1
|
Cao J, Kuyumcu-Martinez MN. Alternative polyadenylation regulation in cardiac development and cardiovascular disease. Cardiovasc Res 2023; 119:1324-1335. [PMID: 36657944 PMCID: PMC10262186 DOI: 10.1093/cvr/cvad014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 01/21/2023] Open
Abstract
Cleavage and polyadenylation of pre-mRNAs is a necessary step for gene expression and function. Majority of human genes exhibit multiple polyadenylation sites, which can be alternatively used to generate different mRNA isoforms from a single gene. Alternative polyadenylation (APA) of pre-mRNAs is important for the proteome and transcriptome landscape. APA is tightly regulated during development and contributes to tissue-specific gene regulation. Mis-regulation of APA is linked to a wide range of pathological conditions. APA-mediated gene regulation in the heart is emerging as a new area of research. Here, we will discuss the impact of APA on gene regulation during heart development and in cardiovascular diseases. First, we will briefly review how APA impacts gene regulation and discuss molecular mechanisms that control APA. Then, we will address APA regulation during heart development and its dysregulation in cardiovascular diseases. Finally, we will discuss pre-mRNA targeting strategies to correct aberrant APA patterns of essential genes for the treatment or prevention of cardiovascular diseases. The RNA field is blooming due to advancements in RNA-based technologies. RNA-based vaccines and therapies are becoming the new line of effective and safe approaches for the treatment and prevention of human diseases. Overall, this review will be influential for understanding gene regulation at the RNA level via APA in the heart and will help design RNA-based tools for the treatment of cardiovascular diseases in the future.
Collapse
Affiliation(s)
- Jun Cao
- Faculty of Environment and Life, Beijing University of Technology, Xueyuan Road, Haidian District, Beijing 100124, PR China
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
| |
Collapse
|
2
|
Zhang J, Zhang X, Zou Y, Han F. CPSF1 mediates retinal vascular dysfunction in diabetes mellitus via the MAPK/ERK pathway. Arch Physiol Biochem 2022; 128:708-715. [PMID: 32046510 DOI: 10.1080/13813455.2020.1722704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This study investigated the expression and underlying molecular mechanism of CPSF1 in diabetic retinopathy. Streptozotocin (STZ)-induced Sprague-Dawley (SD) rats were employed as a diabetic model, and high-glucose (HG)-induced human retinal vascular endothelial cells (HRVECs)were used as an in vitro experimental model to explore the effect of CPSF1. The results showed that CPSF1 was downregulated in diabetic retinopathy (DR) tissues and HRVECs under HG conditions. Adeno-associated viral CPSF1 attenuated histological abnormalities of retinas. CPSF1 regulates the apoptosis, migration, and vascularisation of HRVECs under HG conditions in vitro. CPSF1 mediates retinal vascular dysfunction by suppressing the phosphorylation mechanism in the mitogen-activated protein kinase/extracellular-signal-regulated kinase (MAPK/ERK) pathway in DR. In conclusion, CPSF1 may be associated with the development of DR, and upregulated CPSF1 alleviates apoptosis and migration via MAPK/ERK pathway.
Collapse
Affiliation(s)
- Jingyi Zhang
- The Second Department of Ophthalmology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Xi Zhang
- The Second Department of Ophthalmology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Yuanyuan Zou
- The Second Department of Ophthalmology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Fengmei Han
- The Second Department of Ophthalmology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| |
Collapse
|
3
|
Chhipi-Shrestha JK, Schneider-Poetsch T, Suzuki T, Mito M, Khan K, Dohmae N, Iwasaki S, Yoshida M. Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns. Cell Chem Biol 2022; 29:259-275.e10. [PMID: 34520743 PMCID: PMC8857039 DOI: 10.1016/j.chembiol.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/10/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
Chemical splicing modulators that bind to the spliceosome have provided an attractive avenue for cancer treatment. Splicing modulators induce accumulation and subsequent translation of a subset of intron-retained mRNAs. However, the biological effect of proteins containing translated intron sequences remains unclear. Here, we identify a number of truncated proteins generated upon treatment with the splicing modulator spliceostatin A (SSA) via genome-wide ribosome profiling and bio-orthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry. A subset of these truncated proteins has intrinsically disordered regions, forms insoluble cellular condensates, and triggers the proteotoxic stress response through c-Jun N-terminal kinase (JNK) phosphorylation, thereby inhibiting the mTORC1 pathway. In turn, this reduces global translation. These findings indicate that creating an overburden of condensate-prone proteins derived from introns represses translation and prevents further production of harmful truncated proteins. This mechanism appears to contribute to the antiproliferative and proapoptotic activity of splicing modulators.
