1
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Nan Y, Luo Q, Wu X, Chang W, Zhao P, Liu S, Liu Z. HCP5 prevents ubiquitination-mediated UTP3 degradation to inhibit apoptosis by activating c-Myc transcriptional activity. Mol Ther 2023; 31:552-568. [PMID: 36245126 PMCID: PMC9931552 DOI: 10.1016/j.ymthe.2022.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/06/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Inducing cancer cell apoptosis through cytotoxic reagents is the main therapeutic strategy for diverse cancer types. However, several antiapoptotic factors impede curative cancer therapy by driving cancer cells to resist cytotoxic agent-induced apoptosis, thus leading to refractoriness and relapse. To define critical antiapoptotic factors that contribute to chemoresistance in esophageal squamous cell carcinoma (ESCC), we generated two pairs of parental and apoptosis-resistant cell models through cisplatin (DDP) induction and then performed whole-transcriptome sequencing. We identified the long noncoding RNA (lncRNA) histocompatibility leukocyte antigen complex P5 (HCP5) as the chief culprit for chemoresistance. Mechanistically, HCP5 interacts with UTP3 small subunit processome component (UTP3) and prevents UTP3 degradation from E3 ligase tripartite motif containing 29 (TRIM29)-mediated ubiquitination. UTP3 then recruits c-Myc to activate vesicle-associated membrane protein 3 (VAMP3) expression. Activated VAMP3 suppresses caspase-dependent apoptosis and eventually leads to chemoresistance. Accordingly, the expression level of the HCP5/UTP3/c-Myc/VAMP3 axis in chemoresistant patients is significantly higher than that in chemosensitive patients. Thus, our study demonstrated that the HCP5/UTP3/c-Myc/VAMP3 axis plays an important role in the inhibition of cancer cell apoptosis and that HCP5 may be a promising chemosensitivity target for cancer treatment.
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Affiliation(s)
- Yabing Nan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qingyu Luo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiaowei Wu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wan Chang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Pengfei Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shi Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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2
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Crlz-1 Homozygous Null Knockout Mouse Embryos Are Lethally Stopped in Their Early Development. Genes (Basel) 2022; 13:genes13030511. [PMID: 35328065 PMCID: PMC8951461 DOI: 10.3390/genes13030511] [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: 02/24/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Although the conditional gene knockout (KO) is a better choice for observing its phenotype in a specific cell, tissue, and/or organ, the simple null gene KO could nevertheless be attempted initially to scan its overall phenotypes at the level of the whole-body system, especially for a new gene such as Crlz-1. Therefore, with a hope to glean phenotypic clues for Crlz-1 at the whole-body system, we attempted to generate its null KO mice. Contrary to our original desire, Crlz-1 homozygous null KO mice were not born. However, in the chasing of their homozygous KO embryos, they were found to be lethally impaired from early development, remaining in a state of small globular mass without ever leading to a body shape, indicating the critical role of Crlz-1 as a Wnt target gene for the proliferation and/or differentiation of cells during early mouse embryonic development.
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3
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Measuring the buffering capacity of gene silencing in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2021; 118:2111841118. [PMID: 34857629 PMCID: PMC8670432 DOI: 10.1073/pnas.2111841118] [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] [Accepted: 10/16/2021] [Indexed: 11/18/2022] Open
Abstract
Gene silencing, once established, is stably maintained for several generations. Despite the high fidelity of the inheritance of the silent state, individual components of silenced chromatin are in constant flux. Models suggest that silent loci can tolerate fluctuations in Sir proteins and histone acetylation levels, but the level of tolerance is unknown. To understand the quantitative relationships between H4K16 acetylation, Sir proteins, and silencing, we developed assays to quantitatively alter a H4K16 acetylation mimic allele and Sir protein levels and measure the effects of these changes on silencing. Our data suggest that a two- to threefold change in levels of histone marks and specific Sir proteins affects the stability of the silent state of a large chromatin domain. Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.
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4
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Zhao S, Huang D, Peng J. Nucleolus-localized Def-CAPN3 protein degradation pathway and its role in cell cycle control and ribosome biogenesis. J Genet Genomics 2021; 48:955-960. [PMID: 34452850 DOI: 10.1016/j.jgg.2021.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/25/2022]
Abstract
The nucleolus, as the 'nucleus of the nucleus', is a prominent subcellular organelle in a eukaryocyte. The nucleolus serves as the centre for ribosome biogenesis, as well as an important site for cell-cycle regulation, cellular senescence, and stress response. The protein composition of the nucleolus changes dynamically through protein turnover to meet the needs of cellular activities or stress responses. Recent studies have identified a nucleolus-localized protein degradation pathway in zebrafish and humans, namely the Def-CAPN3 pathway, which is essential to ribosome production and cell-cycle progression, by controlling the turnover of multiple substrates (e.g., ribosomal small-subunit [SSU] processome component Mpp10, transcription factor p53, check-point proteins Chk1 and Wee1). This pathway relies on the Ca2+-dependent cysteine proteinase CAPN3 and is independent of the ubiquitin-mediated proteasome pathway. CAPN3 is recruited by nucleolar protein Def from cytoplasm to nucleolus, where it proteolyzes its substrates which harbor a CAPN3 recognition-motif. Def depletion leads to the exclusion of CAPN3 and accumulation of p53, Wee1, Chk1, and Mpp10 in the nucleolus that result in cell-cycle arrest and rRNA processing abnormality. Here, we summarize the discovery of the Def-CAPN3 pathway and propose its biological role in cell-cycle control and ribosome biogenesis.
