jay College of Criminal Justice; City University of New York ; New York, NY USA
| | - Ken R Gayler
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne, Parkville ; Victoria, Australia
| | - Dixie J Goss
- Department of Chemistry and Graduate Center; Hunter College; City University of New York ; New York, NY USA
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Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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40
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Gonatopoulos-Pournatzis T, Cowling VH. Cap-binding complex (CBC). Biochem J 2014. [PMID: 24354960 DOI: 10.1042/bj2013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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Affiliation(s)
| | - Victoria H Cowling
- *MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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41
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Müller-McNicoll M, Neugebauer KM. Good cap/bad cap: how the cap-binding complex determines RNA fate. Nat Struct Mol Biol 2014; 21:9-12. [DOI: 10.1038/nsmb.2751] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Putting an 'End' to HIV mRNAs: capping and polyadenylation as potential therapeutic targets. AIDS Res Ther 2013; 10:31. [PMID: 24330569 PMCID: PMC3874655 DOI: 10.1186/1742-6405-10-31] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/26/2013] [Indexed: 01/27/2023] Open
Abstract
Like most cellular mRNAs, the 5′ end of HIV mRNAs is capped and the 3′ end matured by the process of polyadenylation. There are, however, several rather unique and interesting aspects of these post-transcriptional processes on HIV transcripts. Capping of the highly structured 5′ end of HIV mRNAs is influenced by the viral TAT protein and a population of HIV mRNAs contains a trimethyl-G cap reminiscent of U snRNAs involved in splicing. HIV polyadenylation involves active repression of a promoter-proximal polyadenylation signal, auxiliary upstream regulatory elements and moonlighting polyadenylation factors that have additional impacts on HIV biology outside of the constraints of classical mRNA 3’ end formation. This review describes these post-transcriptional novelties of HIV gene expression as well as their implications in viral biology and as possible targets for therapeutic intervention.
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The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat Struct Mol Biol 2013; 20:1367-76. [PMID: 24270879 PMCID: PMC3923317 DOI: 10.1038/nsmb.2703] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/04/2013] [Indexed: 11/29/2022]
Abstract
Nuclear processing and quality control of eukaryotic RNA is mediated by the RNA exosome, which is regulated by accessory factors. However, the mechanism of exosome recruitment to its ribonucleoprotein (RNP) targets remains poorly understood. Here we disclose a physical link between the human exosome and the cap-binding complex (CBC). The CBC associates with the ARS2 protein to form CBC-ARS2 (CBCA), and then further connects together with the ZC3H18 protein to the nuclear exosome targeting (NEXT) complex, forming CBC-NEXT (CBCN). RNA immunoprecipitation using CBCN factors as well as the analysis of combinatorial depletion of CBCN and exosome components underscore the functional relevance of CBC-exosome bridging at the level of target RNA. Specifically, CBCA suppresses read-through products of several RNA families by promoting their transcriptional termination. We suggest that the RNP 5′cap links transcription termination to exosomal RNA degradation via CBCN.
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Hallais M, Pontvianne F, Andersen PR, Clerici M, Lener D, Benbahouche NEH, Gostan T, Vandermoere F, Robert MC, Cusack S, Verheggen C, Jensen TH, Bertrand E. CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing. Nat Struct Mol Biol 2013; 20:1358-66. [PMID: 24270878 DOI: 10.1038/nsmb.2720] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/24/2013] [Indexed: 02/07/2023]
Abstract
The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small, capped RNAs such as pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, ARS2 and PHAX, and show that both CBCAP and CBC-ARS2 complexes can be reconstituted from recombinant proteins. ARS2 stimulates PHAX binding to the CBC and snRNA 3'-end processing, thereby coupling maturation with export. In vivo, CBC and ARS2 bind similar capped noncoding and coding RNAs and stimulate their 3'-end processing. The strongest effects are for cap-proximal polyadenylation sites, and this favors premature transcription termination. ARS2 functions partly through the mRNA 3'-end cleavage factor CLP1, which binds RNA Polymerase II through PCF11. ARS2 is thus a major CBC effector that stimulates functional and cryptic 3'-end processing sites.
