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Shehzada S, Noto T, Saksouk J, Mochizuki K. A SUMO E3 ligase promotes long non-coding RNA transcription to regulate small RNA-directed DNA elimination. eLife 2024; 13:e95337. [PMID: 38197489 PMCID: PMC10830130 DOI: 10.7554/elife.95337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Small RNAs target their complementary chromatin regions for gene silencing through nascent long non-coding RNAs (lncRNAs). In the ciliated protozoan Tetrahymena, the interaction between Piwi-associated small RNAs (scnRNAs) and the nascent lncRNA transcripts from the somatic genome has been proposed to induce target-directed small RNA degradation (TDSD), and scnRNAs not targeted for TDSD later target the germline-limited sequences for programmed DNA elimination. In this study, we show that the SUMO E3 ligase Ema2 is required for the accumulation of lncRNAs from the somatic genome and thus for TDSD and completing DNA elimination to make viable sexual progeny. Ema2 interacts with the SUMO E2 conjugating enzyme Ubc9 and enhances SUMOylation of the transcription regulator Spt6. We further show that Ema2 promotes the association of Spt6 and RNA polymerase II with chromatin. These results suggest that Ema2-directed SUMOylation actively promotes lncRNA transcription, which is a prerequisite for communication between the genome and small RNAs.
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Affiliation(s)
- Salman Shehzada
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Tomoko Noto
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Julie Saksouk
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
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2
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Ning YN, Tian D, Tan ML, Luo XM, Zhao S, Feng JX. Regulation of fungal raw-starch-degrading enzyme production depends on transcription factor phosphorylation and recruitment of the Mediator complex. Commun Biol 2023; 6:1032. [PMID: 37828083 PMCID: PMC10570388 DOI: 10.1038/s42003-023-05404-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Filamentous fungus can produce raw-starch-degrading enzyme (RSDE) that efficiently degrades raw starch below starch gelatinization temperature. Employment of RSDE in starch processing can save energy. A key putative transcription factor PoxRsrA (production of raw-starch-degrading enzyme regulation in Penicillium oxalicum) was identified to regulate RSDE production in P. oxalicum; however, its regulatory mechanism remains unclear. Here we show that PoxRsrA1434-1730 was the transcriptional activation domain, with essential residues, D1508, W1509 and M1510. SANT (SWI3, ADA2, N-CoR and TFIIIB)-like domain 1 (SANT1) bound to DNA at the sequence 5'-RHCDDGGD-3' in the promoter regions of genes encoding major amylases, with an essential residue, R866. SANT2 interacted with a putative 3-hydroxyisobutyryl-CoA hydrolase, which suppressed phosphorylation at tyrosines Y1127 and Y1170 of PoxRsrA901-1360, thereby inhibiting RSDE biosynthesis. PoxRsrA1135-1439 regulated mycelial sporulation by interacting with Mediator subunit Med6, whereas PoxRsrA1440-1794 regulated RSDE biosynthesis by binding to Med31. Overexpression of PoxRsrA increased sporulation and RSDE production. These findings provide insights into the regulatory mechanisms of fungal RSDE biosynthesis.
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Affiliation(s)
- Yuan-Ni Ning
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
| | - Di Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
| | - Man-Li Tan
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
| | - Xue-Mei Luo
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
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3
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Nabeel-Shah S, Garg J, Ashraf K, Jeyapala R, Lee H, Petrova A, Burns JD, Pu S, Zhang Z, Greenblatt JF, Pearlman RE, Lambert JP, Fillingham J. Multilevel interrogation of H3.3 reveals a primordial role in transcription regulation. Epigenetics Chromatin 2023; 16:10. [PMID: 37024975 PMCID: PMC10080907 DOI: 10.1186/s13072-023-00484-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Eukaryotic cells can rapidly adjust their transcriptional profile in response to molecular needs. Such dynamic regulation is, in part, achieved through epigenetic modifications and selective incorporation of histone variants into chromatin. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. Although H3.3 has been well studied in metazoans, information regarding the assembly of H3.3 onto chromatin and its possible role in transcription regulation remain poorly documented outside of Opisthokonts. RESULTS We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, to investigate the dynamics of H3 variant function in evolutionarily divergent eukaryotes. Functional proteomics and immunofluorescence analyses of H3.1 and H3.3 revealed a highly conserved role for Nrp1 and Asf1 histone chaperones in nuclear influx of histones. Cac2, a putative subunit of H3.1 deposition complex CAF1, is not required for growth, whereas the expression of the putative ortholog of the H3.3-specific chaperone Hir1 is essential in Tetrahymena. Our results indicate that Cac2 and Hir1 have distinct localization patterns during different stages of the Tetrahymena life cycle and suggest that Cac2 might be dispensable for chromatin assembly. ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over the promoters, gene bodies, and transcription termination sites of highly transcribed genes. H3.3 knockout followed by RNA-seq reveals large-scale transcriptional alterations in functionally important genes. CONCLUSION Our results provide an evolutionary perspective on H3.3's conserved role in maintaining the transcriptional landscape of cells and on the emergence of specialized chromatin assembly pathways.
