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Ntasis VF, Guigó R. Studying relative RNA localization From nucleus to the cytosol. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583744. [PMID: 38559161 PMCID: PMC10979850 DOI: 10.1101/2024.03.06.583744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The precise coordination of important biological processes, such as differentiation and development, is highly dependent on the regulation of expression of the genetic information. The flow of the genetic information is tightly regulated on multiple levels. Among them, RNA export to cytosol is an essential step for the production of proteins in eukaryotic cells. Hence, estimating the relative concentration of RNA molecules of a given transcript species in the nucleus and in the cytosol is of major significance as it contributes to the understanding of the dynamics of RNA trafficking between the nucleus and the cytosol. The most efficient way to estimate the levels of RNA species genome-wide is through RNA sequencing (RNAseq). While RNAseq can be performed separately in the nucleus and in the cytosol, because measured transcript levels are relative to the total volume of RNA in these compartments, and because this volume is usually unknown, the transcript levels in the nucleus and in the cytosol cannot be directly compared. Here we show theoretically that if, in addition to nuclear and cytosolic RNA-seq, whole cell RNA-seq is also performed, then accurate estimations of the localization of transcripts can be obtained. Based on this, we designed a method that estimates, first the fraction of the total RNA volume in the cytosol (nucleus), and then, this fraction for every transcript. We evaluate our methodology on simulated data and nuclear and cytosolic single cell data available. Finally, we use our method to investigate the cellular localization of transcripts using bulk RNAseq data from the ENCODE project.
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Affiliation(s)
- Vasilis F. Ntasis
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
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Fujiwara N, Shigemoto M, Hirayama M, Fujita KI, Seno S, Matsuda H, Nagahama M, Masuda S. MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus. Nucleic Acids Res 2022; 50:8779-8806. [PMID: 35902094 PMCID: PMC9410898 DOI: 10.1093/nar/gkac559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/10/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here, we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent substrate decay by the human exosome. Using RNA polymerase II-transcribed poly(A)+ substrate accumulation as an indicator of a perturbed exosome, we found functional redundancy between RRP6 and MPP6 in the decay of these poly(A)+ transcripts. MTR4 binding to the exosome core via MPP6 was essential for MPP6 to exert its redundancy with RRP6. However, at least for the decay of our identified exosome substrates, MTR4 recruitment by MPP6 was not functionally equivalent to recruitment by RRP6. Genome-wide classification of substrates based on their sensitivity to each exosome component revealed that MPP6 deals with a specific range of substrates and highlights the importance of MTR4 for their decay. Considering recent findings of competitive binding to the exosome between auxiliary complexes, our results suggest that the MPP6-incorporated MTR4-exosome complex is one of the multiple alternative complexes rather than the prevailing one.
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Affiliation(s)
- Naoko Fujiwara
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Maki Shigemoto
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Mizuki Hirayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Ken-Ichi Fujita
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan.,Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Seiji Masuda
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan.,Department of Food Science and Nutrition, Faculty of Agriculture Kindai University, Nara, Nara 631-8505, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Nara 631-8505, Japan.,Antiaging center, Kindai University, Higashiosaka, Osaka 577-8502, Japan
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Wang F, Chen S, Zheng H, Guo B. Design of an Intron-Retained Bioluminescence Reporter and its Application in Imaging of Pre-mRNA Splicing in Living Subjects. Methods Mol Biol 2022; 2524:209-221. [PMID: 35821474 DOI: 10.1007/978-1-0716-2453-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aberrant splicing of precursor messenger RNA (pre-mRNA) can generate abnormal transcripts, and most of the human diseases have been shown to associate with abnormal splicing of pre-mRNA. Conventional methods require sample lysis and thus cannot be used for monitoring pre-mRNA splicing in real time. This chapter guides how to develop an intron-retained bioluminescence (BL) reporter, which simulates the splicing process of pre-mRNA in vitro and in vivo noninvasively. In the following, we illustrate the design and construction of RLuc-intron and the methods of BL experiments in vitro and in vivo. The exemplified results show that our reporter is suitable for high-throughput screening of splicing inhibitors for the therapies of the diseases caused by aberrant splicing.