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Affiliation(s)
- Marie Hallais
- Equipe labellisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
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Ghulam MM, Courtois F, Lerbs-Mache S, Merendino L. Complex processing patterns of mRNAs of the large ATP synthase operon in Arabidopsis chloroplasts. PLoS One 2013; 8:e78265. [PMID: 24223785 PMCID: PMC3817242 DOI: 10.1371/journal.pone.0078265] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/09/2013] [Indexed: 02/03/2023] Open
Abstract
Chloroplasts are photosynthetic cell organelles which have evolved from endosymbiosis of the cyanobacterial ancestor. In chloroplasts, genes are still organized into transcriptional units as in bacteria but the corresponding poly-cistronic mRNAs undergo complex processing events, including inter-genic cleavage and 5′ and 3′ end-definition. The current model for processing proposes that the 3′ end of the upstream cistron transcripts and the 5′ end of the downstream cistron transcripts are defined by the same RNA-binding protein and overlap at the level of the protein-binding site. We have investigated the processing mechanisms that operate within the large ATP synthase (atp) operon, in Arabidopsis thaliana chloroplasts. This operon is transcribed by the plastid-encoded RNA polymerase starting from two promoters, which are upstream and within the operon, respectively, and harbors four potential sites for RNA-binding proteins. In order to study the functional significance of the promoters and the protein-binding sites for the maturation processes, we have performed a detailed mapping of the atp transcript ends. Our data indicate that in contrast to maize, atpI and atpH transcripts with overlapping ends are very rare in Arabidopsis. In addition, atpA mRNAs, which overlap with atpF mRNAs, are even truncated at the 3′ end, thus representing degradation products. We observe, instead, that the 5′ ends of nascent poly-cistronic atp transcripts are defined at the first protein-binding site which follows either one of the two transcription initiation sites, while the 3′ ends are defined at the subsequent protein-binding sites or at hairpin structures that are encountered by the progressing RNA polymerase. We conclude that the overlapping mechanisms of mRNA protection have only a limited role in obtaining stable processed atp mRNAs in Arabidopsis. Our findings suggest that during evolution of different plant species as maize and Arabidopsis, chloroplasts have evolved multiple strategies to produce mature transcripts suitable for translation.
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Affiliation(s)
- Mustafa Malik Ghulam
- Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, CNRS, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, DSV, iRTSV, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, USC1359, INRA, Grenoble, France
| | - Florence Courtois
- Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, CNRS, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, DSV, iRTSV, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, USC1359, INRA, Grenoble, France
| | - Silva Lerbs-Mache
- Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, CNRS, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, DSV, iRTSV, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, USC1359, INRA, Grenoble, France
| | - Livia Merendino
- Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168, CNRS, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, DSV, iRTSV, Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, USC1359, INRA, Grenoble, France
- * E-mail:
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A novel role for Cet1p mRNA 5'-triphosphatase in promoter proximal accumulation of RNA polymerase II in Saccharomyces cerevisiase. Genetics 2013; 196:161-76. [PMID: 24172134 DOI: 10.1534/genetics.113.158535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yeast mRNA 5'-triphosphatase, Cet1p, recognizes phosphorylated-RNA polymerase II as a component of capping machinery via Ceg1p for cotranscriptional formation of mRNA cap structure that recruits cap-binding complex (CBC) and protects mRNA from exonucleases. Here, we show that the accumulation of RNA polymerase II at the promoter proximal site of ADH1 is significantly enhanced in the absence of Cet1p. Similar results are also found at other genes. Cet1p is recruited to the 5' end of the coding sequence, and its absence impairs mRNA capping, and hence CBC recruitment. However, such an impaired recruitment of CBC does not enhance promoter proximal accumulation of RNA polymerase II. Thus, Cet1p specifically lowers the accumulation of RNA polymerase II at the promoter proximal site independently of mRNA cap structure or CBC. Further, we show that Cet1p's N-terminal domain, which is not involved in mRNA capping, decreases promoter proximal accumulation of RNA polymerase II. An accumulation of RNA polymerase II at the promoter proximal site in the absence of Cet1p's N-terminal domain is correlated with reduced transcription. Collectively, our results demonstrate a novel role of Cet1p in regulation of promoter proximal accumulation of RNA polymerase II independently of mRNA capping activity, and hence transcription in vivo.
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Pabis M, Neufeld N, Steiner MC, Bojic T, Shav-Tal Y, Neugebauer KM. The nuclear cap-binding complex interacts with the U4/U6·U5 tri-snRNP and promotes spliceosome assembly in mammalian cells. RNA (NEW YORK, N.Y.) 2013; 19:1054-63. [PMID: 23793891 PMCID: PMC3708526 DOI: 10.1261/rna.037069.112] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 04/24/2013] [Indexed: 05/23/2023]
Abstract
The nuclear cap-binding complex (CBC) binds to the 7-methyl guanosine cap present on every RNA polymerase II transcript. CBC has been implicated in many aspects of RNA biogenesis; in addition to roles in miRNA biogenesis, nonsense-mediated decay, 3'-end formation, and snRNA export from the nucleus, CBC promotes pre-mRNA splicing. An unresolved question is how CBC participates in splicing. To investigate CBC's role in splicing, we used mass spectrometry to identify proteins that copurify with mammalian CBC. Numerous components of spliceosomal snRNPs were specifically detected. Among these, three U4/U6·U5 snRNP proteins (hBrr2, hPrp4, and hPrp31) copurified with CBC in an RNA-independent fashion, suggesting that a significant fraction of CBC forms a complex with the U4/U6·U5 snRNP and that the activity of CBC might be associated with snRNP recruitment to pre-mRNA. To test this possibility, CBC was depleted from HeLa cells by RNAi. Chromatin immunoprecipitation and live-cell imaging assays revealed decreased cotranscriptional accumulation of U4/U6·U5 snRNPs on active transcription units, consistent with a requirement for CBC in cotranscriptional spliceosome assembly. Surprisingly, recruitment of U1 and U2 snRNPs was also affected, indicating that RNA-mediated interactions between CBC and snRNPs contribute to splicing. On the other hand, CBC depletion did not impair snRNP biogenesis, ruling out the possibility that decreased snRNP recruitment was due to changes in nuclear snRNP concentration. Taken together, the data support a model whereby CBC promotes pre-mRNA splicing through a network of interactions with and among spliceosomal snRNPs during cotranscriptional spliceosome assembly.