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Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
- Department of Biology, York University, 4700 Keele St, Toronto, M3J 1P3, Canada
| | - Kanwal Ashraf
- Department of Biology, York University, 4700 Keele St, Toronto, M3J 1P3, Canada
| | - Renu Jeyapala
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, Canada
| | - Alexandra Petrova
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
| | - James D Burns
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele St, Toronto, M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, QC, Canada
- CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City, QC, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada.
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4
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Broad domains of histone marks in the highly compact Paramecium macronuclear genome. Genome Res 2022; 32:710-725. [PMID: 35264449 PMCID: PMC8997361 DOI: 10.1101/gr.276126.121] [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: 08/20/2021] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
Abstract
The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.
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Nabeel-Shah S, Garg J, Saettone A, Ashraf K, Lee H, Wahab S, Ahmed N, Fine J, Derynck J, Pu S, Ponce M, Marcon E, Zhang Z, Greenblatt JF, Pearlman RE, Lambert JP, Fillingham J. Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila. Nucleic Acids Res 2021; 49:6196-6212. [PMID: 34086947 PMCID: PMC8216455 DOI: 10.1093/nar/gkab413] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Retinoblastoma-binding proteins 4 and 7 (RBBP4 and RBBP7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Here, we report that in the ciliate protozoan Tetrahymena thermophila a single orthologue of human RBBP4 and 7 proteins, RebL1, physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Functional proteomics identified conserved functional links for Tetrahymena RebL1 protein as well as human RBBP4 and 7. We found that putative subunits of multiple chromatin-related complexes including CAF1, Hat1, Rpd3, and MuvB, co-purified with RebL1 during Tetrahymena growth and conjugation. Iterative proteomics analyses revealed that the cell cycle regulatory MuvB-complex in Tetrahymena is composed of at least five subunits including evolutionarily conserved Lin54, Lin9 and RebL1 proteins. Genome-wide analyses indicated that RebL1 and Lin54 (Anqa1) bind within genic and intergenic regions. Moreover, Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation. RebL1 depletion inhibited cellular growth and reduced the expression levels of Anqa1 and Lin9. Consistent with observations in glioblastoma tumors, RebL1 depletion suppressed DNA repair protein Rad51 in Tetrahymena, thus underscoring the evolutionarily conserved functions of RBBP4/7 proteins. Our results suggest the essentiality of RebL1 functions in multiple epigenetic regulatory complexes in which it impacts transcription regulation and cellular viability.
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Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada.,Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Kanwal Ashraf
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Hyunmin Lee
- Department of Computer Science, University of Toronto, Toronto M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Suzanne Wahab
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Nujhat Ahmed
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Jacob Fine
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Joanna Derynck
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Marcelo Ponce
- SciNet HPC Consortium, University of Toronto, 661 University Avenue, Suite 1140, Toronto M5G 1M1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, Canada; CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City G1V 4G2, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
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6
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Nabeel-Shah S, Garg J, Kougnassoukou Tchara PE, Pearlman RE, Lambert JP, Fillingham J. Functional proteomics protocol for the identification of interaction partners in Tetrahymena thermophila. STAR Protoc 2021; 2:100362. [PMID: 33786459 PMCID: PMC7988224 DOI: 10.1016/j.xpro.2021.100362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
We describe an optimized protocol for one-step affinity purification of FZZ-tagged proteins followed by mass spectrometry analysis for the identification of protein-protein interactions in the ciliate protozoan Tetrahymena thermophila. The FZZ epitope tag contains 2 protein A moieties (ZZ) and a 3xFLAG separated by a TEV cleavage site, which can also be employed in tandem affinity purification. This protocol is versatile and is suitable to use for other common epitope tags and can be adapted for other ciliates. For complete details on the use and execution of this protocol, please refer to Garg et al. (2019).