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Affiliation(s)
- Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China.
- Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China.
| | - Si Chen
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
| | - Haifeng Zheng
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
| | - Bin Guo
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China
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Miyake S, Masuda S. Inhibition of mitochondrial complex III or dihydroorotate dehydrogenase (DHODH) triggers formation of poly(A) + RNA foci adjacent to nuclear speckles following activation of ATM (ataxia telangiectasia mutated). RNA Biol 2022; 19:1244-1255. [PMID: 36412986 PMCID: PMC9683070 DOI: 10.1080/15476286.2022.2146919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intracellular and intercellular signalling networks play an essential role in optimizing cellular homoeostasis and are thought to be partly reflected in nuclear mRNA dynamics. However, the regulation of nuclear mRNA dynamics by intracellular and intercellular signals remains largely unexplored, and research tools are lacking. Through an original screening based on the mRNA metabolic mechanism, we discovered that eight well-known inhibitors cause significant nuclear poly(A)+ RNA accumulation. Among these inhibitors, we discovered a new mRNA metabolic response in which the addition of antimycin A, an inhibitor of mitochondrial respiratory-chain complex III (complex III), resulted in a marked accumulation of poly(A)+ RNA near the nuclear speckles. Furthermore, dihydroorotate dehydrogenase (DHODH) inhibitors, a rate-limiting enzyme in the intracellular de novo pyrimidine synthesis reaction that specifically exchanges electrons with complex III, also caused a remarkable accumulation of nuclear poly(A)+ RNA adjacent to the nuclear speckles, which was abolished by extracellular uridine supply, indicating that the depletion of intracellular pyrimidine affects poly(A)+ RNA metabolism. Further analysis revealed that ataxia telangiectasia mutated (ATM), a serine and threonine kinase and a master regulator of DNA double-strand break (DSB) and nucleolar stress, is required for this poly(A)+ RNA nuclear accumulation phenomenon. This study reports new insights into novel aspects of nuclear poly(A)+ RNA metabolism, especially the relationship between mitochondrial respiratory-chain functions, pyrimidine metabolism, and nuclear RNA metabolism.
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Affiliation(s)
- Shuntaro Miyake
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Japan,Department of Food Science and Nutrition, Faculty of Agriculture, Kindai University, Nara, Japan,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan,Antiaging Center, Kindai University, Higashiosaka, Japan,CONTACT Seiji Masuda Department of Food Science and Nutrition, Faculty of Agriculture, Kindai University, Nara631-8505, Japan
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Kurata M, Fujiwara N, Fujita KI, Yamanaka Y, Seno S, Kobayashi H, Miyamae Y, Takahashi N, Shibuya Y, Masuda S. Food-Derived Compounds Apigenin and Luteolin Modulate mRNA Splicing of Introns with Weak Splice Sites. iScience 2019; 22:336-352. [PMID: 31809999 PMCID: PMC6909097 DOI: 10.1016/j.isci.2019.11.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/23/2019] [Accepted: 11/15/2019] [Indexed: 01/08/2023] Open
Abstract
Cancer cells often exhibit extreme sensitivity to splicing inhibitors. We identified food-derived flavonoids, apigenin and luteolin, as compounds that modulate mRNA splicing at the genome-wide level, followed by proliferation inhibition. They bind to mRNA splicing-related proteins to induce a widespread change of splicing patterns in treated cells. Their inhibitory activity on splicing is relatively moderate, and introns with weak splice sites tend to be sensitive to them. Such introns remain unspliced, and the resulting intron-containing mRNAs are retained in the nucleus, resulting in the nuclear accumulation of poly(A)+ RNAs in these flavonoid-treated cells. Tumorigenic cells are more susceptible to these flavonoids than nontumorigenic cells, both for the nuclear poly(A)+ RNA-accumulating phenotype and cell viability. This study illustrates the possible mechanism of these flavonoids to suppress tumor progression in vivo that were demonstrated by previous studies and provides the potential of daily intake of moderate splicing inhibitors to prevent cancer development. Food-derived compounds, apigenin and luteolin, modulate mRNA splicing The treatment of these flavonoids causes numerous alternative splicing events Splicing of introns with weak splice sites tend to be inhibited by these flavonoids Tumorigenic cells are more sensitive to these flavonoids than non-tumorigenic cells