Collapse
Affiliation(s)
- Jagat K. Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Khalid Khan
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| |
Collapse
|
4
|
Kikuchi K, Kaida D. CCNE1 and E2F1 Partially Suppress G1 Phase Arrest Caused by Spliceostatin A Treatment. Int J Mol Sci 2021; 22:ijms222111623. [PMID: 34769053 PMCID: PMC8584075 DOI: 10.3390/ijms222111623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023] Open
Abstract
The potent splicing inhibitor spliceostatin A (SSA) inhibits cell cycle progression at the G1 and G2/M phases. We previously reported that upregulation of the p27 cyclin-dependent kinase inhibitor encoded by CDKN1B and its C-terminal truncated form, namely p27*, which is translated from CDKN1B pre-mRNA, is one of the causes of G1 phase arrest caused by SSA treatment. However, the detailed molecular mechanism underlying G1 phase arrest caused by SSA treatment remains to be elucidated. In this study, we found that SSA treatment caused the downregulation of cell cycle regulators, including CCNE1, CCNE2, and E2F1, at both the mRNA and protein levels. We also found that transcription elongation of the genes was deficient in SSA-treated cells. The overexpression of CCNE1 and E2F1 in combination with CDKN1B knockout partially suppressed G1 phase arrest caused by SSA treatment. These results suggest that the downregulation of CCNE1 and E2F1 contribute to the G1 phase arrest induced by SSA treatment, although they do not exclude the involvement of other factors in SSA-induced G1 phase arrest.
Collapse
Affiliation(s)
- Kei Kikuchi
- School of Medicine, University of Toyama, Toyama 930-0194, Japan;
| | - Daisuke Kaida
- Faculty of Medicine, Academic Assembly, University of Toyama, Toyama 930-0194, Japan
- Correspondence:
| |
Collapse
|
5
|
Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
Collapse
Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| |
Collapse
|
6
|
Deng K, Yao J, Huang J, Ding Y, Zuo J. Abnormal alternative splicing promotes tumor resistance in targeted therapy and immunotherapy. Transl Oncol 2021; 14:101077. [PMID: 33774500 PMCID: PMC8039720 DOI: 10.1016/j.tranon.2021.101077] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Abnormal alternative splicing is involve in abnormal expression of genes in cancer. Abnormal alternative splicing events promote malignant progression of cancer. Abnormal alternative splicing develops tumor resistance to targeted therapy by changing the target point and signal transduction pathway. Abnormal alternative splicing develops tumor resistance to immunotherapy by changing cell surface antigens and protein structure.
Abnormally alternative splicing events are common hallmark of diverse types of cancers. Splicing variants with aberrant functions play an important role in cancer development. Most importantly, a growing body of evidence has supported that alternative splicing might play a significant role in the therapeutic resistance of tumors. Targeted therapy and immunotherapy are the future directions of tumor therapy; however, the loss of antigen targets on the tumor cells surface and alterations in drug efficacy have resulted in the failure of targeted therapy and immunotherapy. Interestingly, abnormal alternative splicing, as a strategy to regulate gene expression, is reportedly involved in the reprogramming of cell signaling pathways and epitopes on the tumor cell surface by changing splicing patterns of genes, thus rendering tumors resisted to targeted therapy and immunotherapy. Accordingly, increased knowledge regarding abnormal alternative splicing in tumors may help predict therapeutic resistance during targeted therapy and immunotherapy and lead to novel therapeutic approaches in cancer. Herein, we provide a brief synopsis of abnormal alternative splicing events in cancer progression and therapeutic resistance.
