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Shehzada S, Noto T, Saksouk J, Mochizuki K. A SUMO E3 ligase promotes long non-coding RNA transcription to regulate small RNA-directed DNA elimination. eLife 2024; 13:e95337. [PMID: 38197489 PMCID: PMC10830130 DOI: 10.7554/elife.95337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Small RNAs target their complementary chromatin regions for gene silencing through nascent long non-coding RNAs (lncRNAs). In the ciliated protozoan Tetrahymena, the interaction between Piwi-associated small RNAs (scnRNAs) and the nascent lncRNA transcripts from the somatic genome has been proposed to induce target-directed small RNA degradation (TDSD), and scnRNAs not targeted for TDSD later target the germline-limited sequences for programmed DNA elimination. In this study, we show that the SUMO E3 ligase Ema2 is required for the accumulation of lncRNAs from the somatic genome and thus for TDSD and completing DNA elimination to make viable sexual progeny. Ema2 interacts with the SUMO E2 conjugating enzyme Ubc9 and enhances SUMOylation of the transcription regulator Spt6. We further show that Ema2 promotes the association of Spt6 and RNA polymerase II with chromatin. These results suggest that Ema2-directed SUMOylation actively promotes lncRNA transcription, which is a prerequisite for communication between the genome and small RNAs.
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Affiliation(s)
- Salman Shehzada
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Tomoko Noto
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Julie Saksouk
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
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2
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Bétermier M, Klobutcher LA, Orias E. Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends. Microbiol Mol Biol Rev 2023; 87:e0018422. [PMID: 38009915 PMCID: PMC10732028 DOI: 10.1128/mmbr.00184-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
SUMMARYCiliated protozoa undergo large-scale developmental rearrangement of their somatic genomes when forming a new transcriptionally active macronucleus during conjugation. This process includes the fragmentation of chromosomes derived from the germline, coupled with the efficient healing of the broken ends by de novo telomere addition. Here, we review what is known of developmental chromosome fragmentation in ciliates that have been well-studied at the molecular level (Tetrahymena, Paramecium, Euplotes, Stylonychia, and Oxytricha). These organisms differ substantially in the fidelity and precision of their fragmentation systems, as well as in the presence or absence of well-defined sequence elements that direct excision, suggesting that chromosome fragmentation systems have evolved multiple times and/or have been significantly altered during ciliate evolution. We propose a two-stage model for the evolution of the current ciliate systems, with both stages involving repetitive or transposable elements in the genome. The ancestral form of chromosome fragmentation is proposed to have been derived from the ciliate small RNA/chromatin modification process that removes transposons and other repetitive elements from the macronuclear genome during development. The evolution of this ancestral system is suggested to have potentiated its replacement in some ciliate lineages by subsequent fragmentation systems derived from mobile genetic elements.
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Affiliation(s)
- Mireille Bétermier
- Department of Genome Biology, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Lawrence A. Klobutcher
- Department of Molecular Biology and Biophysics, UCONN Health (University of Connecticut), Farmington, Connecticut, USA
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
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3
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The Conjusome-A Transient Organelle Linking Genome Rearrangements in the Parental and Developing Macronuclei. Microorganisms 2023; 11:microorganisms11020418. [PMID: 36838383 PMCID: PMC9962563 DOI: 10.3390/microorganisms11020418] [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: 12/01/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The conjusome plays an important role in the conjugation events that occur in Tetrahymena thermophila. The conjusome appears in the anterior of conjugant pairs during the early stages of new macronuclei (anlagen) development. It lacks a membrane, and is composed of a network of fibrous, electron dense material, containing background cytoplasm and ribosomes. Several proteins localize to this organelle, including Pdd1p, a chromodomain protein that participates in the formation of chromatin-containing structures in developing macronuclear anlagen, and is associated with the elimination of specific germ-line sequences from developing macronuclei. Conjugants lacking the PDD1 allele in the parental macronucleus do not show Pdd1p antibody staining in conjusomes. Investigations were performed using mutant cell lines, uniparental cytogamy and drug treatment, and show that the conjusome appears to be dependent on parental macronuclei condensation, and is a transitory organelle that traffics nuclear determinants from the parental macronucleus to the developing anlagen. These data, taken together with Pdd1p knockout experiments, suggest the conjusome is involved in the epigenetic phenomena that occur during conjugation and sexual reorganization. This is likely a conserved organelle. Conjusome-like structures were also observed in another Ciliate, Stylonichia. In general, conjusomes have features that resemble germ line P-granules.