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Affiliation(s)
- Shuyi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Delai Huang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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5
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Zhao S, Chen Y, Chen F, Huang D, Shi H, Lo LJ, Chen J, Peng J. Sas10 controls ribosome biogenesis by stabilizing Mpp10 and delivering the Mpp10-Imp3-Imp4 complex to nucleolus. Nucleic Acids Res 2019; 47:2996-3012. [PMID: 30773582 PMCID: PMC6451133 DOI: 10.1093/nar/gkz105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 01/29/2019] [Accepted: 02/09/2019] [Indexed: 01/19/2023] Open
Abstract
Mpp10 forms a complex with Imp3 and Imp4 that serves as a core component of the ribosomal small subunit (SSU) processome. Mpp10 also interacts with the nucleolar protein Sas10/Utp3. However, it remains unknown how the Mpp10-Imp3-Imp4 complex is delivered to the nucleolus and what biological function the Mpp10-Sas10 complex plays. Here, we report that the zebrafish Mpp10 and Sas10 are conserved nucleolar proteins essential for the development of the digestive organs. Mpp10, but not Sas10/Utp3, is a target of the nucleolus-localized Def-Capn3 protein degradation pathway. Sas10 protects Mpp10 from Capn3-mediated cleavage by masking the Capn3-recognition site on Mpp10. Def interacts with Sas10 to form the Def-Sas10-Mpp10 complex to facilitate the Capn3-mediated cleavage of Mpp10. Importantly, we found that Sas10 determines the nucleolar localization of the Mpp10-Imp3-Imp4 complex. In conclusion, Sas10 is essential not only for delivering the Mpp10-Imp3-Imp4 complex to the nucleolus for assembling the SSU processome but also for fine-tuning Mpp10 turnover in the nucleolus during organogenesis.
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Affiliation(s)
- Shuyi Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yayue Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
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6
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Sá-Moura B, Kornprobst M, Kharde S, Ahmed YL, Stier G, Kunze R, Sinning I, Hurt E. Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. PLoS One 2017; 12:e0183272. [PMID: 28813493 PMCID: PMC5558966 DOI: 10.1371/journal.pone.0183272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/01/2017] [Indexed: 11/29/2022] Open
Abstract
In eukaryotes, ribosome assembly is a highly complex process that involves more than 200 assembly factors that ensure the folding, modification and processing of the different rRNA species as well as the timely association of ribosomal proteins. One of these factors, Mpp10 associates with Imp3 and Imp4 to form a complex that is essential for the normal production of the 18S rRNA. Here we report the crystal structure of a complex between Imp4 and a short helical element of Mpp10 to a resolution of 1.88 Å. Furthermore, we extend the interaction network of Mpp10 and characterize two novel interactions. Mpp10 is able to bind the ribosome biogenesis factor Utp3/Sas10 through two conserved motifs in its N-terminal region. In addition, Mpp10 interacts with the ribosomal protein S5/uS7 using a short stretch within an acidic loop region. Thus, our findings reveal that Mpp10 provides a platform for the simultaneous interaction with multiple proteins in the 90S pre-ribosome.
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Affiliation(s)
- Bebiana Sá-Moura
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Markus Kornprobst
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Satyavati Kharde
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Yasar Luqman Ahmed
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Gunter Stier
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Ruth Kunze
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Irmgard Sinning
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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7
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Chen YJC, Wang HJ, Jauh GY. Dual Role of a SAS10/C1D Family Protein in Ribosomal RNA Gene Expression and Processing Is Essential for Reproduction in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006408. [PMID: 27792779 PMCID: PMC5085252 DOI: 10.1371/journal.pgen.1006408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022] Open
Abstract
In eukaryotic cells, ribosomal RNAs (rRNAs) are transcribed, processed, and assembled with ribosomal proteins in the nucleolus. Regulatory mechanisms of rRNA gene (rDNA) transcription and processing remain elusive in plants, especially their connection to nucleolar organization. We performed an in silico screen for essential genes of unknown function in Arabidopsis thaliana and identified Thallo (THAL) encoding a SAS10/C1D family protein. THAL disruption caused enlarged nucleoli in arrested embryos, aberrant processing of precursor rRNAs at the 5' External Transcribed Spacer, and repression of the major rDNA variant (VAR1). THAL overexpression lines showed de-repression of VAR1 and overall reversed effects on rRNA processing sites. Strikingly, THAL overexpression also induced formation of multiple nucleoli per nucleus phenotypic of mutants of heterochromatin factors. THAL physically associated with histone chaperone Nucleolin 1 (NUC1), histone-binding NUC2, and histone demethylase Jumonji 14 (JMJ14) in bimolecular fluorescence complementation assay, suggesting that it participates in chromatin regulation. Furthermore, investigation of truncated THAL proteins revealed that the SAS10 C-terminal domain is likely important for its function in chromatin configuration. THAL also interacted with putative Small Subunit processome components, including previously unreported Arabidopsis homologue of yeast M Phase Phosphoprotein 10 (MPP10). Our results uncovering the dual role of THAL in transcription and processing events critical for proper rRNA biogenesis and nucleolar organization during reproduction are the first to define the function of SAS10/C1D family members in plants.