Collapse
Affiliation(s)
- Kun Deng
- The Laboratory of translational medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang, Hunan 421001, P R China
| | - Jingwei Yao
- The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan 421002, P R China
| | - Jialu Huang
- The Laboratory of translational medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang, Hunan 421001, P R China
| | - Yubo Ding
- The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan 421002, P R China
| | - Jianhong Zuo
- The Laboratory of translational medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang, Hunan 421001, P R China; The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan 421002, P R China; Clinical Laboratory, The Third Affiliated Hospital of University of South China, Hengyang, Hunan 421900, China.
| |
Collapse
|
7
|
Schneider-Poetsch T, Chhipi-Shrestha JK, Yoshida M. Splicing modulators: on the way from nature to clinic. J Antibiot (Tokyo) 2021; 74:603-616. [PMID: 34345042 PMCID: PMC8472923 DOI: 10.1038/s41429-021-00450-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Over the course of more than two decades, natural products isolated from various microorganisms and plants have built the foundation for chemical biology research into the mechanism of pre-mRNA splicing. Hand in hand with advances in scientific methodology small molecule splicing modulators have become powerful tools for investigating, not just the splicing mechanism, but also the cellular effect of altered mRNA processing. Based on thorough structure-activity studies, synthetic analogues have moved on from scientific tool compounds to experimental drugs. With current advances in drug discovery methodology and new means of attacking targets previously thought undruggable, we can expect further advances in both research and therapeutics based on small molecule splicing modulators.
Collapse
Affiliation(s)
- Tilman Schneider-Poetsch
- grid.509461.fChemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan
| | | | - Minoru Yoshida
- grid.509461.fChemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo Japan
| |
Collapse
|
8
|
Kim Guisbert KS, Mossiah I, Guisbert E. Titration of SF3B1 Activity Reveals Distinct Effects on the Transcriptome and Cell Physiology. Int J Mol Sci 2020; 21:ijms21249641. [PMID: 33348896 PMCID: PMC7766730 DOI: 10.3390/ijms21249641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/16/2022] Open
Abstract
SF3B1 is a core component of the U2 spliceosome that is frequently mutated in cancer. We have previously shown that titrating the activity of SF3B1, using the inhibitor pladienolide B (PB), affects distinct steps of the heat shock response (HSR). Here, we identify other genes that are sensitive to different levels of SF3B1 (5 vs. 100 nM PB) using RNA sequencing. Significant changes to mRNA splicing were identified at both low PB and high PB concentrations. Changes in expression were also identified in the absence of alternative splicing, suggesting that SF3B1 influences other gene expression pathways. Surprisingly, gene expression changes identified in low PB are not predictive of changes in high PB. Specific pathways were identified with differential sensitivity to PB concentration, including nonsense-mediated decay and protein-folding homeostasis, both of which were validated using independent reporter constructs. Strikingly, cells exposed to low PB displayed enhanced protein-folding capacity relative to untreated cells. These data reveal that the transcriptome is exquisitely sensitive to SF3B1 and suggests that the activity of SF3B1 is finely regulated to coordinate mRNA splicing, gene expression and cellular physiology.