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4
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Origins of genome-editing excisases as illuminated by the somatic genome of the ciliate Blepharisma. Proc Natl Acad Sci U S A 2023; 120:e2213887120. [PMID: 36669098 PMCID: PMC9942806 DOI: 10.1073/pnas.2213887120] [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] [Indexed: 01/21/2023] Open
Abstract
Massive DNA excision occurs regularly in ciliates, ubiquitous microbial eukaryotes with somatic and germline nuclei in the same cell. Tens of thousands of internally eliminated sequences (IESs) scattered throughout the ciliate germline genome are deleted during the development of the streamlined somatic genome. The genus Blepharisma represents one of the two high-level ciliate clades (subphylum Postciliodesmatophora) and, unusually, has dual pathways of somatic nuclear and genome development. This makes it ideal for investigating the functioning and evolution of these processes. Here we report the somatic genome assembly of Blepharisma stoltei strain ATCC 30299 (41 Mbp), arranged as numerous telomere-capped minichromosomal isoforms. This genome encodes eight PiggyBac transposase homologs no longer harbored by transposons. All appear subject to purifying selection, but just one, the putative IES excisase, has a complete catalytic triad. We hypothesize that PiggyBac homologs were ancestral excisases that enabled the evolution of extensive natural genome editing.
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5
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MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma. Proc Natl Acad Sci U S A 2023; 120:e2213985120. [PMID: 36669106 PMCID: PMC9942856 DOI: 10.1073/pnas.2213985120] [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] [Indexed: 01/21/2023] Open
Abstract
During their development following sexual conjugation, ciliates excise numerous internal eliminated sequences (IESs) from a copy of the germline genome to produce the functional somatic genome. Most IESs are thought to have originated from transposons, but the presumed homology is often obscured by sequence decay. To obtain more representative perspectives on the nature of IESs and ciliate genome editing, we assembled 40,000 IESs of Blepharisma stoltei, a species belonging to a lineage (Heterotrichea) that diverged early from those of the intensively studied model ciliate species. About a quarter of IESs were short (<115 bp), largely nonrepetitive, and with a pronounced ~10 bp periodicity in length; the remainder were longer (up to 7 kbp) and nonperiodic and contained abundant interspersed repeats. Contrary to the expectation from current models, the assembled Blepharisma germline genome encodes few transposases. Instead, its most abundant repeat (8,000 copies) is a Miniature Inverted-repeat Transposable Element (MITE), apparently a deletion derivative of a germline-limited Pogo-family transposon. We hypothesize that MITEs are an important source of IESs whose proliferation is eventually self-limiting and that rather than defending the germline genomes against mobile elements, transposase domestication actually facilitates the accumulation of junk DNA.
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6
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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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7
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Wei F, Pan B, Diao J, Wang Y, Sheng Y, Gao S. The micronuclear histone H3 clipping in the unicellular eukaryote Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:584-594. [PMID: 37078088 PMCID: PMC10077241 DOI: 10.1007/s42995-022-00151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/07/2022] [Indexed: 05/02/2023]
Abstract
Clipping of the histone H3 N-terminal tail has been implicated in multiple fundamental biological processes for a growing list of eukaryotes. H3 clipping, serving as an irreversible process to permanently remove some post-translational modifications (PTMs), may lead to noticeable changes in chromatin dynamics or gene expression. The eukaryotic model organism Tetrahymena thermophila is among the first few eukaryotes that exhibits H3 clipping activity, wherein the first six amino acids of H3 are cleaved off during vegetative growth. Clipping only occurs in the transcriptionally silent micronucleus of the binucleated T. thermophila, thus offering a unique opportunity to reveal the role of H3 clipping in epigenetic regulation. However, the physiological functions of the truncated H3 and its protease(s) for clipping remain elusive. Here, we review the major findings of H3 clipping in T. thermophila and highlight its association with histone modifications and cell cycle regulation. We also summarize the functions and mechanisms of H3 clipping in other eukaryotes, focusing on the high diversity in terms of protease families and cleavage sites. Finally, we predict several protease candidates in T. thermophila and provide insights for future studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00151-0.
