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Nguyen LAC, Mori M, Yasuda Y, Galipon J. Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol 2023; 43:611-628. [PMID: 37937348 PMCID: PMC10761120 DOI: 10.1080/10985549.2023.2270406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Glucose is a major source of carbon and essential for the survival of many organisms, ranging from yeast to human. A sudden 60-fold reduction of glucose in exponentially growing fission yeast induces transcriptome-wide changes in gene expression. This regulation is multilayered, and the boundaries of transcripts are known to vary, with functional consequences at the protein level. By combining direct RNA sequencing with 5'-CAGE and short-read sequencing, we accurately defined the 5'- and 3'-ends of transcripts that are both poly(A) tailed and 5'-capped in glucose starvation, followed by proteome analysis. Our results confirm previous experimentally validated loci with alternative isoforms and reveal several transcriptome-wide patterns. First, we show that sense-antisense gene pairs are more strongly anticorrelated when a time lag is taken into account. Second, we show that the glucose starvation response initially elicits a shortening of 3'-UTRs and poly(A) tails, followed by a shortening of the 5'-UTRs at later time points. These result in domain gains and losses in proteins involved in the stress response. Finally, the relatively poor overlap both between differentially expressed genes (DEGs), differential transcript usage events (DTUs), and differentially detected proteins (DDPs) highlight the need for further study on post-transcriptional regulation mechanisms in glucose starvation.
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Affiliation(s)
- Lan Anh Catherine Nguyen
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Institute of Innovation for Future Society, Nagoya University, Aichi, Nagoya, Japan
| | - Yuji Yasuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Faculty of Environment and Information Studies, Keio University, Kanagawa, Fujisawa, Japan
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Graduate School of Science and Engineering, Yamagata University, Yamagata, Yonezawa, Japan
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Nanopore Direct RNA Sequencing of Monosome- and Polysome-Bound RNA. Methods Mol Biol 2023; 2632:281-297. [PMID: 36781736 DOI: 10.1007/978-1-0716-2996-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Polysome fractionation makes use of density gradients and ultracentrifugation to separate transcripts based on their specific number of bound ribosomes, and can be combined with downstream analysis such as cDNA-seq (commonly known as RNA-seq), microarray analysis, RT-qPCR, or Northern blotting. Here, we describe the application of Nanopore direct RNA sequencing to quantify monosome- and polysome-bound full-length transcripts after polysome fractionation, RNA cleanup, and size selection, using the yeast glucose stress response as an example use case.
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Li J, Liu X, Yin Z, Hu Z, Zhang KQ. An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi. Front Microbiol 2021; 12:638617. [PMID: 33995298 PMCID: PMC8113380 DOI: 10.3389/fmicb.2021.638617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
For decades, more and more long non-coding RNAs (lncRNAs) have been confirmed to play important functions in key biological processes of different organisms. At present, most identified lncRNAs and those with known functional roles are from mammalian systems. However, lncRNAs have also been found in primitive eukaryotic fungi, and they have different functions in fungal development, metabolism, and pathogenicity. In this review, we highlight some recent researches on lncRNAs in the primitive eukaryotic fungi, particularly focusing on the identification of lncRNAs and their regulatory roles in diverse biological processes.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiaoying Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ziyu Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhihong Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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A current view on long noncoding RNAs in yeast and filamentous fungi. Appl Microbiol Biotechnol 2018; 102:7319-7331. [PMID: 29974182 PMCID: PMC6097775 DOI: 10.1007/s00253-018-9187-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are crucial players in epigenetic regulation. They were initially discovered in human, yet they emerged as common factors involved in a number of central cellular processes in several eukaryotes. For example, in the past decade, research on lncRNAs in yeast has steadily increased. Several examples of lncRNAs were described in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Also, screenings for lncRNAs in ascomycetes were performed and, just recently, the first full characterization of a lncRNA was performed in the filamentous fungus Trichoderma reesei. In this review, we provide a broad overview about currently known fugal lncRNAs. We make an attempt to categorize them according to their functional context, regulatory strategies or special properties. Moreover, the potential of lncRNAs as a biotechnological tool is discussed.
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Chen C, Xu G, Yuan K, Sun Y, Bao G, Xu D, Cui Z. Transcriptional analysis of long non-coding RNAs in facet joint osteoarthritis. RSC Adv 2018; 8:33695-33701. [PMID: 35548800 PMCID: PMC9086565 DOI: 10.1039/c8ra04809f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/18/2018] [Accepted: 09/24/2018] [Indexed: 11/21/2022] Open
Abstract
It is recognized that facet joint osteoarthritis (FJOA) is commonly induced by the degeneration of articular cartilage of the facet joint.
