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Zhang L, Cervantes MD, Pan S, Lindsley J, Dabney A, Kapler GM. Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles. Mol Biol Cell 2023; 34:rs1. [PMID: 36475712 PMCID: PMC9930529 DOI: 10.1091/mbc.e22-08-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During vegetative growth, the "cell cycles" of the diploid micronucleus and polyploid macronucleus are offset. Micronuclear S phase initiates just before cytokinesis and is completed in daughter cells before onset of macronuclear DNA replication. Mitotic micronuclear division occurs mid-cell cycle, while macronuclear amitosis is coupled to cell division. Here we report the first RNA-seq cell cycle analysis of a binucleated ciliated protozoan. RNA was isolated across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation. Using MetaCycle, 3244 of the 26,000+ predicted genes were shown to be cell cycle regulated. Proteins present in both nuclei exhibit a single mRNA peak that always precedes their macronuclear function. Nucleus-limited genes, including nucleoporins and importins, are expressed before their respective nucleus-specific role. Cyclin D and A/B gene family members exhibit different expression patterns that suggest nucleus-restricted roles. Periodically expressed genes cluster into seven cyclic patterns. Four clusters have known PANTHER gene ontology terms associated with G1/S and G2/M phase. We propose that these clusters encode known and novel factors that coordinate micro- and macronuclear-specific events such as mitosis, amitosis, DNA replication, and cell division.
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Affiliation(s)
- L. Zhang
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - M. D. Cervantes
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - S. Pan
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - J. Lindsley
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - A. Dabney
- Department of Statistics, Texas A&M University, College Station, TX 77843,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
| | - G. M. Kapler
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
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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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Iwamoto M, Mori C, Osakada H, Koujin T, Hiraoka Y, Haraguchi T. Nuclear localization signal targeting to macronucleus and micronucleus in binucleated ciliate Tetrahymena thermophila. Genes Cells 2018; 23:568-579. [PMID: 29882620 DOI: 10.1111/gtc.12602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/27/2018] [Accepted: 05/08/2018] [Indexed: 01/25/2023]
Abstract
Ciliated protozoa possess two morphologically and functionally distinct nuclei: a macronucleus (MAC) and a micronucleus (MIC). The MAC is transcriptionally active and functions in all cellular events. The MIC is transcriptionally inactive during cell growth, but functions in meiotic events to produce progeny nuclei. Thus, these two nuclei must be distinguished by the nuclear proteins required for their distinct functions during cellular events such as cell proliferation and meiosis. To understand the mechanism of the nuclear transport specific to either MAC or MIC, we identified specific nuclear localization signals (NLSs) in two MAC- and MIC-specific nuclear proteins, macronuclear histone H1 and micronuclear linker histone-like protein (Mlh1), respectively. By expressing GFP-fused fragments of these proteins in Tetrahymena thermophila cells, two distinct regions in macronuclear histone H1 protein were assigned as independent MAC-specific NLSs and two distinct regions in Mlh1 protein were assigned as independent MIC-specific NLSs. These NLSs contain several essential lysine residues responsible for the MAC- and MIC-specific nuclear transport, but neither contains any consensus sequence with known monopartite or bipartite NLSs in other model organisms. Our findings contribute to understanding how specific nuclear targeting is achieved to perform distinct nuclear functions in binucleated ciliates.
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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4
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Qiao J, Xu J, Bo T, Wang W. Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila. PLoS One 2017; 12:e0187475. [PMID: 29095884 PMCID: PMC5667856 DOI: 10.1371/journal.pone.0187475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 10/19/2017] [Indexed: 02/02/2023] Open
Abstract
Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila.
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Affiliation(s)
- Juxia Qiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi, China
- * E-mail:
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5
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Wang Y, Wang Y, Sheng Y, Huang J, Chen X, AL-Rasheid KA, Gao S. A comparative study of genome organization and epigenetic mechanisms in model ciliates, with an emphasis on Tetrahymena , Paramecium and Oxytricha. Eur J Protistol 2017; 61:376-387. [DOI: 10.1016/j.ejop.2017.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
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Cutter AR, Hayes JJ. Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochem Cell Biol 2016; 95:171-178. [PMID: 28177778 DOI: 10.1139/bcb-2016-0097] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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7
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Liao R, Mizzen CA. Interphase H1 phosphorylation: Regulation and functions in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:476-85. [PMID: 26657617 DOI: 10.1016/j.bbagrm.2015.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022]
Abstract
Many metazoan cell types differentially express multiple non-allelic amino acid sequence variants of histone H1. Although early work revealed that H1 variants, collectively, are phosphorylated during interphase and mitosis, differences between individual H1 variants in the sites they possess for mitotic and interphase phosphorylation have been elucidated only relatively recently. Here, we review current knowledge on the regulation and function of interphase H1 phosphorylation, with a particular emphasis on how differences in interphase phosphorylation among the H1 variants of mammalian cells may enable them to have differential effects on transcription and other chromatin processes.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA; Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA.
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8
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Parseghian MH. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS BIOPHYSICS 2015; 2:724-772. [PMID: 31289748 PMCID: PMC6615755 DOI: 10.3934/biophy.2015.4.724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.
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9
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Izzo A, Schneider R. The role of linker histone H1 modifications in the regulation of gene expression and chromatin dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:486-95. [PMID: 26348411 DOI: 10.1016/j.bbagrm.2015.09.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/07/2015] [Accepted: 09/02/2015] [Indexed: 12/27/2022]
Abstract
BACKGROUND Linker histone H1 is a structural component of chromatin. It exists as a family of related proteins known as variants and/or subtypes. H1.1, H1.2, H1.3, H1.4 and H1.5 are present in most somatic cells, whereas other subtypes are mainly expressed in more specialized cells. SCOPE OF REVIEW H1 subtypes have been shown to have unique functions in chromatin structure and dynamics. This can occur at least in part via specific post-translational modifications of distinct H1 subtypes. However, while core histone modifications have been extensively studied, our knowledge of H1 modifications and their molecular functions has remained for a long time limited to phosphorylation. In this review we discuss the current state of knowledge of linker histone H1 modifications and where possible highlight functional differences in the modifications of distinct H1 subtypes. MAJOR CONCLUSIONS AND GENERAL SIGNIFICANCE H1 histones are intensely post-translationally modified. These modifications are located in the N- and C-terminal tails as well as within the globular domain. Recently, advanced mass spectrometrical analysis revealed a large number of novel histone H1 subtype specific modification sites and types. H1 modifications include phosphorylation, acetylation, methylation, ubiquitination, and ADP ribosylation. They are involved in the regulation of all aspects of linker histone functions, however their mechanism of action is often only poorly understood. Therefore systematic functional characterization of H1 modifications will be necessary in order to better understand their role in gene regulation as well as in higher-order chromatin structure and dynamics.
