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Fukuda Y, Akematsu T, Bando H, Kato K. Snf2 Proteins Are Required to Generate Gamete Pronuclei in Tetrahymena thermophila. Microorganisms 2022; 10:microorganisms10122426. [PMID: 36557679 PMCID: PMC9786623 DOI: 10.3390/microorganisms10122426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
During sexual reproduction/conjugation of the ciliate Tetrahymena thermophila, the germinal micronucleus undergoes meiosis resulting in four haploid micronuclei (hMICs). All hMICs undergo post-meiotic DNA double-strand break (PM-DSB) formation, cleaving their genome. DNA lesions are subsequently repaired in only one ‘selected’ hMIC, which eventually produces gametic pronuclei. DNA repair in the selected hMIC involves chromatin remodeling by switching from the heterochromatic to the euchromatic state of its genome. Here, we demonstrate that, among the 15 Tetrahymena Snf2 family proteins, a core of the ATP-dependent chromatin remodeling complex in Tetrahymena, the germline nucleus specific Iswi in Tetrahymena IswiGTt and Rad5Tt is crucial for the generation of gametic pronuclei. In either gene knockout, the selected hMIC which shows euchromatin markers such as lysine-acetylated histone H3 does not appear, but all hMICs in which markers for DNA lesions persist are degraded, indicating that both IswiGTt and Rad5Tt have important roles in repairing PM-DSB DNA lesions and remodeling chromatin for the euchromatic state in the selected hMIC.
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Affiliation(s)
- Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
- Correspondence: ; Tel.: +81-229-84-7387
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan
| | - Hironori Bando
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
| | - Kentaro Kato
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
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2
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Singh A, Maurer‐Alcalá XX, Solberg T, Häußermann L, Gisler S, Ignarski M, Swart EC, Nowacki M. Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium. EMBO J 2022; 41:e111839. [PMID: 36221862 PMCID: PMC9670198 DOI: 10.15252/embj.2022111839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 01/13/2023] Open
Abstract
Small RNAs mediate the silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. The unicellular ciliate Paramecium is a model to study dynamic genome organization in eukaryotic cells, given its unique feature of nuclear dimorphism. Here, the formation of the somatic macronucleus during sexual reproduction requires eliminating thousands of transposon remnants (IESs) and transposable elements scattered throughout the germline micronuclear genome. The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries. Here we show that IES recognition and precise excision are facilitated by recruiting ISWI1, a Paramecium homolog of the chromatin remodeler ISWI. ISWI1 knockdown substantially inhibits DNA elimination, quantitatively similar to development-specific sRNA gene knockdowns but with much greater aberrant IES excision at alternative boundaries. We also identify key development-specific sRNA biogenesis and transport proteins, Ptiwi01 and Ptiwi09, as ISWI1 cofactors in our co-immunoprecipitation studies. Nucleosome profiling indicates that increased nucleosome density correlates with the requirement for ISWI1 and other proteins necessary for IES excision. We propose that chromatin remodeling together with small RNAs is essential for efficient and precise DNA elimination in Paramecium.
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Affiliation(s)
- Aditi Singh
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland,Max Planck Institute for BiologyTubingenGermany
| | | | - Therese Solberg
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | | | - Silvan Gisler
- Institute of Cell BiologyUniversity of BernBernSwitzerland
| | | | - Estienne C Swart
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Max Planck Institute for BiologyTubingenGermany
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3
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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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4
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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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Garg J, Saettone A, Nabeel-Shah S, Cadorin M, Ponce M, Marquez S, Pu S, Greenblatt J, Lambert JP, Pearlman RE, Fillingham J. The Med31 Conserved Component of the Divergent Mediator Complex in Tetrahymena thermophila Participates in Developmental Regulation. Curr Biol 2019; 29:2371-2379.e6. [PMID: 31280994 DOI: 10.1016/j.cub.2019.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/18/2019] [Accepted: 06/18/2019] [Indexed: 11/24/2022]
Abstract
Mediator is a large protein complex required for basal and regulated expression of most RNA polymerase II (RNAP II)-transcribed genes, in part due to its interaction with and phosphorylation of the conserved C-terminal domain (CTD) of Rpb1 [1, 2]. Mediator has been implicated in many aspects of gene expression including chromatin looping [3], higher-order chromatin folding [4], mRNA processing [5] and export [6], and transcriptional memory [7]. Mediator is thought to have played a major role during eukaryotic diversification [8, 9], although its function remains unknown in evolutionarily deep branching eukaryotes lacking canonical CTD heptad repeats. We used the ciliate protozoan Tetrahymena thermophila as a model organism whose genome encodes a highly divergent Rpb1 lacking canonical CTD heptad repeats. We endogenously tagged the Med31 subunit of the Mediator complex and performed affinity purification coupled with mass spectrometry (AP-MS) to identify Mediator subunits. We found that Med31 physically interacts with a large number of proteins (>20), several of which share similarities to canonical Mediator subunits in yeast and humans as well as Tetrahymena-specific proteins. Furthermore, Med31 ChIP-seq analysis suggested a global role for Mediator in transcription regulation. We demonstrated that MED31 knockdown in growing Tetrahymena results in the ectopic expression of developmental genes important for programmed DNA rearrangements. In addition, indirect immunofluorescence revealed Med31 localization in meiotic micronuclei, implicating Mediator in RNAPII-dependent ncRNA transcription. Our results reveal structural and functional insights and implicate Mediator as an ancient cellular machinery for transcription regulation with a possible involvement in global transcription of ncRNAs.