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Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, QC, Canada
- CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City, QC, G1V 4G2, Canada
| | - Ronald E. Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, QC, Canada
- CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City, QC, G1V 4G2, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
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Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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8
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Nucleus-specific linker histones Hho1 and Mlh1 form distinct protein interactions during growth, starvation and development in Tetrahymena thermophila. Sci Rep 2020; 10:168. [PMID: 31932604 PMCID: PMC6957481 DOI: 10.1038/s41598-019-56867-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
Chromatin organization influences most aspects of gene expression regulation. The linker histone H1, along with the core histones, is a key component of eukaryotic chromatin. Despite its critical roles in chromatin structure and function and gene regulation, studies regarding the H1 protein-protein interaction networks, particularly outside of Opisthokonts, are limited. The nuclear dimorphic ciliate protozoan Tetrahymena thermophila encodes two distinct nucleus-specific linker histones, macronuclear Hho1 and micronuclear Mlh1. We used a comparative proteomics approach to identify the Hho1 and Mlh1 protein-protein interaction networks in Tetrahymena during growth, starvation, and sexual development. Affinity purification followed by mass spectrometry analysis of the Hho1 and Mlh1 proteins revealed a non-overlapping set of co-purifying proteins suggesting that Tetrahymena nucleus-specific linker histones are subject to distinct regulatory pathways. Furthermore, we found that linker histones interact with distinct proteins under the different stages of the Tetrahymena life cycle. Hho1 and Mlh1 co-purified with several Tetrahymena-specific as well as conserved interacting partners involved in chromatin structure and function and other important cellular pathways. Our results suggest that nucleus-specific linker histones might be subject to nucleus-specific regulatory pathways and are dynamically regulated under different stages of the Tetrahymena life cycle.
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Saettone A, Ponce M, Nabeel-Shah S, Fillingham J. RACS: rapid analysis of ChIP-Seq data for contig based genomes. BMC Bioinformatics 2019; 20:533. [PMID: 31664892 PMCID: PMC6819487 DOI: 10.1186/s12859-019-3100-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA sequences on a genomic scale. ChIP-Seq generates large quantities of data that is difficult to process and analyze, particularly for organisms with a contig-based sequenced genomes that typically have minimal annotation on their associated set of genes other than their associated coordinates primarily predicted by gene finding programs. Poorly annotated genome sequence makes comprehensive analysis of ChIP-Seq data difficult and as such standardized analysis pipelines are lacking. RESULTS We present a one-stop computational pipeline, "Rapid Analysis of ChIP-Seq data" (RACS), that utilizes traditional High-Performance Computing (HPC) techniques in association with open source tools for processing and analyzing raw ChIP-Seq data. RACS is an open source computational pipeline available from any of the following repositories https://bitbucket.org/mjponce/RACS or https://gitrepos.scinet.utoronto.ca/public/?a=summary&p=RACS . RACS is particularly useful for ChIP-Seq in organisms with contig-based genomes that have poor gene annotation to aid protein function discovery.To test the performance and efficiency of RACS, we analyzed ChIP-Seq data previously published in a model organism Tetrahymena thermophila which has a contig-based genome. We assessed the generality of RACS by analyzing a previously published data set generated using the model organism Oxytricha trifallax, whose genome sequence is also contig-based with poor annotation. CONCLUSIONS The RACS computational pipeline presented in this report is an efficient and reliable tool to analyze genome-wide raw ChIP-Seq data generated in model organisms with poorly annotated contig-based genome sequence. Because RACS segregates the found read accumulations between genic and intergenic regions, it is particularly efficient for rapid downstream analyses of proteins involved in gene expression.
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Affiliation(s)
- Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St, Toronto, M5B 2K3 Canada
| | - Marcelo Ponce
- SciNet High Performance Computing Consortium, University of Toronto, 661 University Ave, Toronto, M5G 1M1 Canada
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, 1 King’s College Cir, Toronto, M5S 1A8 Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St, Toronto, M5B 2K3 Canada
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Abstract
Mediator is a large, multi-module complex that plays a key role in transcription regulation in eukaryotes. A divergent Mediator from a unicellular eukaryote has been identified and characterized, revealing novel adaptations to mRNA and ncRNA transcription.
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Affiliation(s)
- Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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