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Affiliation(s)
- Annalisa Izzo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France.
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10
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Cutter AR, Hayes JJ. A brief review of nucleosome structure. FEBS Lett 2015; 589:2914-22. [PMID: 25980611 DOI: 10.1016/j.febslet.2015.05.016] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 12/23/2022]
Abstract
The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States.
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11
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Aeschlimann SH, Jönsson F, Postberg J, Stover NA, Petera RL, Lipps HJ, Nowacki M, Swart EC. The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. Genome Biol Evol 2014; 6:1707-23. [PMID: 24951568 PMCID: PMC4122937 DOI: 10.1093/gbe/evu139] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: A small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia’s macronucleus has a very unusual architecture, comprised variably and highly amplified “nanochromosomes,” each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between S. lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation, and copy number. Protein domain searches in Stylonychia revealed two new telomere-binding protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements.
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Affiliation(s)
| | - Franziska Jönsson
- Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, Germany
| | - Jan Postberg
- Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, GermanyDepartment of Neonatology, HELIOS Children's Hospital, Witten/Herdecke University, Wuppertal, Germany
| | | | | | - Hans-Joachim Lipps
- Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, Germany
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12
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Takagi M, Imamoto N. Control of nuclear size by NPC proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:571-91. [PMID: 24563366 DOI: 10.1007/978-1-4899-8032-8_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The architecture of the cell nucleus in cancer cells is often altered in a manner associated with the tumor type and aggressiveness. Therefore, it has been the central criterion in the pathological diagnosis and prognosis of cancer. However, the molecular mechanism behind these observed changes in nuclear morphology, including size, remains completely unknown. Based on our current understanding of the physiology of the nuclear pore complex (NPC) and its constituents, which are collectively referred to as nucleoporins (Nups), we discuss how the structural and functional ablation of the NPC and Nups could directly or indirectly contribute to the changes in nuclear size observed in cancer cells.
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Affiliation(s)
- Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN, WAKO, Saitama, 351-0198, Japan,
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13
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Abstract
Research using ciliates revealed early examples of epigenetic phenomena and continues to provide novel findings. These protozoans maintain separate germline and somatic nuclei that carry transcriptionally silent and active genomes, respectively. Examining the differences in chromatin within distinct nuclei of Tetrahymena identified histone variants and established that transcriptional regulators act by modifying histones. Formation of somatic nuclei requires both transcriptional activation of silent chromatin and large-scale DNA elimination. This somatic genome remodeling is directed by homologous RNAs, acting with an RNA interference (RNAi)-related machinery. Furthermore, the content of the parental somatic genome provides a homologous template to guide this genome restructuring. The mechanisms regulating ciliate DNA rearrangements reveal the surprising power of homologous RNAs to remodel the genome and transmit information transgenerationally.
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Affiliation(s)
- Douglas L Chalker
- Department of Biology, Washington University, St. Louis, Missouri 63130
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14
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Harshman SW, Young NL, Parthun MR, Freitas MA. H1 histones: current perspectives and challenges. Nucleic Acids Res 2013; 41:9593-609. [PMID: 23945933 PMCID: PMC3834806 DOI: 10.1093/nar/gkt700] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
H1 and related linker histones are important both for maintenance of higher-order chromatin structure and for the regulation of gene expression. The biology of the linker histones is complex, as they are evolutionarily variable, exist in multiple isoforms and undergo a large variety of posttranslational modifications in their long, unstructured, NH2- and COOH-terminal tails. We review recent progress in understanding the structure, genetics and posttranslational modifications of linker histones, with an emphasis on the dynamic interactions of these proteins with DNA and transcriptional regulators. We also discuss various experimental challenges to the study of H1 and related proteins, including limitations of immunological reagents and practical difficulties in the analysis of posttranslational modifications by mass spectrometry.
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Affiliation(s)
- Sean W Harshman
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA, College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA and Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
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15
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Edrissi B, Taghizadeh K, Dedon PC. Quantitative analysis of histone modifications: formaldehyde is a source of pathological n(6)-formyllysine that is refractory to histone deacetylases. PLoS Genet 2013; 9:e1003328. [PMID: 23468656 PMCID: PMC3585032 DOI: 10.1371/journal.pgen.1003328] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 01/03/2013] [Indexed: 01/07/2023] Open
Abstract
Aberrant protein modifications play an important role in the pathophysiology of many human diseases, in terms of both dysfunction of physiological modifications and the formation of pathological modifications by reaction of proteins with endogenous electrophiles. Recent studies have identified a chemical homolog of lysine acetylation, N6-formyllysine, as an abundant modification of histone and chromatin proteins, one possible source of which is the reaction of lysine with 3′-formylphosphate residues from DNA oxidation. Using a new liquid chromatography-coupled to tandem mass spectrometry method to quantify all N6-methyl-, -acetyl- and -formyl-lysine modifications, we now report that endogenous formaldehyde is a major source of N6-formyllysine and that this adduct is widespread among cellular proteins in all compartments. N6-formyllysine was evenly distributed among different classes of histone proteins from human TK6 cells at 1–4 modifications per 104 lysines, which contrasted strongly with lysine acetylation and mono-, di-, and tri-methylation levels of 1.5-380, 5-870, 0-1400, and 0-390 per 104 lysines, respectively. While isotope labeling studies revealed that lysine demethylation is not a source of N6-formyllysine in histones, formaldehyde exposure was observed to cause a dose-dependent increase in N6-formyllysine, with use of [13C,2H2]-formaldehyde revealing unchanged levels of adducts derived from endogenous sources. Inhibitors of class I and class II histone deacetylases did not affect the levels of N6-formyllysine in TK6 cells, and the class III histone deacetylase, SIRT1, had minimal activity (<10%) with a peptide substrate containing the formyl adduct. These data suggest that N6-formyllysine is refractory to removal by histone deacetylases, which supports the idea that this abundant protein modification could interfere with normal regulation of gene expression if it arises at conserved sites of physiological protein secondary modification. Oxidative stress and inflammation lead to the generation of a multitude of electrophiles in cells that in turn react with nucleophilic macromolecules such as DNA, RNA, polyunsaturated fatty acids, and proteins, leading to progression of a variety of disorders and diseases. Emerging evidence points to widespread modification of cellular proteins by N6-formylation of lysine as a result of adventitious reactions with endogenous electrophiles. N6-Formyllysine is a chemical homolog of the biologically important N6-acetyllysine and thus may interfere with acetylation signaling in cells. While N6-formyllysine adducts are now well recognized as abundant protein modifications in cells, the source of these pathological adducts remains unclear. Our previous study proposed N6-formylation of lysine in histone proteins occurred by reaction of lysine with 3′-formylphosphate residues arising from DNA oxidation. Here, we investigate additional sources as well as the fate of this abundant pathological protein modification. Our results reveal that endogenous formaldehyde is a major source of N6-formyllysine and that this adduct is widely distributed among proteins in all cell compartments. We also demonstrate for the first time that N6-formyllysine modifications do not undergo appreciable removal by histone deacetylases, which suggests that they persist in proteins and possibly interfere with the signaling functions at conserved lysine positions in histone proteins.