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Affiliation(s)
- Fan Wei
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jinghan Diao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yuanyuan Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yalan Sheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Shan Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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8
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Tian M, Cai X, Liu Y, Liucong M, Howard-Till R. A practical reference for studying meiosis in the model ciliate Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:595-608. [PMID: 37078080 PMCID: PMC10077211 DOI: 10.1007/s42995-022-00149-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/28/2022] [Indexed: 05/03/2023]
Abstract
Meiosis is a critical cell division program that produces haploid gametes for sexual reproduction. Abnormalities in meiosis are often causes of infertility and birth defects (e.g., Down syndrome). Most organisms use a highly specialized zipper-like protein complex, the synaptonemal complex (SC), to guide and stabilize pairing of homologous chromosomes in meiosis. Although the SC is critical for meiosis in many eukaryotes, there are organisms that perform meiosis without a functional SC. However, such SC-less meiosis is poorly characterized. To understand the features of SC-less meiosis and its adaptive significance, the ciliated protozoan Tetrahymena was selected as a model. Meiosis research in Tetrahymena has revealed intriguing aspects of the regulatory programs utilized in its SC-less meiosis, yet additional efforts are needed for obtaining an in-depth comprehension of mechanisms that are associated with the absence of SC. Here, aiming at promoting a wider application of Tetrahymena for meiosis research, we introduce basic concepts and core techniques for studying meiosis in Tetrahymena and then suggest future directions for expanding the current Tetrahymena meiosis research toolbox. These methodologies could be adopted for dissecting meiosis in poorly characterized ciliates that might reveal novel features. Such data will hopefully provide insights into the function of the SC and the evolution of meiosis from a unique perspective. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00149-8.
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Affiliation(s)
- Miao Tian
- 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, 266237 China
- Institute of Human Genetics, CNRS, University of Montpellier, 34090 Montpellier, France
| | - Xia Cai
- 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, 266237 China
| | - Yujie Liu
- 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, 266237 China
| | - Mingmei Liucong
- 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, 266237 China
| | - Rachel Howard-Till
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA USA
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9
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Wang C, Solberg T, Maurer-Alcalá XX, Swart EC, Gao F, Nowacki M. A small RNA-guided PRC2 complex eliminates DNA as an extreme form of transposon silencing. Cell Rep 2022; 40:111263. [PMID: 36001962 PMCID: PMC10073204 DOI: 10.1016/j.celrep.2022.111263] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/27/2022] [Accepted: 08/04/2022] [Indexed: 01/04/2023] Open
Abstract
In animal germlines, transposons are silenced at the transcriptional or post-transcriptional level to prevent deleterious expression. Ciliates employ a more direct approach by physically eliminating transposons from their soma, utilizing piRNAs to recognize transposons and imprecisely excise them. Ancient, mutated transposons often do not require piRNAs and are precisely eliminated. Here, we characterize the Polycomb Repressive Complex 2 (PRC2) in Paramecium and demonstrate its involvement in the removal of transposons and transposon-derived DNA. Our results reveal a striking difference between the elimination of new and ancient transposons at the chromatin level and show that the complex may be guided by Piwi-bound small RNAs (sRNAs). We propose that imprecise elimination in ciliates originates from an ancient transposon silencing mechanism, much like in plants and metazoans, through sRNAs, repressive methylation marks, and heterochromatin formation. However, it is taken a step further by eliminating DNA as an extreme form of transposon silencing.
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Affiliation(s)
- Chundi Wang
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laboratory of Marine Protozoan Biodiversity & Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Therese Solberg
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Xyrus X Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland; Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Estienne C Swart
- Max Planck Institute for Biology, Max Planck Ring 5, 72076 Tuebingen, Germany
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
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10
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Smith SA, Santoferrara LF, Katz LA, McManus GB. Genome architecture used to supplement species delineation in two cryptic marine ciliates. Mol Ecol Resour 2022; 22:2880-2896. [PMID: 35675173 DOI: 10.1111/1755-0998.13664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%-0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.
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11
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Plattner H. Ciliate Research. From Myth to Trendsetting Science. J Eukaryot Microbiol 2022; 69:e12926. [PMID: 35608570 DOI: 10.1111/jeu.12926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
Abstract
This special issue of the Journal of Eukaryotic Microbiology (JEM) summarizes achievements obtained by generations of researchers with ciliates in widely different disciplines. In fact, ciliates range among the first cells seen under the microscope centuries ago. Their beauty made them an object of scientia amabilis and their manifold reactions made them attractive for college experiments and finally challenged causal analyses at the cellular level. Some of this work was honored by a Nobel Prize. Some observations yielded a baseline for additional novel discoveries, occasionally facilitated by specific properties of some ciliates. This also offers some advantage in the exploration of closely related parasites (malaria). Articles contributed here by colleagues from all over the world encompass a broad spectrum of ciliate life, from genetics to evolution, from molecular cell biology to ecology, from intercellular signaling to epigenetics etc. This introductory chapter, largely based on my personal perception, aims at integrating work presented in this special issue of JEM into a broader historical context up to current research.