Collapse
|
9
|
Muraoka S, Fukumura K, Hayashi M, Kataoka N, Mayeda A, Kaida D. Rbm38 Reduces the Transcription Elongation Defect of the SMEK2 Gene Caused by Splicing Deficiency. Int J Mol Sci 2020; 21:ijms21228799. [PMID: 33233740 PMCID: PMC7699959 DOI: 10.3390/ijms21228799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/14/2020] [Accepted: 11/19/2020] [Indexed: 11/30/2022] Open
Abstract
Pre-mRNA splicing is an essential mechanism for ensuring integrity of the transcriptome in eukaryotes. Therefore, splicing deficiency might cause a decrease in functional proteins and the production of nonfunctional, aberrant proteins. To prevent the production of such aberrant proteins, eukaryotic cells have several mRNA quality control mechanisms. In addition to the known mechanisms, we previously found that transcription elongation is attenuated to prevent the accumulation of pre-mRNA under splicing-deficient conditions. However, the detailed molecular mechanism behind the defect in transcription elongation remains unknown. Here, we showed that the RNA binding protein Rbm38 reduced the transcription elongation defect of the SMEK2 gene caused by splicing deficiency. This reduction was shown to require the N- and C-terminal regions of Rbm38, along with an important role being played by the RNA-recognition motif of Rbm38. These findings advance our understanding of the molecular mechanism of the transcription elongation defect caused by splicing deficiency.
Collapse
Affiliation(s)
- Shintaro Muraoka
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; (S.M.); (M.H.)
| | - Kazuhiro Fukumura
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan; (K.F.); (A.M.)
| | - Megumi Hayashi
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; (S.M.); (M.H.)
| | - Naoyuki Kataoka
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan; (K.F.); (A.M.)
| | - Daisuke Kaida
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; (S.M.); (M.H.)
- Correspondence:
| |
Collapse
|
10
|
Takeuchi A, Iida K, Tsubota T, Hosokawa M, Denawa M, Brown JB, Ninomiya K, Ito M, Kimura H, Abe T, Kiyonari H, Ohno K, Hagiwara M. Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain. Cell Rep 2019; 23:1326-1341. [PMID: 29719248 DOI: 10.1016/j.celrep.2018.03.141] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/19/2018] [Accepted: 03/30/2018] [Indexed: 12/13/2022] Open
Abstract
Genes specifically expressed in neurons contain members with extended long introns. Longer genes present a problem with respect to fulfilment of gene length transcription, and evidence suggests that dysregulation of long genes is a mechanism underlying neurodegenerative and psychiatric disorders. Here, we report the discovery that RNA-binding protein Sfpq is a critical factor for maintaining transcriptional elongation of long genes. We demonstrate that Sfpq co-transcriptionally binds to long introns and is required for sustaining long-gene transcription by RNA polymerase II through mediating the interaction of cyclin-dependent kinase 9 with the elongation complex. Phenotypically, Sfpq disruption caused neuronal apoptosis in developing mouse brains. Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases. The identified molecular machinery yields directions for targeted investigations of the association between long-gene transcriptopathy and neuronal diseases.
Collapse
Affiliation(s)
- Akihide Takeuchi
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kei Iida
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Toshiaki Tsubota
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - J B Brown
- Laboratory for Molecular Biosciences, Life Science Informatics Research Unit, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takaya Abe
- Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Hiroshi Kiyonari
- Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan; Animal Resource Development Unit, R IKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| |
Collapse
|
11
|
Targeting cleavage and polyadenylation specific factor 1 via shRNA inhibits cell proliferation in human ovarian cancer. J Biosci 2018; 42:417-425. [PMID: 29358555 DOI: 10.1007/s12038-017-9701-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cleavage and polyadenylation specificity factor 1 (CPSF1), a member of CPSF complex, has been reported to play a key role in pre-mRNA 3'-end formation, but its possible role in ovarian cancer remains unclear. In the present study, we found the mRNA level of CPSF1 was overexpressed in ovarian cancer tissues using Oncomine Cancer Microarray database. Then the loss-of-function assays, including CCK-8, colony formation and flow cytometry assays, were performed to determine the effects of CPSF1 on cell viability, proliferation, cell cycle and apoptosis of human ovarian cancer cell lines (SKOV-3 and OVCAR-3). The results indicated that depletion of CPSF1 suppressed cell viability, impaired colony formation ability, induced cell cycle arrest at G0/G1 phase and promoted cell apoptosis in ovarian cancer cells. Furthermore, knockdown of CPSF1 upregulated the expression of cleaved caspase-3 and PARP and downregulated CDK4/cyclin D1 expression. These data suggested that CPSF1 could promote ovarian cancer cell growth and proliferation in vitro and its depletion might serve as a potential therapeutic target for human ovarian cancer.