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Affiliation(s)
- Ying-Jiun C. Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Huei-Jing Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taichung, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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8
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Jackson RA, Wu JS, Chen ES. C1D family proteins in coordinating RNA processing, chromosome condensation and DNA damage response. Cell Div 2016; 11:2. [PMID: 27030795 PMCID: PMC4812661 DOI: 10.1186/s13008-016-0014-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/22/2016] [Indexed: 12/02/2022] Open
Abstract
Research on the involvement of C1D and its yeast homologues Rrp47 (S. cerevisiae) and Cti1 (S. pombe) in DNA damage repair and RNA processing has remained mutually exclusive, with most studies predominantly concentrating on Rrp47. This review will look to reconcile the functions of these proteins in their involvement with the RNA exosome, in the regulation of chromatin architecture, and in the repair of DNA double-strand breaks, focusing on non-homologous end joining and homologous recombination. We propose that C1D is situated in a central position to maintain genomic stability at highly transcribed gene loci by coordinating these processes through the timely recruitment of relevant regulatory factors. In the event that the damage is beyond repair, C1D induces apoptosis in a p53-dependent manner.
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Affiliation(s)
- Rebecca A Jackson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Jocelyn Shumei Wu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore ; National University Health System (NUHS), Singapore, 119228 Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119228 Singapore
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9
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An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide. Sci Rep 2015; 5:13370. [PMID: 26311515 PMCID: PMC4550835 DOI: 10.1038/srep13370] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/23/2015] [Indexed: 12/11/2022] Open
Abstract
The molecular weight (MW) of a protein can be predicted based on its amino acids (AA) composition. However, in many cases a non-chemically modified protein shows an SDS PAGE-displayed MW larger than its predicted size. Some reports linked this fact to high content of acidic AA in the protein. However, the exact relationship between the acidic AA composition and the SDS PAGE-displayed MW is not established. Zebrafish nucleolar protein Def is composed of 753 AA and shows an SDS PAGE-displayed MW approximately 13 kDa larger than its predicted MW. The first 188 AA in Def is defined by a glutamate-rich region containing ~35.6% of acidic AA. In this report, we analyzed the relationship between the SDS PAGE-displayed MW of thirteen peptides derived from Def and the AA composition in each peptide. We found that the difference between the predicted and SDS PAGE-displayed MW showed a linear correlation with the percentage of acidic AA that fits the equation y = 276.5x − 31.33 (x represents the percentage of acidic AA, 11.4% ≤ x ≤ 51.1%; y represents the average ΔMW per AA). We demonstrated that this equation could be applied to predict the SDS PAGE-displayed MW for thirteen different natural acidic proteins.
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10
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Li M, Yin X, Sakata K, Yang P, Komatsu S. Proteomic Analysis of Phosphoproteins in the Rice Nucleus During the Early Stage of Seed Germination. J Proteome Res 2015; 14:2884-96. [DOI: 10.1021/acs.jproteome.5b00215] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ming Li
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Xiaojian Yin
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Katsumi Sakata
- Department
of Life Science and Informatics, Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Pingfang Yang
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Setsuko Komatsu
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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11
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Park SK, Son Y, Kang CJ. A strong promoter activity of pre-B cell stage-specific Crlz1 gene is caused by one distal LEF-1 and multiple proximal Ets sites. Mol Cells 2011; 32:67-76. [PMID: 21544627 PMCID: PMC3887653 DOI: 10.1007/s10059-011-1031-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/09/2011] [Accepted: 04/15/2011] [Indexed: 12/12/2022] Open
Abstract
The promoter of pre-B cell stage-specific Crlz1 gene, whose protein translocates the cytoplasmic core binding factor β (CBFβ) into the nucleus and thereby allows its heterodimerization with Runx, has a very strong activity, which is about 25% of cytomegalovirus (CMV) promoter activity and comparable to the EF-1α promoter activity. Its transcription start site was mapped at 155 nt upstream of translation initiation codon. 5'-truncation analysis of charged amino acids rich leucine zipper 1 (Crlz1) promoter revealed that one distal region from -612 to -536 and one proximal region from -198 to -100 as numbered from the transcription start site were critical for the promoter activity. The 3'-truncation analysis of the promoter revealed that the basal promoter sequence around the transcription start site, which should be necessary for the assembly of transcription initiation complex and the start of RNA polymerase II, was also essential, although not sufficient by itself. When transcription factor binding sites within those two critical regions were searched by in vivo footprinting, one distal LEF-1 and multiple proximal Ets consensus-like sites were found to be footprinted. Indeed, the protein causing a footprint over the distal region was found to be LEF-1, and the ones causing three footprints over the proximal region were found to be such Ets family members as Fli-1 and GABP, as verified by EMSA and ChIP analyses. Furthermore, those LEF-1 and Ets sites were shown to drive additively a strong transcription of Crlz1 gene.