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Affiliation(s)
- Bahar Edrissi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Koli Taghizadeh
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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16
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Abstract
Nuclear dualism is a characteristic feature of the ciliated protozoa. Tetrahymena have two different nuclei in each cell. The larger, polyploid, somatic macronucleus (MAC) is the site of transcriptional activity in the vegetatively growing cell. The smaller, diploid micronucleus (MIC) is transcriptionally inactive in vegetative cells, but is transcriptionally active in mating cells and responsible for the genetic continuity during sexual reproduction. Although the MICs and MACs develop from mitotic products of a common progenitor and reside in a common cytoplasm, they are different from one another in almost every respect.
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Affiliation(s)
- Kathleen M Karrer
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
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Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain. Mol Cell Biol 2011; 31:2341-8. [PMID: 21464206 DOI: 10.1128/mcb.05145-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Linker histones play essential roles in the chromatin structure of higher eukaryotes. While binding to the surface of nucleosomes is directed by an ∼ 80-amino-acid-residue globular domain, the structure and interactions of the lysine-rich ∼ 100-residue C-terminal domain (CTD), primarily responsible for the chromatin-condensing functions of linker histones, are poorly understood. By quantitatively analyzing binding of a set of H1 CTD deletion mutants to nucleosomes containing various lengths of linker DNA, we have identified interactions between distinct regions of the CTD and nucleosome linker DNA at least 21 bp from the edge of the nucleosome core. Importantly, partial CTD truncations caused increases in H1 binding affinity, suggesting that significant entropic costs are incurred upon binding due to CTD folding. van't Hoff entropy/enthalpy analysis and intramolecular fluorescent resonance energy transfer (FRET) studies indicate that the CTD undergoes substantial nucleosome-directed folding, in a manner that is distinct from that which occurs upon H1 binding to naked DNA. In addition to defining critical interactions between the H1 CTD and linker DNA, our data indicate that the H1 CTD is an intrinsically disordered domain and provide important insights into the biological function of this protein.
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Iwamoto M, Asakawa H, Hiraoka Y, Haraguchi T. Nucleoporin Nup98: a gatekeeper in the eukaryotic kingdoms. Genes Cells 2010; 15:661-9. [PMID: 20545767 DOI: 10.1111/j.1365-2443.2010.01415.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The nucleoporin Nup98 is an essential component of the nuclear pore complex. This peripheral nucleoporin with its Gly-Leu-Phe-Gly (GLFG) repeat domain contributes to nuclear-cytoplasmic trafficking, including mRNA export. In addition, accumulating studies indicate that Nup98 plays roles in several important biological events such as gene expression, mitotic checkpoint, and pathogenesis. Nup98 is well conserved among organisms belonging to the fungi and animal kingdoms. These kingdoms belong to the eukaryotic supergroup Opisthokonta. However, there is considerable diversity in the Nup98 orthologs expressed in organisms belonging to other eukaryotic supergroups. Intriguingly, in ciliates, a unicellular organism having two functionally distinct nuclei, GLFG-Nup98 is present in one of the nuclei and a distinct Nup98 ortholog is present in the other nucleus, and these different Nup98s participate in a nucleus-selective transport mechanism. In this review, we focus on Nup98 function and discuss how this nucleoporin has evolved in eukaryotic kingdoms.
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Affiliation(s)
- Masaaki Iwamoto
- Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, Japan
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19
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Raghuram N, Carrero G, Th’ng J, Hendzel MJ. Molecular dynamics of histone H1This paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2009; 87:189-206. [DOI: 10.1139/o08-127] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The histone H1 family of nucleoproteins represents an important class of structural and architectural proteins that are responsible for maintaining and stabilizing higher-order chromatin structure. Essential for mammalian cell viability, they are responsible for gene-specific regulation of transcription and other DNA-dependent processes. In this review, we focus on the wealth of information gathered on the molecular kinetics of histone H1 molecules using novel imaging techniques, such as fluorescence recovery after photobleaching. These experiments have shed light on the effects of H1 phosphorylation and core histone acetylation in influencing chromatin structure and dynamics. We also delineate important concepts surrounding the C-terminal domain of H1, such as the intrinsic disorder hypothesis, and how it affects H1 function. Finally, we address the biochemical mechanisms behind low-affinity H1 binding.
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Affiliation(s)
- Nikhil Raghuram
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
| | - Gustavo Carrero
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
| | - John Th’ng
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
| | - Michael J. Hendzel
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
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Nucleus-specific importin alpha proteins and nucleoporins regulate protein import and nuclear division in the binucleate Tetrahymena thermophila. EUKARYOTIC CELL 2008; 7:1487-99. [PMID: 18676955 DOI: 10.1128/ec.00193-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ciliate Tetrahymena thermophila, having both germ line micronuclei and somatic macronuclei, must possess a specialized nucleocytoplasmic transport system to import proteins into the correct nucleus. To understand how Tetrahymena can target proteins to distinct nuclei, we first characterized FG repeat-containing nucleoporins and found that micro- and macronuclei utilize unique subsets of these proteins. This finding implicates these proteins in the differential permeability of the two nuclei and implies that nuclear pores with discrete specificities are assembled within a single cell. To identify the import machineries that interact with these different pores, we characterized the large families of karyopherin homologs encoded within the genome. Localization studies of 13 putative importin (imp) alpha- and 11 imp beta-like proteins revealed that imp alpha-like proteins are nucleus specific--nine localized to the germ line micronucleus--but that most imp beta-like proteins localized to both types of nuclei. These data suggest that micronucleus-specific proteins are transported by specific imp alpha adapters. The different imp alpha proteins exhibit substantial sequence divergence and do not appear to be simply redundant in function. Disruption of the IMA10 gene encoding an imp alpha-like protein that accumulates in dividing micronuclei results in nuclear division defects and lethality. Thus, nucleus-specific protein import and nuclear function in Tetrahymena are regulated by diverse, specialized karyopherins.