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Affiliation(s)
- Jyoti Garg
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Matthew Cadorin
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Marcelo Ponce
- SciNet HPC Consortium, University of Toronto, 661 University Avenue, Suite 1140, Toronto, ON M5G 1M1, Canada
| | - Susanna Marquez
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, Canada; CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec, QC G1V 4G2, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
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6
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Ashraf K, Nabeel-Shah S, Garg J, Saettone A, Derynck J, Gingras AC, Lambert JP, Pearlman RE, Fillingham J. Proteomic Analysis of Histones H2A/H2B and Variant Hv1 in Tetrahymena thermophila Reveals an Ancient Network of Chaperones. Mol Biol Evol 2019; 36:1037-1055. [PMID: 30796450 PMCID: PMC6502085 DOI: 10.1093/molbev/msz039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Epigenetic information, which can be passed on independently of the DNA sequence, is stored in part in the form of histone posttranslational modifications and specific histone variants. Although complexes necessary for deposition have been identified for canonical and variant histones, information regarding the chromatin assembly pathways outside of the Opisthokonts remains limited. Tetrahymena thermophila, a ciliated protozoan, is particularly suitable to study and unravel the chromatin regulatory layers due to its unique physical separation of chromatin states in the form of two distinct nuclei present within the same cell. Using a functional proteomics pipeline, we carried out affinity purification followed by mass spectrometry of endogenously tagged T. thermophila histones H2A, H2B and variant Hv1.We identified a set of interacting proteins shared among the three analyzed histones that includes the FACT-complex, as well as H2A- or Hv1-specific chaperones. We find that putative subunits of T. thermophila versions of SWR- and INO80-complexes, as well as transcription-related histone chaperone Spt6Tt specifically copurify with Hv1. We also identified importin β6 and the T. thermophila ortholog of nucleoplasmin 1 (cNpl1Tt) as H2A–H2B interacting partners. Our results further implicate Poly [ADP-ribose] polymerases in histone metabolism. Molecular evolutionary analysis, reciprocal affinity purification coupled to mass spectrometry experiments, and indirect immunofluorescence studies using endogenously tagged Spt16Tt (FACT-complex subunit), cNpl1Tt, and PARP6Tt underscore the validity of our approach and offer mechanistic insights. Our results reveal a highly conserved regulatory network for H2A (Hv1)–H2B concerning their nuclear import and assembly into chromatin.
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Affiliation(s)
- Kanwal Ashraf
- Department of Biology, York University, Toronto, ON, Canada
| | - Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jyoti Garg
- Department of Biology, York University, Toronto, ON, Canada
| | - Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Joanna Derynck
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec, QC, Canada.,CHU de Québec Research Center, CHUL, Québec, QC, Canada
| | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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7
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Saettone A, Nabeel-Shah S, Garg J, Lambert JP, Pearlman RE, Fillingham J. Functional Proteomics of Nuclear Proteins in Tetrahymena thermophila: A Review. Genes (Basel) 2019; 10:E333. [PMID: 31052454 PMCID: PMC6562869 DOI: 10.3390/genes10050333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Abstract
Identification and characterization of protein complexes and interactomes has been essential to the understanding of fundamental nuclear processes including transcription, replication, recombination, and maintenance of genome stability. Despite significant progress in elucidation of nuclear proteomes and interactomes of organisms such as yeast and mammalian systems, progress in other models has lagged. Protists, including the alveolate ciliate protozoa with Tetrahymena thermophila as one of the most studied members of this group, have a unique nuclear biology, and nuclear dimorphism, with structurally and functionally distinct nuclei in a common cytoplasm. These features have been important in providing important insights about numerous fundamental nuclear processes. Here, we review the proteomic approaches that were historically used as well as those currently employed to take advantage of the unique biology of the ciliates, focusing on Tetrahymena, to address important questions and better understand nuclear processes including chromatin biology of eukaryotes.