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Affiliation(s)
| | | | - Chang-Joong Kang
- Graduate School of Biotechnology, Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Korea
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12
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Costello JL, Stead JA, Feigenbutz M, Jones RM, Mitchell P. The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3'-maturation. J Biol Chem 2010; 286:4535-43. [PMID: 21135092 PMCID: PMC3039359 DOI: 10.1074/jbc.m110.162826] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cells lacking the exosome-associated protein Rrp47 show similar defects in stable RNA processing to those observed in the absence of the catalytic subunit Rrp6, but the precise mechanism(s) by which Rrp47 functions together with Rrp6 remains unclear. Deletion complementation analyses defined an N-terminal region of Rrp47, largely coincident with the bioinformatically defined Sas10/C1D domain, which was sufficient for protein function in vivo. In vitro protein interaction studies demonstrated that this domain of Rrp47 binds the PMC2NT domain of Rrp6. Expression of the N-terminal domain of Rrp47 in yeast complemented most RNA-processing defects associated with the rrp47Δ mutant but failed to complement the defect observed in 3′-end maturation of box C/D small nucleolar RNAs. Consistent with these results, protein capture assays revealed an interaction between the C-terminal region of Rrp47 and the small nucleolar ribonucleoproteins Nop56 and Nop58. Filter binding assays demonstrated that deletion of the lysine-rich sequence at the C terminus of Rrp47 blocked RNA binding in vitro. Furthermore, a protein mutated both at the C terminus and within the N-terminal domain showed a synergistic defect in RNA binding without impacting on its ability to interact with Rrp6. These studies provide evidence for a role of Rrp47 in registering a small nucleolar ribonucleoprotein particle assembly, functionally characterize the Sas10/C1D domain of Rrp47, and show that both the C terminus of Rrp47 and the N-terminal domain contribute to its RNA-binding activity.
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Affiliation(s)
- Joe L Costello
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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13
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Abstract
The Sas10/C1D domain is found in a small group of eukaryotic proteins that have functions in RNA processing events, translational control and DNA repair mechanisms. The domain is predicted to be alpha-helical in nature and comprises approx. 80 amino acid residues. Whereas the Sas10/C1D domain has yet to be functionally characterized, available results suggest that this domain forms a binding surface for specific interactions with other proteins and can concomitantly interact with RNA or DNA. This property of the Sas10/C1D domain may facilitate this family of proteins to dock other proteins on to nucleic acid substrates.
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14
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NOF1 encodes an Arabidopsis protein involved in the control of rRNA expression. PLoS One 2010; 5:e12829. [PMID: 20877469 PMCID: PMC2942902 DOI: 10.1371/journal.pone.0012829] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 08/13/2010] [Indexed: 02/01/2023] Open
Abstract
The control of ribosomal RNA biogenesis is essential for the regulation of protein synthesis in eukaryotic cells. Here, we report the characterization of NOF1 that encodes a putative nucleolar protein involved in the control of rRNA expression in Arabidopsis. The gene has been isolated by T-DNA tagging and its function verified by the characterization of a second allele and genetic complementation of the mutants. The nof1 mutants are affected in female gametogenesis and embryo development. This result is consistent with the detection of NOF1 mRNA in all tissues throughout plant life's cycle, and preferentially in differentiating cells. Interestingly, the closely related proteins from zebra fish and yeast are also necessary for cell division and differentiation. We showed that the nof1-1 mutant displays higher rRNA expression and hypomethylation of rRNA promoter. Taken together, the results presented here demonstrated that NOF1 is an Arabidopsis gene involved in the control of rRNA expression, and suggested that it encodes a putative nucleolar protein, the function of which may be conserved in eukaryotes.
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15
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Butler JS, Mitchell P. Rrp6, Rrp47 and Cofactors of the Nuclear Exosome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:91-104. [DOI: 10.1007/978-1-4419-7841-7_8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Park SK, Lim JH, Kang CJ. Crlz1 activates transcription by mobilizing cytoplasmic CBFbeta into the nucleus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:702-8. [PMID: 19735751 DOI: 10.1016/j.bbagrm.2009.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 08/18/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
Abstract
Transcriptional function of a novel Crlz1 protein was examined by using the CBF site-containing IgJ enhancer, because it was originally cloned due to its ability to bind CBFbeta, a subunit of CBF heterodimer, of which Runx is the other subunit. In a cotransfection experiment, Crlz1 was shown to increase the IgJ enhancer activity due to its CBF sites, as verified by both the absence of Crlz1 effect on the CBF-site mutated IgJ enhancer and the presence of transcriptional synergy between Crlz1 and CBFbeta. Most significantly, the cytoplasmic CBFbeta was shown to be mobilized into the nucleus when it was coexpressed with the nuclear Crlz1. This mobilized nuclear CBFbeta could then heterodimerize with the nuclear Runx to bind to its target DNA site with a high affinity. Furthermore, in our coimmunoprecipitation and chromatin immunoprecipitation experiments, Crlz1 was found to be bound to the resulting CBF heterodimer in a form of ternary complex and to remain in that ternary complex even when CBF bound to its target DNA site such as IgJ enhancer.