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21
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Brosch G, Loidl P, Graessle S. Histone modifications and chromatin dynamics: a focus on filamentous fungi. FEMS Microbiol Rev 2008; 32:409-39. [PMID: 18221488 PMCID: PMC2442719 DOI: 10.1111/j.1574-6976.2007.00100.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 11/13/2007] [Indexed: 12/19/2022] Open
Abstract
The readout of the genetic information of eukaryotic organisms is significantly regulated by modifications of DNA and chromatin proteins. Chromatin alterations induce genome-wide and local changes in gene expression and affect a variety of processes in response to internal and external signals during growth, differentiation, development, in metabolic processes, diseases, and abiotic and biotic stresses. This review aims at summarizing the roles of histone H1 and the acetylation and methylation of histones in filamentous fungi and links this knowledge to the huge body of data from other systems. Filamentous fungi show a wide range of morphologies and have developed a complex network of genes that enables them to use a great variety of substrates. This fact, together with the possibility of simple and quick genetic manipulation, highlights these organisms as model systems for the investigation of gene regulation. However, little is still known about regulation at the chromatin level in filamentous fungi. Understanding the role of chromatin in transcriptional regulation would be of utmost importance with respect to the impact of filamentous fungi in human diseases and agriculture. The synthesis of compounds (antibiotics, immunosuppressants, toxins, and compounds with adverse effects) is also likely to be regulated at the chromatin level.
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Affiliation(s)
- Gerald Brosch
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Fritz-Pregl-Strasse 3, Innsbruck, Austria
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22
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Huvos PE. Extensive changes in the locations and sequence content of developmentally deleted DNA between Tetrahymena thermophila and its closest relative, T. malaccensis. J Eukaryot Microbiol 2007; 54:73-82. [PMID: 17300523 DOI: 10.1111/j.1550-7408.2006.00148.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tetrahymena thermophila has two different types of nuclei in a single cell. The development of the transcriptionally active macronucleus from a transcriptionally inert micronucleus is accompanied by the elimination of numerous DNA segments, called deletion elements or internally eliminated sequences (IESs). To try to distinguish between alternative modes for the generation of IESs during evolution, DNA sequences at three loci that contain IESs in T. thermophila were examined in Tetrahymena malaccensis, the closest relative of T. thermophila. In T. malaccensis, two loci examined do not seem to contain IESs. At one of these sites, the presence of the IES in T. thermophila can be accounted for either by insertion of a novel IES into T. thermophila or its precise deletion from T. malaccensis. At a third locus, the newly discovered EFZ IES (named after neighboring EF-hand/Zinc finger genes), both T. thermophila and T. malaccensis contain IESs, but of different length and sequence content. If the three locations examined are a representative sample, the evolution of IESs seems to have been very rapid, and has led to substantial changes in the IES content of these two closely related species. Although insertion-deletion events are likely to have shaped IES evolution, none of the IESs examined here could be identified as transposon-like elements.
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Affiliation(s)
- Piroska E Huvos
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA.
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23
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Juranek SA, Lipps HJ. New Insights into the Macronuclear Development in Ciliates. INTERNATIONAL REVIEW OF CYTOLOGY 2007; 262:219-51. [PMID: 17631190 DOI: 10.1016/s0074-7696(07)62005-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During macronuclear differentiation in ciliated protozoa, most amazing "DNA gymnastics" takes place, which includes DNA excision, DNA elimination, DNA reorganization, and DNA-specific amplification. Although the morphological events occurring during macronuclear development are well described, a detailed knowledge of the molecular mechanisms and the regulation of this differentiation process is still missing. However, recently several models have been proposed for the molecular regulation of macronuclear differentiation, but these models have yet to be verified experimentally. The scope of this review is to summarize recent discoveries in different ciliate species and to compare and discuss the different models proposed. Results obtained in these studies are not only relevant for our understanding of nuclear differentiation in ciliates, but also for cellular differentiation in eukaryotic organisms in general as well as for other disciplines such as bioinformatics and computational biology.
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Affiliation(s)
- Stefan A Juranek
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York 10021, USA
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24
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Abstract
Protozoan parasites are early branching eukaryotes causing significant morbidity and mortality in humans and livestock. Single-celled parasites have evolved complex life cycles, which may involve multiple host organisms, and strategies to evade host immune responses. Consequently, two key aspects of virulence that underlie pathogenesis are parasite differentiation and antigenic variation, both of which require changes in the expressed genome. Complicating these requisite alterations in the parasite transcriptome is chromatin, which serves as a formidable barrier to DNA processes including transcription, repair, replication and recombination. Considerable progress has been made in the study of chromatin dynamics in other eukaryotes, and there is much to be gained in extending these analyses to protozoan parasites. Much of the work completed to date has focused on histone acetylation and methylation in the apicomplexans and trypanosomatids. As we describe in this review, such studies provide a unique vantage point of the evolutionary picture of eukaryotic cell development, and reveal unique phenomena that could be exploited pharmacologically to treat protozoal diseases.