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12
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Paramecium Polycomb repressive complex 2 physically interacts with the small RNA-binding PIWI protein to repress transposable elements. Dev Cell 2022; 57:1037-1052.e8. [DOI: 10.1016/j.devcel.2022.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/10/2022] [Accepted: 03/21/2022] [Indexed: 12/30/2022]
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13
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Ahsan R, Blanche W, Katz LA. Macronuclear development in ciliates, with a focus on nuclear architecture. J Eukaryot Microbiol 2022; 69:e12898. [PMID: 35178799 DOI: 10.1111/jeu.12898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei varies tremendously among ciliates. Except just after conjugation (i.e. the nuclear exchange in sexual cycle), the germline micronucleus is transcriptionally-inactive and contains canonical chromosomes that will be inherited between generations. In contrast, the transcriptionally-active macronucleus contains chromosomes that vary in size in different classes of ciliates, with some lineages having extensively-fragmented gene-sized somatic chromosomes while others contain longer multigene chromosomes. Here, we describe the variation in somatic macronuclear architecture in lineages sampled across the ciliate tree of life, specifically focusing on lineages with extensively fragmented chromosomes (e.g. the classes Phyllopharyngea and Spirotrichea). Further, we synthesize information from the literature on the development of ciliate macronuclei, focusing on changes in nuclear architecture throughout life cycles. These data highlight the tremendous diversity among ciliate nuclear cycles, extend our understanding of patterns of genome evolution, and provide insight into different germline and somatic nuclear features (e.g. nuclear structure and development) among eukaryotes.
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Affiliation(s)
- Ragib Ahsan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
| | - Wumei Blanche
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
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14
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Vijayanathan M, Trejo-Arellano MG, Mozgová I. Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective. EPIGENOMES 2022; 6:3. [PMID: 35076495 PMCID: PMC8788455 DOI: 10.3390/epigenomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
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Affiliation(s)
- Mallika Vijayanathan
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - María Guadalupe Trejo-Arellano
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - Iva Mozgová
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
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15
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Zangarelli C, Arnaiz O, Bourge M, Gorrichon K, Jaszczyszyn Y, Mathy N, Escoriza L, Bétermier M, Régnier V. Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics. Genome Res 2022; 32:2028-2042. [PMID: 36418061 PMCID: PMC9808624 DOI: 10.1101/gr.277027.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022]
Abstract
With its nuclear dualism, the ciliate Paramecium constitutes a unique model to study how host genomes cope with transposable elements (TEs). P. tetraurelia harbors two germline micronuclei (MICs) and a polyploid somatic macronucleus (MAC) that develops from one MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of approximately 45,000 TE-derived internal eliminated sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by noncoding RNAs and repressive chromatin marks. A subset of IESs is excised independently of this epigenetic control, raising the question of how IESs are targeted for elimination. To gain insight into the determinants of IES excision, we established the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with high-throughput sequencing. Essentially all IESs are excised within only one endoreplication round (32C to 64C), whereas TEs are eliminated at a later stage. We show that DNA elimination proceeds independently of replication. We defined four IES classes according to excision timing. The earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends, and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision by acquiring stronger sequence determinants and escaping epigenetic control.
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Affiliation(s)
- Coralie Zangarelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Olivier Arnaiz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Mickaël Bourge
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Kevin Gorrichon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Nathalie Mathy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Loïc Escoriza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Vinciane Régnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France;,Université Paris Cité, UFR Sciences du Vivant, 75205 Paris Cedex 13, France
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16
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Catania F, Rothering R, Vitali V. One Cell, Two Gears: Extensive Somatic Genome Plasticity Accompanies High Germline Genome Stability in Paramecium. Genome Biol Evol 2021; 13:6443145. [PMID: 34849843 PMCID: PMC8670300 DOI: 10.1093/gbe/evab263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/15/2022] Open
Abstract
Mutation accumulation (MA) experiments are conventionally employed to study spontaneous germline mutations. However, MA experiments can also shed light on somatic genome plasticity in a habitual and genetic drift-maximizing environment. Here, we revisit an MA experiment that uncovered extraordinary germline genome stability in Paramecium tetraurelia, a single-celled eukaryote with nuclear dimorphism. Our re-examination of isogenic P. tetraurelia MA lines propagated in nutrient-rich medium for >40 sexual cycles reveals that their polyploid somatic genome accrued hundreds of intervening DNA segments (IESs), which are normally eliminated during germline-soma differentiation. These IESs frequently occupy a fraction of the somatic DNA copies of a given locus, producing IES excision/retention polymorphisms, and preferentially fall into a class of epigenetically controlled sequences. Relative to control lines, retained IESs are flanked by stronger cis-acting signals and interrupt an excess of highly expressed coding exons. These findings suggest that P. tetraurelia’s elevated germline DNA replication fidelity is associated with pervasive somatic genome plasticity. They show that MA regimes are powerful tools for investigating the role that developmental plasticity, somatic mutations, and epimutations have in ecology and evolution.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Germany.,Institute of Environmental Radioactivity, Fukushima University, Japan