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Affiliation(s)
- Sung-Kyun Park
- Graduate School of Biotechnology, Institute of Life Science and Resources, Kyung Hee University, 1 Seocheon, Giheung, Yongin, Gyeonggi-do 446-701, Republic of Korea
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17
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Sihn CR, Lee YS, Jeong JS, Park K, Kim SH. CANu1, a novel nucleolar protein, accumulated on centromere in response to DNA damage. Genes Cells 2008; 13:787-96. [DOI: 10.1111/j.1365-2443.2008.01205.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Tu S, Bulloch EMM, Yang L, Ren C, Huang WC, Hsu PH, Chen CH, Liao CL, Yu HM, Lo WS, Freitas MA, Tsai MD. Identification of histone demethylases in Saccharomyces cerevisiae. J Biol Chem 2007; 282:14262-71. [PMID: 17369256 PMCID: PMC2855503 DOI: 10.1074/jbc.m609900200] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Based on the prediction that histone lysine demethylases may contain the JmjC domain, we examined the methylation patterns of five knock-out strains (ecm5Delta, gis1Delta, rph1Delta, jhd1Delta, and jhd2Delta (yjr119cDelta)) of Saccharomyces cerevisiae. Mass spectrometry (MS) analyses of histone H3 showed increased modifications in all mutants except ecm5Delta. High-resolution MS was used to unequivocally differentiate trimethylation from acetylation in various tryptic fragments. The relative abundance of specific fragments indicated that histones K36me3 and K4me3 accumulate in rph1Delta and jhd2Delta strains, respectively, whereas both histone K36me2 and K36me accumulate in gis1Delta and jhd1Delta strains. Analyses performed with strains overexpressing the JmjC proteins yielded changes in methylation patterns that were the reverse of those obtained in the complementary knock-out strains. In vitro enzymatic assays confirmed that the JmjC domain of Rph1 specifically demethylates K36me3 primarily and K36me2 secondarily. Overexpression of RPH1 generated a growth defect in response to UV irradiation. The demethylase activity of Rph1 is responsible for the phenotype. Collectively, in addition to Jhd1, our results identified three novel JmjC domain-containing histone demethylases and their sites of action in budding yeast S. cerevisiae. Furthermore, the methodology described here will be useful for identifying histone demethylases and their target sites in other organisms.
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Affiliation(s)
- Shengjiang Tu
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | | | - Lanhao Yang
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Chen Ren
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Wei-Chieh Huang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Pang-Hung Hsu
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chein-Hung Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chung-Lin Liao
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hui-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Sheng Lo
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
- To whom correspondence may be addressed.
| | - Michael A. Freitas
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Ming-Daw Tsai
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
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19
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Lim JH, Cho SJ, Park SK, Kim J, Cho D, Lee WJ, Kang CJ. Stage-specific expression of two neighboring Crlz1 and IgJ genes during B cell development is regulated by their chromatin accessibility and histone acetylation. THE JOURNAL OF IMMUNOLOGY 2007; 177:5420-9. [PMID: 17015728 DOI: 10.4049/jimmunol.177.8.5420] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The IgJ gene is expressed in the plasma cell stage. However, its neighboring charged amino acid-rich leucine zipper 1 (Crlz1) gene, which is mapped 30 kb upstream of the IgJ gene in mice, is shown to be expressed in the pre-B cell stage. These stage-specific expressions of two neighboring genes are found to be regulated by their chromatin accessibility and acetylation. Hypersensitive site 1 on the IgJ promoter is opened in the plasma cells, whereas hypersensitive sites 9/10 on the Crlz1 promoter are opened in the pre-B cells. Furthermore, H3 and H4 histones toward the chromatin of the Crlz1 gene are found to be hyperacetylated, especially on H3, in the pre-B cells, whereas those toward the chromatin of the IgJ gene are found to be hyperacetylated in the plasma cells. Consistently, the hyperacetylation of H3 and H4 toward the chromatin of the IgJ gene but not the Crlz1 gene is induced by an IL-2 treatment of BCL1, which is a model cell line for studying the terminal differentiation of B cells.
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Affiliation(s)
- Jung-Hyun Lim
- Graduate School of Biotechnology, Institute of Life Science and Resources, Kyung Hee University, Yongin, Gyeonggi-do, Korea
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20
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Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol 2006; 2:2006.0003. [PMID: 16738550 PMCID: PMC1681477 DOI: 10.1038/msb4100045] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 12/06/2005] [Indexed: 01/30/2023] Open
Abstract
Here, we develop computational methods to assess and consolidate large, diverse protein interaction data sets, with the objective of identifying proteins involved in the coupling of multicomponent complexes within the yeast gene expression pathway. From among approximately 43 000 total interactions and 2100 proteins, our methods identify known structural complexes, such as the spliceosome and SAGA, and functional modules, such as the DEAD-box helicases, within the interaction network of proteins involved in gene expression. Our process identifies and ranks instances of three distinct, biologically motivated motifs, or patterns of coupling among distinct machineries involved in different subprocesses of gene expression. Our results confirm known coupling among transcription, RNA processing, and export, and predict further coupling with translation and nonsense-mediated decay. We systematically corroborate our analysis with two independent, comprehensive experimental data sets. The methods presented here may be generalized to other biological processes and organisms to generate principled, systems-level network models that provide experimentally testable hypotheses for coupling among biological machines.