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Affiliation(s)
- Marta Pabis
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Noa Neufeld
- The Mina & Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Michaela C. Steiner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Teodora Bojic
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Karla M. Neugebauer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. Mol Cell 2013; 50:104-15. [PMID: 23523372 DOI: 10.1016/j.molcel.2013.02.017] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 01/24/2013] [Accepted: 02/14/2013] [Indexed: 12/27/2022]
Abstract
Recently, we reported that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5' end-capped messenger RNAs (mRNAs). Here, we report that their mammalian homolog, Dom3Z (referred to as DXO), possesses pyrophosphohydrolase, decapping, and 5'-to-3' exoribonuclease activities. Surprisingly, we found that DXO preferentially degrades defectively capped pre-mRNAs in cells. Additional studies show that incompletely capped pre-mRNAs are inefficiently spliced at all introns, a fact that contrasts with current understanding, and are also poorly cleaved for polyadenylation. Crystal structures of DXO in complex with substrate mimic and products at a resolution of up to 1.5Å provide elegant insights into the catalytic mechanism and molecular basis for their three apparently distinct activities. Our data reveal a pre-mRNA 5' end capping quality control mechanism in mammalian cells, indicating DXO as the central player for this mechanism, and demonstrate an unexpected intimate link between proper 5' end capping and subsequent pre-mRNA processing.
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Abstract
RNAs containing a variety of terminal and internal modifications can be produced using bacteriophage polymerases often with a few simple adjustments to standard transcription protocols. RNAs containing a single phosphate or a cap structure at their 5' ends can readily be generated either co-transcriptionally or through enzymatic treatments of transcription products. Likewise, a variety of modified bases, including fluorescent or biotinylated species, can be effectively incorporated co-transcriptionally. The key to effective co-transcriptional incorporation lies in determining the efficiency of incorporation of modified base relative to its standard counterpart. Finally, an approach to place a poly(A) tail at the exact 3' end of a desired transcription product is presented. Collectively, these protocols allow one to synthesize RNAs with a variety of modifications to serve as versatile molecules to analyze biological questions.
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Rehfeld A, Plass M, Krogh A, Friis-Hansen L. Alterations in polyadenylation and its implications for endocrine disease. Front Endocrinol (Lausanne) 2013; 4:53. [PMID: 23658553 PMCID: PMC3647115 DOI: 10.3389/fendo.2013.00053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms with different 3' untranslated regions (3' UTRs) and in some cases different coding regions. Two thirds of all human genes undergo APA. The efficiency of the polyadenylation process regulates gene expression and APA plays an important part in post-transcriptional regulation, as the 3' UTR contains various cis-elements associated with post-transcriptional regulation, such as target sites for micro-RNAs and RNA-binding proteins. Implications of alterations in polyadenylation for endocrine disease: Alterations in polyadenylation have been found to be causative of neonatal diabetes and IPEX (immune dysfunction, polyendocrinopathy, enteropathy, X-linked) and to be associated with type I and II diabetes, pre-eclampsia, fragile X-associated premature ovarian insufficiency, ectopic Cushing syndrome, and many cancer diseases, including several types of endocrine tumor diseases. PERSPECTIVES Recent developments in high-throughput sequencing have made it possible to characterize polyadenylation genome-wide. Antisense elements inhibiting or enhancing specific poly(A) site usage can induce desired alterations in polyadenylation, and thus hold the promise of new therapeutic approaches. SUMMARY This review gives a detailed description of alterations in polyadenylation in endocrine disease, an overview of the current literature on polyadenylation and summarizes the clinical implications of the current state of research in this field.
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Affiliation(s)
- Anders Rehfeld
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
| | - Mireya Plass
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Anders Krogh
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Lennart Friis-Hansen
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
- *Correspondence: Lennart Friis-Hansen, Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 4113, Blegdamsvej 9, DK2100 Copenhagen, Denmark. e-mail:
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