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Affiliation(s)
- Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| | - Jyoti Garg
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada.
- CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, QC, G1V 4G2, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
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8
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Saettone A, Garg J, Lambert JP, Nabeel-Shah S, Ponce M, Burtch A, Thuppu Mudalige C, Gingras AC, Pearlman RE, Fillingham J. The bromodomain-containing protein Ibd1 links multiple chromatin-related protein complexes to highly expressed genes in Tetrahymena thermophila. Epigenetics Chromatin 2018. [PMID: 29523178 PMCID: PMC5844071 DOI: 10.1186/s13072-018-0180-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1. Results Using affinity purification coupled to mass spectrometry (AP–MS) we identified members of a SWI/SNF complex (SWI/SNFTt) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt, Swi1Tt, Swi3Tt, Snf12Tt, Brg1Tt, two proteins with potential chromatin-interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals. SWI/SNFTt subunits localize exclusively to the transcriptionally active macronucleus during growth and development, consistent with a role in transcription. While Tetrahymena Brg1 does not contain a BRD, our AP–MS results identified a BRD-containing SWI/SNFTt component, Ibd1 that associates with SWI/SNFTt during growth but not development. AP–MS analysis of epitope-tagged Ibd1 revealed it to be a subunit of several additional protein complexes, including putative SWRTt, and SAGATt complexes as well as a putative H3K4-specific histone methyl transferase complex. Recombinant Ibd1 recognizes acetyl-lysine marks on histones correlated with active transcription. Consistent with our AP–MS and histone array data suggesting a role in regulation of gene expression, ChIP-Seq analysis of Ibd1 indicated that it primarily binds near promoters and within gene bodies of highly expressed genes during growth. Conclusions Our results suggest that through recognizing specific histones marks, Ibd1 targets active chromatin regions of highly expressed genes in Tetrahymena where it subsequently might coordinate the recruitment of several chromatin-remodeling complexes to regulate the transcriptional landscape of vegetatively growing Tetrahymena cells. Electronic supplementary material The online version of this article (10.1186/s13072-018-0180-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada
| | - Jyoti Garg
- Department of Biology, York University, 4700 Keele St., Toronto, M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, M5G 1X5, Canada.,Department of Molecular Medicine, Université Laval, Quebec, Canada.,Centre Hospitalier Universitaire de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, G1V 4G2, Canada
| | - Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Marcelo Ponce
- SciNet HPC Consortium, University of Toronto, 661 University Ave, Suite 1140, Toronto, M5G 1M1, Canada
| | - Alyson Burtch
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada
| | - Cristina Thuppu Mudalige
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, M5G 1X5, 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
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada.
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9
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Xiong J, Gao S, Dui W, Yang W, Chen X, Taverna SD, Pearlman RE, Ashlock W, Miao W, Liu Y. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Res 2016; 44:10091-10105. [PMID: 27488188 PMCID: PMC5137421 DOI: 10.1093/nar/gkw684] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/21/2016] [Accepted: 07/24/2016] [Indexed: 02/06/2023] Open
Abstract
The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.
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Affiliation(s)
- Jie Xiong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,These authors contributed equally to this work as first authors
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China,These authors contributed equally to this work as first authors
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences and The Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ronald E. Pearlman
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Wendy Ashlock
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,Correspondence may also be addressed to Wei Miao.