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Affiliation(s)
- Karolina Maciag
- Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA
| | - Steven J Altschuler
- Department of Pharmacology and Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael D Slack
- Department of Pharmacology and Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nevan J Krogan
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Jack F Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Tom Maniatis
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Lani F Wu
- Department of Pharmacology and Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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21
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Kimura M, Ishihama A. Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions. Nucleic Acids Res 2004; 32:6706-15. [PMID: 15616156 PMCID: PMC545442 DOI: 10.1093/nar/gkh1000] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TFIIF is a general transcription factor (GTF) that binds to RNA polymerase II (pol II) for subsequent recruitment of pol II to a promoter. TFIIF of Saccharomyces cerevisiae contains a small subunit, designated Tfg3, in addition to two conserved subunits, TFIIFalpha (Tfg1) and TFIIFbeta (Tfg2). In this study, we characterized Tfg3 of Schizosaccharomyces pombe. Using Tfg3 fused to green fluorescent protein (GFP), we found that Tfg3 is located in nuclei, and it is assembled into the C-terminal domain phosphatase (Fcp1)/TFIIF/pol II complex via interactions with TFIIFalpha and TFIIFbeta. As in the case of S.cerevisiae, Tfg3 in S.pombe forms part of another GTF, namely TFIID. The TFIID complex isolated from S.pombe that had been cultured at elevated temperatures included increased levels of Tfg3. The interaction of recombinant Tfg3 with TATA-binding protein (TBP), the central subunit of TFIID, was temperature-dependent. Moreover, a mutant of S.pombe that lacked the gene for Tfg3 was sensitive to a battery of stresses including temperature up-shift. Starting from a mutant with tfg3- mutation, we isolated five species of multicopy suppressors. Expression levels of the suppressor genes were lower in the mutant cell than in wild-type cell at an elevated temperature. Taken together, we propose that Tfg3 is involved in transcriptional regulation under stress conditions, in particular, at high temperatures.
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Affiliation(s)
- Makoto Kimura
- Gene Engineering Division, BioResource Center, RIKEN (Institute of Physical and Chemical Research), Tsukuba, Ibaraki 305-0074, Japan and Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan.
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22
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Oki M, Valenzuela L, Chiba T, Ito T, Kamakaka RT. Barrier proteins remodel and modify chromatin to restrict silenced domains. Mol Cell Biol 2004; 24:1956-67. [PMID: 14966276 PMCID: PMC350565 DOI: 10.1128/mcb.24.5.1956-1967.2004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptionally active and inactive domains are frequently found adjacent to one another in the eukaryotic nucleus. To better understand the underlying mechanisms by which domains maintain opposing transcription patterns, we performed a systematic genomewide screen for proteins that may block the spread of silencing in yeast. This analysis identified numerous proteins with efficient silencing blocking activities, and some of these have previously been shown to be involved in chromatin dynamics. We isolated subunits of Swi/Snf, mediator, and TFIID, as well as subunits of the Sas-I, SAGA, NuA3, NuA4, Spt10p, Rad6p, and Dot1p complexes, as barrier proteins. We demonstrate that histone acetylation and chromatin remodeling occurred at the barrier and correlated with a block to the spread of silencing. Our data suggest that multiple overlapping mechanisms were involved in delimiting silenced and active domains in vivo.
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Affiliation(s)
- Masaya Oki
- Unit on Chromatin and Transcription, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
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23
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Crotti LB, Basrai MA. Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J 2004; 23:1804-14. [PMID: 15057281 PMCID: PMC394231 DOI: 10.1038/sj.emboj.7600161] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 02/16/2004] [Indexed: 11/09/2022] Open
Abstract
The kinetochore (centromeric DNA and associated proteins) mediates the attachment of chromosomes to the mitotic spindle apparatus and is required for faithful chromosome transmission. We established that evolutionarily conserved Saccharomyces cerevisiae SPT4, previously identified in genetic screens for defects in chromosome transmission fidelity (ctf), encodes a new structural component of specialized chromatin at kinetochores and heterochromatic loci, with roles in kinetochore function and gene silencing. Using chromatin immunoprecipitation assays (ChIP), we determined that kinetochore proteins Ndc10p, Cac1p, and Hir1p are required for the association of Spt4p to centromeric (CEN) loci. Absence of functional Spt4p leads to altered chromatin structure at the CEN DNA and mislocalization of the mammalian CENP-A homolog Cse4p to noncentromeric loci. Spt4p associates with telomeres (TEL) and HMRa loci in a Sir3p-dependent manner and is required for transcriptional gene silencing. We show that a human homolog of SPT4 (HsSPT4) complements Scspt4-silencing defects and associates with ScCEN DNA in an Ndc10p-dependent manner. Our results highlight the evolutionary conservation of pathways required for genome stability in yeast and humans.
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Affiliation(s)
| | - Munira A Basrai
- Genetics Branch, National Cancer Institute, Bethesda, MD, USA
- Genetics Branch, National Cancer Institute, NNMC Bldg. 8, Room 5101, 8901 Wisconsin Avenue, Bethesda, MD 20889-5105, USA. Tel.: +1 301 402 2552; Fax: +1 301 480 0380; E-mail:
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24
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Peters NT, Rohrbach JA, Zalewski BA, Byrkett CM, Vaughn JC. RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. RNA (NEW YORK, N.Y.) 2003; 9:698-710. [PMID: 12756328 PMCID: PMC1370437 DOI: 10.1261/rna.2120703] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Accepted: 03/06/2003] [Indexed: 05/19/2023]
Abstract
We have previously described an example of extensively A-to-G edited cDNA derived from adult heads of the fruitfly Drosophila melanogaster. In that study, the source of the predicted antisense RNA pairing strand for template recognition by dADAR editase was not identified, and the biological significance of the observed hyperediting was not known. Here, we address each of these questions. 4f-rnp and sas-10 are closely adjacent X-linked genes located on opposite DNA strands that produce convergent transcripts. We show that developmentally regulated antisense sas-10 readthrough mRNA arises by activation of an upstream promoter P2 during the late embryo stage of fly development. The sas-10 readthrough transcripts pair with 4f-rnp mRNA to form double-stranded molecules, as indicated by A-to-G editing observed in both RNA strands. It would be predicted that perfect RNA duplexes would be targeted for modification/degradation by enzyme pathways that recognize double-stranded RNAs, leading to decline in 4f-rnp mRNA levels, and this is what we observe. The observation using quantitative RT-PCR that sas-10 readthrough and 4f-rnp transcript levels are inversely related suggests a role for the antisense RNA in posttranscriptional regulation of 4f-rnp gene expression during development. Potential molecular mechanisms that could lead to this result are discussed, one of which is targeted transcript degradation via the RNAi pathway. Insofar as the dADAR editase and RNAi pathways are known to be constitutive in this system, it is likely that control of antisense RNA transcription is the rate-limiting factor. The results provide insight into roles of naturally occurring antisense RNAs in regulation of eukaryotic gene expression.