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Affiliation(s)
- William J Sullivan
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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25
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Woodcock CL, Skoultchi AI, Fan Y. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Res 2006; 14:17-25. [PMID: 16506093 DOI: 10.1007/s10577-005-1024-3] [Citation(s) in RCA: 327] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Despite a great deal of attention over many years, the structural and functional roles of the linker histone H1 remain enigmatic. The earlier concepts of H1 as a general transcriptional inhibitor have had to be reconsidered in the light of experiments demonstrating a minor effect of H1 deletion in unicellular organisms. More recent work analysing the results of depleting H1 in mammals through genetic knockouts of selected H1 subtypes in the mouse has shown that cells and tissues can tolerate a surprisingly low H1 content. One common feature of H1-depleted nuclei is a reduction in nucleosome repeat length (NRL). Moreover, there is a robust linear relationship between H1 stoichiometry and NRL, suggesting an inherent homeostatic mechanism that maintains intranuclear electrostatic balance. It is also clear that the 1 H1 per nucleosome paradigm for higher eukaryotes is the exception rather than the rule. This, together with the high mobility of H1 within the nucleus, prompts a reappraisal of the role of linker histone as an obligatory chromatin architectural protein.
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Affiliation(s)
- Christopher L Woodcock
- Biology Department and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, 01003, USA.
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26
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Jacobs ME, Cortezzo DE, Klobutcher LA. Assessing the effectiveness of coding and non-coding regions in antisense ribosome inhibition of gene expression in Tetrahymena. J Eukaryot Microbiol 2005; 51:536-41. [PMID: 15537088 DOI: 10.1111/j.1550-7408.2004.tb00289.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Tetrahymena thermophila, an "antisense ribosome" technology has been developed for inhibiting gene expression and generating novel mutants. Short segments of genes are inserted in antisense orientation into an rDNA vector in a region corresponding to an external loop of the folded rRNA. DNA segments derived from the 5'-ends of genes have proven most effective in reducing cognate gene expression. To investigate the efficacy of other genic regions, we generated Tetrahymena cell lines with antisense ribosome constructs containing 100-bp DNA segments derived from the 5'-ends, 3'-ends, and internal coding regions of two non-essential genes, granule lattice protein 1 and macronuclear histone H1. The 5'- and 3'-end constructs inhibited gene expression, but antisense ribosomes derived exclusively from coding regions had little effect.
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Affiliation(s)
- Mary Ellen Jacobs
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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27
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Mochizuki K, Gorovsky MA. Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement. Genes Dev 2004; 18:2068-73. [PMID: 15314029 PMCID: PMC515285 DOI: 10.1101/gad.1219904] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We proposed a scan-RNA model for genome rearrangement based on finding small RNAs that hybridized preferentially to micronuclear-specific sequences and on the properties of Twi1p, a PPD protein required for both sequence elimination and small RNA accumulation in Tetrahymena. Here we show that Twi1p interacts with the small RNAs in both the old and the developing macronucleus, and is required for their stability. We show that the specificity of the small RNAs for micronuclear-limited sequences increases during conjugation. These results indicate that the small RNAs observed in conjugating cells have the properties predicted for scan RNAs.
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Affiliation(s)
- Kazufumi Mochizuki
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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28
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Galindo M, Varela N, Espinoza I, Toro GC, Hellman U, Wernstedt C, Galanti N. Chromatin from two classes of platyhelminthes display both protist H1 and higher eukaryote core histones. FEBS Lett 2004; 567:225-9. [PMID: 15178327 DOI: 10.1016/j.febslet.2004.04.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2003] [Revised: 04/20/2004] [Accepted: 04/23/2004] [Indexed: 11/25/2022]
Abstract
Histones from the parasitic platyhelminthes, Echinococcus granulosus and Fasciola hepatica, were systematically characterized. Core histones H2A, H2B, H3 and H4, which were identified on the basis of amino acid sequencing and mass spectrometry data, showed conserved electrophoretic patterns. Histones H1, identified on the basis of physicochemical properties, amino acid composition and amino acid sequencing, showed divergence, both in their number and electrophoretic mobilities, between the two species and among other organisms. According to these data, core histones but not H1 histones, would be stabilized during evolution at the level of platyhelminthes.
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Affiliation(s)
- Mario Galindo
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Casilla 70061, Correo 7, Santiago, Chile
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29
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Folco HD, Freitag M, Ramón A, Temporini ED, Alvarez ME, García I, Scazzocchio C, Selker EU, Rosa AL. Histone H1 Is required for proper regulation of pyruvate decarboxylase gene expression in Neurospora crassa. EUKARYOTIC CELL 2003; 2:341-50. [PMID: 12684383 PMCID: PMC154839 DOI: 10.1128/ec.2.2.341-350.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 12/20/2002] [Indexed: 11/20/2022]
Abstract
We show that Neurospora crassa has a single histone H1 gene, hH1, which encodes a typical linker histone with highly basic N- and C-terminal tails and a central globular domain. A green fluorescent protein-tagged histone H1 chimeric protein was localized exclusively to nuclei. Mutation of hH1 by repeat-induced point mutation (RIP) did not result in detectable defects in morphology, DNA methylation, mutagen sensitivity, DNA repair, fertility, RIP, chromosome pairing, or chromosome segregation. Nevertheless, hH1 mutants had mycelial elongation rates that were lower than normal on all tested carbon sources. This slow linear growth phenotype, however, was less evident on medium containing ethanol. The pyruvate decarboxylase gene, cfp, was abnormally derepressed in hH1 mutants on ethanol-containing medium. This derepression was also found when an ectopically integrated fusion of the cfp gene promoter to the reporter gene hph was analyzed. Thus, Neurospora histone H1 is required for the proper regulation of cfp, a gene with a key role in the respiratory-fermentative pathway.
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Affiliation(s)
- H Diego Folco
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, 5016 Córdoba, Argentina
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30
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Mizzen CA. Purification and Analyses of Histone H1 Variants and H1 Posttranslational Modifications. Methods Enzymol 2003; 375:278-97. [PMID: 14870674 DOI: 10.1016/s0076-6879(03)75019-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Affiliation(s)
- Craig A Mizzen
- Department of Cell & Structural Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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31
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Dou Y, Bowen J, Liu Y, Gorovsky MA. Phosphorylation and an ATP-dependent process increase the dynamic exchange of H1 in chromatin. J Cell Biol 2002; 158:1161-70. [PMID: 12356861 PMCID: PMC2173238 DOI: 10.1083/jcb.200202131] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In Tetrahymena cells, phosphorylation of linker histone H1 regulates transcription of specific genes. Phosphorylation acts by creating a localized negative charge patch and phenocopies the loss of H1 from chromatin, suggesting that it affects transcription by regulating the dissociation of H1 from chromatin. To test this hypothesis, we used FRAP of GFP-tagged H1 to analyze the effects of mutations that either eliminate or mimic phosphorylation on the binding of H1 to chromatin both in vivo and in vitro. We demonstrate that phosphorylation can increase the rate of dissociation of H1 from chromatin, providing a mechanism by which it can affect H1 function in vivo. We also demonstrate a previously undescribed ATP-dependent process that has a global effect on the dynamic binding of linker histone to chromatin.