Collapse
|
12
|
Schneider-Poetsch T, Yoshida M. Along the Central Dogma-Controlling Gene Expression with Small Molecules. Annu Rev Biochem 2018; 87:391-420. [PMID: 29727582 DOI: 10.1146/annurev-biochem-060614-033923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation. Small molecules offer significant advantages over genetic tools, as they allow inhibiting a process at any desired time point, whereas mutating or altering the gene of an important regulator would likely result in a dead organism. With the advent of modern sequencing technology, it has become possible to monitor global cellular effects of small-molecule treatment and thereby overcome the limitations of classical biochemistry, which usually looks at a biological system in isolation. This review focuses on several molecules, especially natural products, that have played an important role in dissecting gene expression and have opened up new fields of investigation as well as clinical venues for disease treatment.
Collapse
Affiliation(s)
- Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan;
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan; .,Department of Biotechnology, University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
13
|
Overexpression of USP39 predicts poor prognosis and promotes tumorigenesis of prostate cancer via promoting EGFR mRNA maturation and transcription elongation. Oncotarget 2017; 7:22016-30. [PMID: 26959883 PMCID: PMC5008341 DOI: 10.18632/oncotarget.7882] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/23/2016] [Indexed: 12/14/2022] Open
Abstract
Castration resistance is a serious problem facing clinical treatment of prostate cancer (PCa). The underlying molecular mechanisms of acquired proliferation ability of tumor cells upon androgen deprivation are largely undetermined. In the present study, we identified that ubiquitin specific peptidase 39 (USP39) was significantly upregulated in PCa samples and cell lines. Elevated USP39 expression was positively correlated with Gleason score, predicted a poor outcome, and functioned as an independent risk factor for biochemical recurrence (BCR) especially in patients with a Gleason score ≤7. Our cell-based study showed that the expression level of USP39 was the highest in AR-negative PCa cell lines. Knockdown of USP39 in PCa cells inhibited cancer colony formation and tumor cell growth, and induced G2/M arrest and cell apoptosis. Microarray analysis suggested that knockdown of USP39 caused a reduced expression of EGFR. Silencing of USP39 inhibited the expression of EGFR 3′-end, and presented a remarkable block to the maturation of EGFR mRNA, suggesting that silencing of USP39 decreased the transcriptional elongation and maturation of EGFR mRNA. Oncomine datasets analysis showed that USP39 expression was positively correlated with EGFR level. The above findings suggest that USP39 plays a vital oncogenic role in the tumorigenesis of PCa and may prove to be a potential biomarker for predicting the prognosis of PCa patients.
Collapse
|
14
|
Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP. Nat Commun 2017; 8:2100. [PMID: 29235465 PMCID: PMC5727392 DOI: 10.1038/s41467-017-02007-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/30/2017] [Indexed: 01/21/2023] Open
Abstract
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3′ splice sites to these drugs. Sequences 5′ from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs. Drug-induced exon skipping preferentially affects shorter alternatively spliced regions with weaker BPs. Remarkably, structurally similar drugs display both common and differential effects on splicing regulation, SSA generally displaying stronger effects on intron retention, and Sudemycins more acute effects on exon skipping. Collectively, our results illustrate how splicing modulation is exquisitely sensitive to the sequence context of 3′ splice sites and to small structural differences between drugs. Several families of natural compounds target core components of the pre-mRNA splicing machinery and display anti-tumor activity. Here the authors show that particular sequence features can be linked to drug response, and that drugs with very similar chemical structures display substantially different effects on splicing regulation.
Collapse
|
15
|
Pham D, Koide K. Discoveries, target identifications, and biological applications of natural products that inhibit splicing factor 3B subunit 1. Nat Prod Rep 2017; 33:637-47. [PMID: 26812544 DOI: 10.1039/c5np00110b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Covering: 1992 to 2015The natural products FR901464, pladienolide, and herboxidiene were discovered as activators of reporter gene systems. Unexpectedly, these compounds target neither transcription nor translation; rather, they target splicing factor 3B subunit 1 of the spliceosome, causing changes in splicing patterns. All of them showed anticancer activity in a low nanomolar range. Since their discovery, these molecules have been used in a variety of biological applications.