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Affiliation(s)
- Nick T Peters
- Department of Zoology, Miami University, Oxford, Ohio 45056, USA
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25
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Dragon F, Gallagher JEG, Compagnone-Post PA, Mitchell BM, Porwancher KA, Wehner KA, Wormsley S, Settlage RE, Shabanowitz J, Osheim Y, Beyer AL, Hunt DF, Baserga SJ. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 2002; 417:967-70. [PMID: 12068309 DOI: 10.1038/nature00769] [Citation(s) in RCA: 535] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the U3 small nucleolar RNA (snoRNA), a member of the box C/D class of snoRNAs, was identified with the spliceosomal small nuclear RNAs (snRNAs) over 30 years ago, its function and its associated protein components have remained more elusive. The U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA in all organisms where it has been tested. Biochemical and genetic analyses suggest that U3 pre-rRNA base-pairing interactions mediate endonucleolytic pre-rRNA cleavages. Here we have purified a large ribonucleoprotein (RNP) complex from Saccharomyces cerevisiae that contains the U3 snoRNA and 28 proteins. Seventeen new proteins (Utp1 17) and Rrp5 were present, as were ten known components. The Utp proteins are nucleolar and specifically associated with the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. On the basis of its large size (80S; calculated relative molecular mass of at least 2,200,000) and function, this complex may correspond to the terminal knobs present at the 5' ends of nascent pre-rRNAs. We have termed this large RNP the small subunit (SSU) processome.
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MESH Headings
- Cell Nucleolus/genetics
- Cell Nucleolus/metabolism
- Chromatin/genetics
- Chromatin/metabolism
- Macromolecular Substances
- Microscopy, Electron
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal, 18S/biosynthesis
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- François Dragon
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520-8040, USA
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26
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Sakuma T, Li QL, Jin Y, Choi LB, Kim EG, Ito K, Ito Y, Nomura S, Bae SC. Cloning and expression pattern of a novel PEBP2 beta-binding protein (charged amino acid rich leucine zipper-1[Crl-1]) in the mouse. Mech Dev 2001; 104:151-4. [PMID: 11404095 DOI: 10.1016/s0925-4773(01)00366-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PEBP2 beta/Cbf beta is the beta subunit of PEBP2/Cbf, which has been demonstrated to have important biological activities in hematopoiesis and osteogenesis. However, PEBP2 beta is ubiquitously expressed, suggesting that PEBP2 has other additionally important physiological activities. In an effort to elucidate other possible functions for PEBP2, we have isolated a novel gene that encodes a PEBP2 beta-interacting protein from a mouse cDNA library. We have called this gene Crl-1 for charged amino acid rich leucine zipper-1 (Crl-1) because it is rich in charged amino acids and contains a putative leucine zipper region. Expression studies in a 17.5 days post-coitum mouse embryo demonstrated Crl-1 expression mainly in the olfactory bulb and cerebral cortex. Post-natally, Crl-1 expression was additionally observed in the cerebellar cortex with strong expression in the hippocampus. These findings show that this novel PEBP2 beta-interacting protein is expressed mainly in subsets of neuronal cells, suggesting that Crl-1 plays some role in the developing mouse brain.
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Affiliation(s)
- T Sakuma
- Department of Pathology, Medical School, Osaka University, Osaka 565-0871, Japan
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27
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Dhillon N, Kamakaka RT. A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol Cell 2000; 6:769-80. [PMID: 11090616 DOI: 10.1016/s1097-2765(00)00076-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Silencing at HMR requires silencers, and one of the roles of the silencer is to recruit Sir proteins. This work focuses on the function of Sir1p once it is recruited to the silencer. We have generated mutants of Sir1p that are recruited to the silencer but are unable to silence, and we have utilized these mutants to identify four proteins, Sir3p, Sir4p, Esc2p, and Htz1p, that when overexpressed, restored silencing. The isolation of Sir3p and Sir4p validated this screen. Molecular analysis suggested that Esc2p contributed to silencing in a manner similar to Sir1p and probably helped recruit or stabilize the other Sir proteins, while Htz1p present at HMR assembled a specialized chromatin structure necessary for silencing.