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Affiliation(s)
- Yali Dou
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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32
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Karrer KM, VanNuland TA. Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1. Nucleic Acids Res 2002; 30:1364-70. [PMID: 11884634 PMCID: PMC101364 DOI: 10.1093/nar/30.6.1364] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There are about 50 copies of each chromosome in the somatic macronucleus of the ciliated protozoan TETRAHYMENA: Approximately 0.8% of the adenine residues in the macronuclear DNA of Tetrahymena are methylated to N6-methyladenine. The degree of methylation varies between sites from a very low percentage to >90%. In this study a correlation was found between nucleosome positioning and DNA methylation. Eight GATC sites with different levels of methylation were examined. There was a direct correlation between the degree of methylation and proximity to linker DNA at these sites. Although methylation occurs preferentially in linker DNA, the patterns and extent of methylation in a histone H1 knockout strain were virtually indistinguishable from those in wild-type cells.
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Affiliation(s)
- Kathleen M Karrer
- Department of Biology, Wehr Life Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, USA.
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33
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Triana O, Galanti N, Olea N, Hellman U, Wernstedt C, Lujan H, Medina C, Toro GC. Chromatin and histones from Giardia lamblia: a new puzzle in primitive eukaryotes. J Cell Biochem 2001; 82:573-82. [PMID: 11500935 DOI: 10.1002/jcb.1159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The three deepest eukaryote lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microsporidia, Metamonada, and Parabasalia. They are followed by either the Euglenozoa (e.g., Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eukaryotes. Considering the great divergence of histone proteins in protozoa we have extended our studies of histones from Trypanosomes (Trypanosoma cruzi, Crithidia fasciculata and Leishmania mexicana) to the Metamonada Giardia lamblia, since Giardia is thought to be one of the most primitive eukaryotes. In the present work, the structure of G. lamblia chromatin and the histone content of the soluble chromatin were investigated and compared with that of higher eukaryotes, represented by calf thymus. The chromatin is present as nucleosome filaments which resemble the calf thymus array in that they show a more regular arrangement than those described for Trypanosoma. SDS-polyacrylamide gel electrophoresis and protein characterization revealed that the four core histones described in Giardia are in the same range of divergence with the histones from other lower eukaryotes. In addition, G. lamblia presented an H1 histone with electrophoretic mobility resembling the H1 of higher eukaryotes, in spite of the fact that H1 has a different molecular mass in calf thymus. Giardia also presents a basic protein which was identified as an HU-like DNA-binding protein usually present in eubacteria, indicating a chimaeric composition for the DNA-binding protein set in this species. Finally, the phylogenetic analysis of selected core histone protein sequences place Giardia divergence before Trypanosoma, despite the fact that Trypanosoma branch shows an acceleration in the evolutionary rate pointing to an unusual evolutionary behavior in this lineage.
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Affiliation(s)
- O Triana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 7, Chile
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34
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Abstract
Genes encoding linker histone variants have evolved to link their expression to signals controlling the proliferative capacities of cells, i.e. cycling and growth-arrested cells express distinct and specific H1 subtypes. In metazoan, these variants show a tripartite structure, with considerably divergent sequences in their amino and carboxyl terminus domains. The aim of this review is to show how specific regulatory signals control the expression of an individual H1 and to discuss the functional significance of the two variables associated with a linker histone: its primary sequence and the timing of its expression.
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Affiliation(s)
- S Khochbin
- Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation - INSERM U309, Equipe chromatine et expression des gènes, Institut Albert Bonniot, Faculté de Médecine, Domaine de la Merci, 38706 La Tronche Cedex, France.
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35
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Green GR. Phosphorylation of histone variant regions in chromatin: Unlocking the linker? Biochem Cell Biol 2001. [DOI: 10.1139/o01-075] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Histone variants illuminate the behavior of chromatin through their unique structures and patterns of postsynthetic modification. This review examines the literature on heteromorphous histone structures in chromatin, structures that are primary targets for histone kinases and phosphatases in vivo. Special attention is paid to certain well-studied experimental systems: mammalian culture cells, chicken erythrocytes, sea urchin sperm, wheat sprouts, Tetrahymena, and budding yeast. A common theme emerges from these studies. Specialized, highly basic structures in histone variants promote chromatin condensation in a variety of developmental situations. Before, and sometimes after condensed chromatin is formed, the chromatin is rendered soluble by phosphorylation of the heteromorphous regions, preventing their interaction with linker DNA. A simple structural model accounting for histone variation and phosphorylation is presented.Key words: phosphorylation, histone variants, chromatin, linker DNA.
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36
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Dou Y, Gorovsky MA. Phosphorylation of linker histone H1 regulates gene expression in vivo by creating a charge patch. Mol Cell 2000; 6:225-31. [PMID: 10983971 DOI: 10.1016/s1097-2765(00)00024-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In Tetrahymena, histone H1 phosphorylation can regulate transcription and mimics loss of H1 from chromatin. We investigated the mechanism by which H1 phosphorylation affects transcription. Tetrahymena strains were created containing mutations in H1 that mimicked the charge of the phosphorylated region without mimicking the structure or increased hydrophilicity of the phosphorylated residues. Whenever the charge resembled that of the phosphorylated state, the induced expression of the CyP1 gene was greatly inhibited. Whenever the charge was similar to that of the dephosphorylated state, the CyP1 gene was induced normally. These results argue strongly that phosphorylation of H1 acts by changing the overall charge of a small domain, not by phosphate recognition or by creating a site-specific charge.
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Affiliation(s)
- Y Dou
- Department of Biology, University of Rochester, New York 14627, USA
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37
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Ramón A, Muro-Pastor MI, Scazzocchio C, Gonzalez R. Deletion of the unique gene encoding a typical histone H1 has no apparent phenotype in Aspergillus nidulans. Mol Microbiol 2000; 35:223-33. [PMID: 10632892 DOI: 10.1046/j.1365-2958.2000.01702.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have cloned the H1 histone gene (hhoA) of Aspergillus nidulans. This single-copy gene codes for a typical linker histone with one central globular domain. The open reading frame is interrupted by six introns. The position of the first intron is identical to that of introns found in some plant histones. An H1-GFP fusion shows exclusive nuclear localization, whereas chromosomal localization can be observed during condensation at mitosis. Surprisingly, the deletion of hhoA results in no obvious phenotype. The nucleosomal repeat length and susceptibility to micrococcal nuclease digestion of A. nidulans chromatin are unchanged in the deleted strain. The nucleosomal organization of a number of promoters, including in particular the strictly regulated niiA-niaD bidirectional promoter is not affected.