Collapse
Affiliation(s)
- Dianne Pham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
| |
Collapse
|
16
|
Gotic I, Schibler U. Posttranscriptional mechanisms controlling diurnal gene expression cycles by body temperature rhythms. RNA Biol 2017; 14:1294-1298. [PMID: 28267416 DOI: 10.1080/15476286.2017.1285481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
In mammals, body temperature oscillates in a daily fashion around a set point of 36°C-37°C. These fluctuations are controlled by the circadian master clock residing in the brain's suprachiasmatic nucleus and, despite their small amplitudes, contribute to the diurnal expression of genes throughout the organism. By focusing on the mechanisms underlying the temperature-dependent accumulation of the cold-inducible RNA-binding protein CIRBP - a factor involved in the tuning of amplitude and phase in circadian clocks of peripheral tissues - we have recently identified a novel mechanism governing temperature-dependent gene expression. This mechanism involves the differential spicing efficiency of primary RNA transcripts under different temperature conditions and thereby determines the fraction of Cirbp pre-mRNA processed into mature mRNA. A genome-wide transcriptome analysis revealed that this mechanism affects the output of hundreds of genes. Here we discuss our findings and future directions toward the identification of specific factors and parameters governing temperature-sensitive splicing efficacy.
Collapse
Affiliation(s)
- Ivana Gotic
- a Department of Molecular Biology , University of Geneva, Quai Ernest-Ansermet , Geneva , Switzerland
| | - Ueli Schibler
- a Department of Molecular Biology , University of Geneva, Quai Ernest-Ansermet , Geneva , Switzerland
| |
Collapse
|
17
|
Yoshimoto R, Kaida D, Furuno M, Burroughs AM, Noma S, Suzuki H, Kawamura Y, Hayashizaki Y, Mayeda A, Yoshida M. Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA (NEW YORK, N.Y.) 2017; 23:47-57. [PMID: 27754875 PMCID: PMC5159648 DOI: 10.1261/rna.058065.116] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/03/2016] [Indexed: 05/27/2023]
Abstract
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA's antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B pre-mRNA, which is involved in SSA-induced cell-cycle arrest. However, it is still unclear whether pre-mRNAs are uniformly exported from the nucleus following SSA treatment. We performed RNA-seq analysis on nuclear and cytoplasmic fractions of SSA-treated cells. Our statistical analyses showed that intron retention is the major consequence of SSA treatment, and a small number of intron-containing pre-mRNAs leak into the cytoplasm. Using a series of reporter plasmids to investigate the roles of intronic sequences in the pre-mRNA leakage, we showed that the strength of the 5' splice site affects pre-mRNA leakage. Additionally, we found that the level of pre-mRNA leakage is related to transcript length. These results suggest that the strength of the 5' splice site and the length of the transcripts are determinants of the pre-mRNA leakage induced by SF3b inhibitors.