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Affiliation(s)
- N Dhillon
- Unit on Chromatin and Transcription, NICHD/NIH, Bethesda, Maryland 20892, USA
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28
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Munakata T, Adachi N, Yokoyama N, Kuzuhara T, Horikoshi M. A human homologue of yeast anti-silencing factor has histone chaperone activity. Genes Cells 2000; 5:221-33. [PMID: 10759893 DOI: 10.1046/j.1365-2443.2000.00319.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Structural changes in chromatin play essential roles in regulating eukaryotic gene expression. Silencing, potent repression of transcription in Saccharomyces cerevisiae, occurs near telomeres and at the silent mating-type loci, as well as at rDNA loci. This type of repression relates to the condensation of chromatin that occurs in the heterochromatin of multicellular organisms. Anti-silencing is a reaction by which silenced loci are de-repressed. Genetic studies revealed that several factors participate in the anti-silencing reaction. However, actions of factors and molecular mechanisms underlying anti-silencing remain unknown. RESULTS Here we report the functional activity of a highly evolutionarily conserved human factor termed CIA (CCG1-interacting factor A), whose budding yeast homologue ASF1 has anti-silencing activity. Using yeast two-hybrid screening, we isolated histone H3 as an interacting factor of CIA. We also showed that CIA binds to histones H3/H4 in vitro, and that the interacting region of histone H3 is located in the C-terminal helices. Considering the functional role of CIA as a histone-interacting protein, we found that CIA forms a nucleosome-like structure with DNA and histones. CONCLUSIONS These results show that human CIA, whose yeast homologue ASF1 is an anti-silencing factor, possesses histone chaperone activity. This leads to a better understanding of the relationship between chromatin structural changes and anti-silencing processes.
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Affiliation(s)
- T Munakata
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo,1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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29
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Smith JS, Caputo E, Boeke JD. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 1999; 19:3184-97. [PMID: 10082585 PMCID: PMC84112 DOI: 10.1128/mcb.19.4.3184] [Citation(s) in RCA: 186] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae occurs at several genetic loci, including the ribosomal DNA (rDNA). Silencing at telomeres (telomere position effect [TPE]) and the cryptic mating-type loci (HML and HMR) depends on the silent information regulator genes, SIR1, SIR2, SIR3, and SIR4. However, silencing of polymerase II-transcribed reporter genes integrated within the rDNA locus (rDNA silencing) requires only SIR2. The mechanism of rDNA silencing is therefore distinct from TPE and HM silencing. Few genes other than SIR2 have so far been linked to the rDNA silencing process. To identify additional non-Sir factors that affect rDNA silencing, we performed a genetic screen designed to isolate mutations which alter the expression of reporter genes integrated within the rDNA. We isolated two classes of mutants: those with a loss of rDNA silencing (lrs) phenotype and those with an increased rDNA silencing (irs) phenotype. Using transposon mutagenesis, lrs mutants were found in 11 different genes, and irs mutants were found in 22 different genes. Surprisingly, we did not isolate any genes involved in rRNA transcription. Instead, multiple genes associated with DNA replication and modulation of chromatin structure were isolated. We describe these two gene classes, and two previously uncharacterized genes, LRS4 and IRS4. Further characterization of the lrs and irs mutants revealed that many had alterations in rDNA chromatin structure. Several lrs mutants, including those in the cdc17 and rfc1 genes, caused lengthened telomeres, consistent with the hypothesis that telomere length modulates rDNA silencing. Mutations in the HDB (RPD3) histone deacetylase complex paradoxically increased rDNA silencing by a SIR2-dependent, SIR3-independent mechanism. Mutations in rpd3 also restored mating competence selectively to sir3Delta MATalpha strains, suggesting restoration of silencing at HMR in a sir3 mutant background.
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MESH Headings
- Chromatin/metabolism
- Chromatin/ultrastructure
- DNA Replication
- DNA, Ribosomal/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Fungal Proteins/genetics
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Genes, Mating Type, Fungal
- Histone Deacetylases
- Models, Genetic
- Mutation
- Phenotype
- RNA, Ribosomal/biosynthesis
- Repressor Proteins/genetics
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Selection, Genetic
- Silent Information Regulator Proteins, Saccharomyces cerevisiae
- Sirtuin 2
- Sirtuins
- Telomere/genetics
- Telomere-Binding Proteins
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription Factors/genetics
- Transcription, Genetic
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Affiliation(s)
- J S Smith
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Gardner KA, Rine J, Fox CA. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in saccharomyces cerevisiae. Genetics 1999; 151:31-44. [PMID: 9872946 PMCID: PMC1460464 DOI: 10.1093/genetics/151.1.31] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Silencing of the cryptic mating-type loci HMR and HML requires the recognition of DNA sequence elements called silencers by the Sir1p, one of four proteins dedicated to the assembly of silenced chromatin in Saccharomyces cerevisiae. The Sir1p is thought to recognize silencers indirectly through interactions with proteins that bind the silencer DNA directly, such as the origin recognition complex (ORC). Eight recessive alleles of SIR1 were discovered that encode mutant Sir1 proteins specifically defective in their ability to recognize the HMR-E silencer. The eight missense mutations all map within a 17-amino-acid segment of Sir1p, and this segment was also required for Sir1p's interaction with Orc1p. The mutant Sir1 proteins could function in silencing if tethered to a silencer directly through a heterologous DNA-binding domain. Thus the amino acids identified are required for Sir1 protein's recognition of the HMR-E silencer and interaction with Orc1p, but not for its ability to function in silencing per se. The approach used to find these mutations may be applicable to defining interaction surfaces on proteins involved in other processes that require the assembly of macromolecular complexes.
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Affiliation(s)
- K A Gardner
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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