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Affiliation(s)
- Masashi Kurata
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan
| | - Naoko Fujiwara
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ken-Ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yasutaka Yamanaka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yusaku Miyamae
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Nobuyuki Takahashi
- Department of Nutritional Science and Food Safety, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yasuyuki Shibuya
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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Kurata M, Murata Y, Momma K, Fouad Ali Mursi I, Takahashi M, Miyamae Y, Kambe T, Nagao M, Narita H, Shibuya Y, Masuda S. The isoflavone fraction from soybean presents mRNA maturation inhibition activity. Biosci Biotechnol Biochem 2017; 81:551-554. [PMID: 27776450 DOI: 10.1080/09168451.2016.1249451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/05/2016] [Indexed: 01/29/2023]
Abstract
Recent findings indicate that mRNA splicing inhibitors can be potential anticancer candidates. We have previously established a screening system which monitors mRNA processing in order to identify mRNA processing inhibitors. Among a number of dietary resources, isoflavone fractions showed an inhibitory effect of mRNA processing. These findings demonstrate that a variety of dietary sources have an impact on mRNA biogenesis.
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Affiliation(s)
- Masashi Kurata
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
- b Department of Oral and Maxillofacial Surgery , Graduate School of Medical Sciences, Nagoya City University , Nagoya , Japan
| | - Yuki Murata
- c Department of Food and Nutrition , Kyoto Women's University , Kyoto , Japan
| | - Keiko Momma
- d Department of Living and Welfare , Kyoto Women's University , Kyoto , Japan
| | - Intisar Fouad Ali Mursi
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Masakazu Takahashi
- e Department of Bioscience , Fukui Prefectural University , Fukui , Japan
| | - Yusaku Miyamae
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Taiho Kambe
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Masaya Nagao
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Hiroshi Narita
- c Department of Food and Nutrition , Kyoto Women's University , Kyoto , Japan
| | - Yasuyuki Shibuya
- b Department of Oral and Maxillofacial Surgery , Graduate School of Medical Sciences, Nagoya City University , Nagoya , Japan
| | - Seiji Masuda
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
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7
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Establishment of a Monitoring System to Detect Inhibition of mRNA Processing. Biosci Biotechnol Biochem 2012; 76:1248-51. [DOI: 10.1271/bbb.120226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Aihara Y, Fujiwara N, Yamazaki T, Kambe T, Nagao M, Hirose Y, Masuda S. Enhancing recombinant protein production in human cell lines with a constitutive transport element and mRNA export proteins. J Biotechnol 2011; 153:86-91. [PMID: 21473891 DOI: 10.1016/j.jbiotec.2011.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 03/05/2011] [Accepted: 03/29/2011] [Indexed: 11/16/2022]
Abstract
Recent research into mRNA maturation processes in the nucleus has identified a number of proteins involved in mRNA transcription, capping, splicing, end processing and export. Among them, the Tap-p15 heterodimer acts as an mRNA export receptor. Tap-p15 is recruited onto fully processed mRNA in the nucleus, which is ready for export to the cytoplasm, through associating with Aly or SR proteins on mRNA, or by directly associating with a constitutive transport element (CTE), an RNA element derived from type D retroviruses. mRNA containing a CTE is exported to the cytoplasm by directly associating with Tap-p15, even in the absence of Tap-recruiting proteins such as Aly or SR proteins on the mRNA. Here, we showed that the use of a CTE enhanced the expression of recombinant protein in human cell lines. The co-expression of reporter proteins and Tap-p15 also enhanced recombinant protein expression. Moreover, the use of a CTE and Tap-p15 synergistically further enhanced the recombinant protein expression. In addition to Tap-p15, several Tap-p15-recruiting proteins, including Aly and SR proteins, enhanced recombinant protein expression, albeit independently of the CTE. The incorporation of a CTE and Tap-p15-recruiting proteins into protein expression system is useful to increase recombinant protein yield in human cells.
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Affiliation(s)
- Yuki Aihara
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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