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Affiliation(s)
- A Ramón
- Institut de Génétique et Microbiologie, Bâtiment 409, Université Paris-Sud, UMR 8621, 91405 Orsay Cedex, France
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38
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Barra JL, Rhounim L, Rossignol JL, Faugeron G. Histone H1 is dispensable for methylation-associated gene silencing in Ascobolus immersus and essential for long life span. Mol Cell Biol 2000; 20:61-9. [PMID: 10594009 PMCID: PMC85047 DOI: 10.1128/mcb.20.1.61-69.2000] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/1999] [Accepted: 09/28/1999] [Indexed: 11/20/2022] Open
Abstract
A gene encoding a protein that shows sequence similarity with the histone H1 family only was cloned in Ascobolus immersus. The deduced peptide sequence presents the characteristic three-domain structure of metazoan linker histones, with a central globular region, an N-terminal tail, and a long positively charged C-terminal tail. By constructing an artificial duplication of this gene, named H1, it was possible to methylate and silence it by the MIP (methylation induced premeiotically) process. This resulted in the complete loss of the Ascobolus H1 histone. Mutant strains lacking H1 displayed normal methylation-associated gene silencing, underwent MIP, and showed the same methylation-associated chromatin modifications as did wild-type strains. However, they displayed an increased accessibility of micrococcal nuclease to chromatin, whether DNA was methylated or not, and exhibited a hypermethylation of the methylated genome compartment. These features are taken to imply that Ascobolus H1 histone is a ubiquitous component of chromatin which plays no role in methylation-associated gene silencing. Mutant strains lacking histone H1 reproduced normally through sexual crosses and displayed normal early vegetative growth. However, between 6 and 13 days after germination, they abruptly and consistently stopped growing, indicating that Ascobolus H1 histone is necessary for long life span. This constitutes the first observation of a physiologically important phenotype associated with the loss of H1.
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Affiliation(s)
- J L Barra
- Institut Jacques Monod, UMR 7592, CNRS/Université Paris 7/Université Paris 6, 75251 Paris Cedex 05, France
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39
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Abstract
Nucleosome positioning in the somatic macronuclear genome of the ciliated protozoan Tetrahymena thermophila was analyzed by indirect end labeling. Nucleosomes were positioned nonrandomly in three different regions of the Tetrahymena genome. Nucleosome repeat length varied between adjacent nucleosomes. Nucleosome positioning in a histone H1 knockout strain was indistinguishable from that in a strain with wild type histone H1.
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Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53201-1881, USA. kathleen,
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40
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Dou Y, Mizzen CA, Abrams M, Allis CD, Gorovsky MA. Phosphorylation of linker histone H1 regulates gene expression in vivo by mimicking H1 removal. Mol Cell 1999; 4:641-7. [PMID: 10549296 DOI: 10.1016/s1097-2765(00)80215-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two Tetrahymena strains were created by gene replacement. One contained H1 with all phosphorylation sites mutated to alanine, preventing phosphorylation. The other had these sites changed to glutamic acid, mimicking the fully phosphorylated state. Global gene expression was not detectably changed in either strain. Instead, H1 phosphorylation activated or repressed specific genes in a manner that was remarkably similar to the effects of knocking out the gene encoding H1. These studies demonstrate a role for H1 phosphorylation in the regulation of transcription in vivo and suggest that it acts by mimicking the partial removal of H1.
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Affiliation(s)
- Y Dou
- Department of Biology, University of Rochester, New York 14627, USA
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41
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Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53201, USA
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42
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Mizzen C, Kuo MH, Smith E, Brownell J, Zhou J, Ohba R, Wei Y, Monaco L, Sassone-Corsi P, Allis CD. Signaling to chromatin through histone modifications: how clear is the signal? COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:469-81. [PMID: 10384311 DOI: 10.1101/sqb.1998.63.469] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- C Mizzen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, France
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43
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Mizzen CA, Dou Y, Liu Y, Cook RG, Gorovsky MA, Allis CD. Identification and mutation of phosphorylation sites in a linker histone. Phosphorylation of macronuclear H1 is not essential for viability in tetrahymena. J Biol Chem 1999; 274:14533-6. [PMID: 10329641 DOI: 10.1074/jbc.274.21.14533] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linker histone phosphorylation has been suggested to play roles in both chromosome condensation and transcriptional regulation. In the ciliated protozoan Tetrahymena, in contrast to many eukaryotes, histone H1 of macronuclei is highly phosphorylated during interphase. Macronuclei divide amitotically without overt chromosome condensation in this organism, suggesting that requirements for phosphorylation of macronuclear H1 may be limited to transcriptional regulation. Here we report the major sites of phosphorylation of macronuclear H1 in Tetrahymena thermophila. Five phosphorylation sites, present in a single cluster, were identified by sequencing 32P-labeled peptides isolated from tryptic peptide maps. Phosphothreonine was detected within two TPVK motifs and one TPTK motif that resemble established p34(cdc2) kinase consensus sequences. Phosphoserine was detected at two non-proline-directed sites that do not resemble known kinase consensus sequences. Phosphorylation at the two noncanonical sites appears to be hierarchical because it was observed only when a nearby p34(cdc2) site was also phosphorylated. Cells expressing macronuclear H1 containing alanine substitutions at all five of these phosphorylation sites were viable even though macronuclear H1 phosphorylation was abolished. These data suggest that the five sites identified comprise the entire collection of sites utilized by Tetrahymena and demonstrate that phosphorylation of macronuclear H1, like the protein itself, is not essential for viability in Tetrahymena.
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Affiliation(s)
- C A Mizzen
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
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44
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Abstract
Linker histones (LH) represent a diverse family of proteins that bind to nucleosomes and bring them together to form a 30-nm chromatin fiber. Although the structure of the globular domain of linker histones H1 and H5 has been solved, the details of its interaction with the nucleosome are not understood in full. Recent data on the location of LH in nucleosome are discussed here.