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Affiliation(s)
- Chu Chen
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Guanhua Xu
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Kun Yuan
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Yuyu Sun
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Guofeng Bao
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Dawei Xu
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Zhiming Cui
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
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Adachi A, Senmatsu S, Asada R, Abe T, Hoffman CS, Ohta K, Hirota K. Interplay between chromatin modulators and histone acetylation regulates the formation of accessible chromatin in the upstream regulatory region of fission yeast fbp1. Genes Genet Syst 2017; 92:267-276. [PMID: 28674280 DOI: 10.1266/ggs.17-00018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Numerous noncoding RNA transcripts are detected in eukaryotic cells. Noncoding RNAs transcribed across gene promoters are involved in the regulation of mRNA transcription via chromatin modulation. This function of noncoding RNA transcription was first demonstrated for the fission yeast fbp1 gene, where a cascade of noncoding RNA transcription events induces chromatin remodeling to facilitate transcription factor binding. We recently demonstrated that the noncoding RNAs from the fbp1 upstream region facilitate binding of the transcription activator Atf1 and thereby promote histone acetylation. Histone acetylation by histone acetyl transferases (HATs) and ATP-dependent chromatin remodelers (ADCRs) are implicated in chromatin remodeling, but the interplay between HATs and ADCRs in this process has not been fully elucidated. Here, we examine the roles played by two distinct ADCRs, Snf22 and Hrp3, and by the HAT Gcn5 in the transcriptional activation of fbp1. Snf22 and Hrp3 redundantly promote disassembly of chromatin in the fbp1 upstream region. Gcn5 critically contributes to nucleosome eviction in the absence of either Snf22 or Hrp3, presumably by recruiting Hrp3 in snf22∆ cells and Snf22 in hrp3∆ cells. Conversely, Gcn5-dependent histone H3 acetylation is impaired in snf22∆/hrp3∆ cells, suggesting that both redundant ADCRs induce recruitment of Gcn5 to the chromatin array in the fbp1 upstream region. These results reveal a previously unappreciated interplay between ADCRs and histone acetylation in which histone acetylation facilitates recruitment of ADCRs, while ADCRs are required for histone acetylation.
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Affiliation(s)
- Akira Adachi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Satoshi Senmatsu
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Ryuta Asada
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | | | - Kunihiro Ohta
- Department of Life Sciences, The University of Tokyo
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University
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Cai X, Qian C, Wu W, Lei H, Ding Q, Zou W, Xiang D, Wang X. An exonic missense mutation c.28G>A is associated with weak B blood group by affecting RNA splicing of the ABO gene. Transfusion 2017; 57:2140-2149. [PMID: 28653406 DOI: 10.1111/trf.14209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 05/08/2017] [Accepted: 05/11/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND The amino acid substitutions caused by ABO gene mutations are usually predicted to impact glycosyltransferase's function or its biosynthesis. Here we report an ABO exonic missense mutation that affects B-antigen expression by decreasing the mRNA level of the ABO gene rather than the amino acid change. STUDY DESIGN AND METHODS Serologic studies including plasma total GTB transfer capacity were performed. The exon sequences of the ABO gene were analyzed by Sanger sequencing. B310 cDNA with c.28G>A (p.G10R) mutation was expressed in HeLa cells and total GTB transfer capacity in cell supernatant was measured. Flow cytometry was performed on these HeLa cells after transfection, and agglutination of Hela-Bweak cells was also examined. The mRNA of the ABO gene was analyzed by direct sequencing and real-time reverse transcriptase-polymerase chain reaction. A minigene construct was prepared to evaluate the potential of splicing. RESULTS While plasma total GTB transfer capacity was undetectable in this B3 -like individual, the relative percentage of antigen-expressing cells and mean fluorescence index of the Bweak red blood cells (RBCs) were 19 and 14% of normal B RBCs, respectively. There was no significant difference of total GTB transfer capacity in cell supernatant and B-antigen expression on cell surfaces between HeLa cells transfected with B310 cDNA and B cDNA. The mRNA expression level of B310 in peripheral whole blood was significantly reduced. The amount of splicing is significantly lower in c.28G>A construct compared to that in wild-type construct after transfection in K562 cells. CONCLUSION ABO c.28G>A mutation may cause B3 -like subgroup by affecting RNA splicing of the ABO gene.
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Affiliation(s)
- Xiaohong Cai
- Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Chengrui Qian
- Blood Group Reference Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Wenman Wu
- Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Hang Lei
- Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Qiulan Ding
- Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zou
- Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
| | - Dong Xiang
- Blood Group Reference Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Xuefeng Wang
- Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China
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