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,To whom correspondence should be addressed. Tel: +1 734 6154239;
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10
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LIA4 encodes a chromoshadow domain protein required for genomewide DNA rearrangements in Tetrahymena thermophila. EUKARYOTIC CELL 2014; 13:1300-11. [PMID: 25084866 DOI: 10.1128/ec.00125-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Extensive DNA elimination occurs as part of macronuclear differentiation during Tetrahymena sexual reproduction. The identification of sequences to excise is guided by a specialized RNA interference (RNAi) machinery that targets the methylation of histone H3 lysine 9 (K9) and K27 on chromatin associated with these internal eliminated sequences (IESs). This modified chromatin is reorganized into heterochromatic subnuclear foci, which is a hallmark of their subsequent elimination. Here, we demonstrate that Lia4, a chromoshadow domain-containing protein, is an essential component in this DNA elimination pathway. LIA4 knockout (ΔLIA4) lines fail to excise IESs from their developing somatic genome and arrest at a late stage of conjugation. Lia4 acts after RNAi-guided heterochromatin formation, as both H3K9 and H3K27 methylation are established. Nevertheless, without LIA4, these cells fail to form the heterochromatic foci associated with DNA rearrangement, and Lia4 accumulates in the foci, indicating that Lia4 plays a key role in their structure. These data indicate a critical role for Lia4 in organizing the nucleus during Tetrahymena macronuclear differentiation.
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11
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Garg J, Lambert JP, Karsou A, Marquez S, Nabeel-Shah S, Bertucci V, Retnasothie DV, Radovani E, Pawson T, Gingras AC, Pearlman RE, Fillingham JS. Conserved Asf1-importin β physical interaction in growth and sexual development in the ciliate Tetrahymena thermophila. J Proteomics 2013; 94:311-26. [PMID: 24120531 DOI: 10.1016/j.jprot.2013.09.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/07/2013] [Accepted: 09/23/2013] [Indexed: 01/14/2023]
Abstract
UNLABELLED How the eukaryotic cell specifies distinct chromatin domains is a central problem in molecular biology. The ciliate protozoan Tetrahymena thermophila features a separation of structurally and functionally distinct germ-line and somatic chromatin into two distinct nuclei, the micronucleus (MIC) and macronucleus (MAC) respectively. To address questions about how distinct chromatin states are assembled in the MAC and MIC, we have initiated studies to define protein-protein interactions for T. thermophila chromatin-related proteins. Affinity purification followed by mass spectrometry analysis of the conserved Asf1 histone chaperone in T. thermophila revealed that it forms a complex with an importin β, ImpB6. Furthermore, these proteins co-localized to both the MAC and MIC in growth and development. We suggest that newly synthesized histones H3 and H4 in T. thermophila are transported via Asf1-ImpB6 in an evolutionarily conserved pathway to both nuclei where they then enter nucleus-specific chromatin assembly pathways. These studies set the stage for further use of functional proteomics to elucidate details of the characterization and functional analysis of the unique chromatin domains in T. thermophila. BIOLOGICAL SIGNIFICANCE Asf1 is an evolutionarily conserved chaperone of H3 and H4 histones that functions in replication dependent and independent chromatin assembly. Although Asf1 has been well studied in humans and yeast (members of the Opisthokonta lineage of eukaryotes), questions remain concerning its mechanism of function. To obtain additional insight into the Asf1 function we have initiated a proteomic analysis in the ciliate protozoan T. thermophila, a member of the Alveolata lineage of eukaryotes. Our results suggest that an evolutionarily conserved function of Asf1 is mediating the nuclear transport of newly synthesized histones H3 and H4.
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Affiliation(s)
- Jyoti Garg
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
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Kwon CS, Wagner D. Unwinding chromatin for development and growth: a few genes at a time. Trends Genet 2007; 23:403-12. [PMID: 17566593 DOI: 10.1016/j.tig.2007.05.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 05/01/2007] [Accepted: 05/30/2007] [Indexed: 01/11/2023]
Abstract
SWI/SNF chromatin remodeling ATPases control accessibility of the information stored in the genome. However, the in vivo role of these remodelers has remained poorly understood because null mutations in these result in embryonic lethality in most organisms. Recently, the study of conditional mutants in mammals and viable null mutants in plants, combined with genome wide expression studies in mammals, flies and plants, have implicated chromatin remodeling ATPases in the regulation of many developmental pathways in multicellular eukaryotes. In addition, these studies reveal striking functional specificity for chromatin remodeling in individual developmental processes.
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Affiliation(s)
- Chang Seob Kwon
- Department of Biology, University of Pennsylvania, Philadelphia, USA
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