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Affiliation(s)
- S Belikov
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Stockholm, Sweden.
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45
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Huvos PE, Wu M, Gorovsky MA. A developmentally eliminated sequence in the flanking region of the histone H1 gene in Tetrahymena thermophila contains short repeats. J Eukaryot Microbiol 1998; 45:189-97. [PMID: 9561773 DOI: 10.1111/j.1550-7408.1998.tb04524.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Tetrahymena, as in other ciliated protozoans, a transcriptionally active, 'somatic' macronucleus develops from a transcriptionally inactive 'germline' micronucleus after conjugation. The process of development involves elimination of germline DNA segments at thousands of locations in the genome. The characterization of one of these segments in Tetrahymena thermophila is described here. This micronucleus-specific DNA has been identified by comparing the sequence of the corresponding micronuclear and macronuclear regions. The micronucleus-specific DNA is over 1 kb long, is AT-rich and has TTT direct repeats at its termini. At one end of the micronuclear sequence there is a 130 bp duplication, and at the other end there are several related repeats of a 13-mer. Short G-rich sections are found in the middle of the eliminated DNA, as well as on one side of the rearrangement junction. Short G-rich segments are also detectable in three previously described micronucleus-specific sequences. The micronuclear sequence described here is a member of a repeat family. Cross-hybridizing sequences are also detectable in some other Tetrahymena species. The distribution of cross-hybridizing sequences among related species is not consistent with the phylogenetic tree.
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Affiliation(s)
- P E Huvos
- Department of Medical Biochemistry, Southern Illinois University, Carbondale 62901, USA.
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46
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Abstract
Knockout experiments in Tetrahymena show that linker histone H1 is not essential for nuclear assembly or cell viability. These results, together with a series of biochemical and cell biological observations, challenge the existing paradigm that requires linker histones to be a key organizing component of higher-order chromatin structure. The H1 knockouts also reveal a much more subtle role for H1. Instead of acting as a general transcriptional repressor, H1 is found to regulate a limited number of specific genes. Surprisingly, H1 can both activate and repress transcription. We discuss how this architectural protein might accomplish this important regulatory role.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892-5430, USA.
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47
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Abstract
In a linker histone H1 knockout strain (delta H1) of Tetrahymena thermophila, the number of mature RNAs produced by genes transcribed by pol I and pol III and of most genes transcribed by pol II remains unchanged. However, H1 is required for the normal basal repression of a gene (ngoA) in growing cells but is not required for its activated expression in starved cells. Surprisingly, H1 is required for the activated expression of another gene (CyP) in starved cells but not for its repression in growing cells. Thus, H1 does not have a major effect on global transcription but can act as either a positive or negative gene-specific regulator of transcription in vivo.
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Affiliation(s)
- X Shen
- Department of Biology University of Rochester, New York 14627, USA
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48
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Liu X, Gorovsky MA. Cloning and characterization of the major histone H2A genes completes the cloning and sequencing of known histone genes of Tetrahymena thermophila. Nucleic Acids Res 1996; 24:3023-30. [PMID: 8760889 PMCID: PMC146061 DOI: 10.1093/nar/24.15.3023] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A truncated cDNA clone encoding Tetrahymena thermophila histone H2A2 was isolated using synthetic degenerate oligonucleotide probes derived from H2A protein sequences of Tetrahymena pyriformis. The cDNA clone was used as a homologous probe to isolate a truncated genomic clone encoding H2A1. The remaining regions of the genes for H2A1 (HTA1) and H2A2 (HTA2) were then isolated using inverse PCR on circularized genomic DNA fragments. These partial clones were assembled into intact HTA1 and HTA2 clones. Nucleotide sequences of the two genes were highly homologous within the coding region but not in the noncoding regions. Comparison of the deduced amino acid sequences with protein sequences of T. pyriformis H2As showed only two and three differences respectively, in a total of 137 amino acids for H2A1, and 132 amino acids for H2A2, indicating the two genes arose before the divergence of these two species. The HTA2 gene contains a TAA triplet within the coding region, encoding a glutamine residue. In contrast with the T. thermophila HHO and HTA3 genes, no introns were identified within the two genes. The 5'- and 3'-ends of the histone H2A mRNAs; were determined by RNase protection and by PCR mapping using RACE and RLM-RACE methods. Both genes encode polyadenylated mRNAs and are highly expressed in vegetatively growing cells but only weakly expressed in starved cultures. With the inclusion of these two genes, T. thermophila is the first organism whose entire complement of known core and linker histones, including replication-dependent and basal variants, has been cloned and sequenced.
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Affiliation(s)
- X Liu
- Department of Biology, University of Rochester, NY 14627, USA
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49
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Zlatanova J, van Holde K. The linker histones and chromatin structure: new twists. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:217-59. [PMID: 8821262 DOI: 10.1016/s0079-6603(08)60968-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J Zlatanova
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA
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50
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Huvos P. Developmental DNA rearrangements and micronucleus-specific sequences in five species within the Tetrahymena pyriformis species complex. Genetics 1995; 141:925-36. [PMID: 8582637 PMCID: PMC1206855 DOI: 10.1093/genetics/141.3.925] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In Tetrahymena thermophila, the development of a transcriptionally active macronucleus from a transcriptionally inert micronucleus includes the elimination of many segments of DNA, the bulk of which belong to repetitive sequence families. Two approaches were used to study the interspecies variations in developmentally eliminated DNA segments. First, the occurrence of restriction fragments crosshybridizing to developmentally eliminated DNA segments isolated from T. thermophila was examined in other species of Tetrahymena. Most micronucleus-specific sequence families examined showed large differences in numbers and intensities of crosshybridizing bands in different species, indicating the possibility of gain or loss of repeats within each of the sequence families. Second, the presence of developmentally excisable DNA segments, i.e., of rearrangement sites, was examined in the same set of species at a number of unique loci. This was carried out by comparing the hybridization patterns of seven unique macronucleus-retained sequences in the micro- and macronuclei of each of the species. Essentially all of the loci displayed variability with respect to the presence of rearrangement sites among the species examined. Results from the two approaches indicate that generation or loss of developmental rearrangements can occur among the species examined here.
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Affiliation(s)
- P Huvos
- Department of Medical Biochemistry, Southern Illinois University, Carbondale 62901, USA
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