Collapse
Affiliation(s)
- Rei Yoshimoto
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Daisuke Kaida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Frontier Research Core for Life Sciences, University of Toyama, Toyama-shi, Toyama 930-0194, Japan
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama-shi, Toyama 930-0194, Japan
| | - Masaaki Furuno
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - A Maxwell Burroughs
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Shohei Noma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Kawamura
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Japan Science and Technology Corporation, CREST Research Project, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
18
|
Gotic I, Omidi S, Fleury-Olela F, Molina N, Naef F, Schibler U. Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp. Genes Dev 2016; 30:2005-17. [PMID: 27633015 PMCID: PMC5066242 DOI: 10.1101/gad.287094.116] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/19/2016] [Indexed: 12/28/2022]
Abstract
Gotic et al. show that the temperature-dependent accumulation of cold-inducible RNA-binding protein (Cirbp) mRNA is controlled primarily by the regulation of splicing efficiency. As revealed by genome-wide “approach-to-steady-state” kinetics, this post-transcriptional mechanism is widespread in the temperature-dependent control of gene expression. In mammals, body temperature fluctuates diurnally around a mean value of 36°C–37°C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, likely, animals. Here we studied the mechanisms responsible for the temperature-dependent expression of cold-inducible RNA-binding protein (CIRBP). In NIH3T3 fibroblasts exposed to simulated mouse body temperature cycles, Cirbp mRNA oscillates about threefold in abundance, as it does in mouse livers. This daily mRNA accumulation cycle is directly controlled by temperature oscillations and does not depend on the cells’ circadian clocks. Here we show that the temperature-dependent accumulation of Cirbp mRNA is controlled primarily by the regulation of splicing efficiency, defined as the fraction of Cirbp pre-mRNA processed into mature mRNA. As revealed by genome-wide “approach to steady-state” kinetics, this post-transcriptional mechanism is widespread in the temperature-dependent control of gene expression.
Collapse
Affiliation(s)
- Ivana Gotic
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Saeed Omidi
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Fabienne Fleury-Olela
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Nacho Molina
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ueli Schibler
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| |
Collapse
|
19
|
Ahn JH, Rechsteiner A, Strome S, Kelly WG. A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans. PLoS Genet 2016; 12:e1006227. [PMID: 27541139 PMCID: PMC4991786 DOI: 10.1371/journal.pgen.1006227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023] Open
Abstract
The elongation phase of transcription by RNA Polymerase II (Pol II) involves numerous events that are tightly coordinated, including RNA processing, histone modification, and chromatin remodeling. RNA splicing factors are associated with elongating Pol II, and the interdependent coupling of splicing and elongation has been documented in several systems. Here we identify a conserved, multi-domain cyclophilin family member, SIG-7, as an essential factor for both normal transcription elongation and co-transcriptional splicing. In embryos depleted for SIG-7, RNA levels for over a thousand zygotically expressed genes are substantially reduced, Pol II becomes significantly reduced at the 3' end of genes, marks of transcription elongation are reduced, and unspliced mRNAs accumulate. Our findings suggest that SIG-7 plays a central role in both Pol II elongation and co-transcriptional splicing and may provide an important link for their coordination and regulation.
Collapse
Affiliation(s)
- Jeong H. Ahn
- Biology Department, Emory University, Atlanta, Georgia, United States of America
- Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, United States of America
| | - Andreas Rechsteiner
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - William G. Kelly
- Biology Department, Emory University, Atlanta, Georgia, United States of America
| |
Collapse
|
20
|
Koga M, Hayashi M, Kaida D. Splicing inhibition decreases phosphorylation level of Ser2 in Pol II CTD. Nucleic Acids Res 2015. [PMID: 26202968 PMCID: PMC4787822 DOI: 10.1093/nar/gkv740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Phosphorylation of the C-terminal domain of the largest subunit of RNA polymerase II (Pol II), especially Ser2 and Ser5 residues, plays important roles in transcription and mRNA processing, including 5′ end capping, splicing and 3′ end processing. These phosphorylation events stimulate mRNA processing, however, it is not clear whether splicing activity affects the phosphorylation status of Pol II. In this study, we found that splicing inhibition by potent splicing inhibitors spliceostatin A (SSA) and pladienolide B or by antisense oligos against snRNAs decreased phospho-Ser2 level, but had little or no effects on phospho-Ser5 level. In contrast, transcription and translation inhibitors did not decrease phospho-Ser2 level, therefore inhibition of not all the gene expression processes cause the decrease of phospho-Ser2. SSA treatment caused early dissociation of Pol II and decrease in phospho-Ser2 level of chromatin-bound Pol II, suggesting that splicing inhibition causes downregulation of phospho-Ser2 through at least these two mechanisms.
Collapse
Affiliation(s)
- Mitsunori Koga
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Megumi Hayashi
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-0194, Japan
| |
Collapse
|