| | - Rebecca Rothering
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Valerio Vitali
- Institute for Evolution and Biodiversity, University of Münster, Germany
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17
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Weiner AKM, Cerón-Romero MA, Yan Y, Katz LA. Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes. Genome Biol Evol 2021; 12:2196-2210. [PMID: 33049043 DOI: 10.1093/gbe/evaa198] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
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18
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Seah BKB, Swart EC. BleTIES: Annotation of natural genome editing in ciliates using long read sequencing. Bioinformatics 2021; 37:3929-3931. [PMID: 34487139 DOI: 10.1093/bioinformatics/btab613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/18/2021] [Indexed: 01/10/2023] Open
Abstract
SUMMARY Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads, but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads. AVAILABILITY AND IMPLEMENTATION BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license), and also distributed via Bioconda. SUPPLEMENTARY INFORMATION Benchmarking of BleTIES with published sequence data.
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Affiliation(s)
- Brandon K B Seah
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Estienne C Swart
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
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19
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Abstract
The evolutionary theory of aging has set the foundations for a comprehensive understanding of aging. The biology of aging has listed and described the "hallmarks of aging," i.e., cellular and molecular mechanisms involved in human aging. The present paper is the first to infer the order of appearance of the hallmarks of bilaterian and thereby human aging throughout evolution from their presence in progressively narrower clades. Its first result is that all organisms, even non-senescent, have to deal with at least one mechanism of aging - the progressive accumulation of misfolded or unstable proteins. Due to their cumulation, these mechanisms are called "layers of aging." A difference should be made between the first four layers of unicellular aging, present in some unicellular organisms and in all multicellular opisthokonts, that stem and strike "from the inside" of individual cells and span from increasingly abnormal protein folding to deregulated nutrient sensing, and the last four layers of metacellular aging, progressively appearing in metazoans, that strike the cells of a multicellular organism "from the outside," i.e., because of other cells, and span from transcriptional alterations to the disruption of intercellular communication. The evolution of metazoans and eumetazoans probably solved the problem of aging along with the problem of unicellular aging. However, metacellular aging originates in the mechanisms by which the effects of unicellular aging are kept under control - e.g., the exhaustion of stem cells that contribute to replace damaged somatic cells. In bilaterians, additional functions have taken a toll on generally useless potentially limited lifespan to increase the fitness of organisms at the price of a progressively less efficient containment of the damage of unicellular aging. In the end, this picture suggests that geroscience should be more efficient in targeting conditions of metacellular aging rather than unicellular aging itself.
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Affiliation(s)
- Maël Lemoine
- CNRS, ImmunoConcEpT, UMR 5164, Univ. Bordeaux, Bordeaux, France
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20
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Abstract
The presence of meiosis, which is a conserved component of sexual reproduction, across organisms from all eukaryotic kingdoms, strongly argues that sex is a primordial feature of eukaryotes. However, extant meiotic structures and processes can vary considerably between organisms. The ciliated protist Tetrahymena thermophila, which diverged from animals, plants, and fungi early in evolution, provides one example of a rather unconventional meiosis. Tetrahymena has a simpler meiosis compared with most other organisms: It lacks both a synaptonemal complex (SC) and specialized meiotic machinery for chromosome cohesion and has a reduced capacity to regulate meiotic recombination. Despite this, it also features several unique mechanisms, including elongation of the nucleus to twice the cell length to promote homologous pairing and prevent recombination between sister chromatids. Comparison of the meiotic programs of Tetrahymena and higher multicellular organisms may reveal how extant meiosis evolved from proto-meiosis.
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Affiliation(s)
- Josef Loidl
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
- * E-mail:
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21
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New contribution to epigenetic studies: Isolation of micronuclei with high purity and DNA integrity in the model ciliated protist, Tetrahymena thermophila. Eur J Protistol 2021; 80:125804. [PMID: 34062315 DOI: 10.1016/j.ejop.2021.125804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 10/24/2022]
Abstract
The ciliated protist Tetrahymena thermophila is a well-known model organism with typical nuclear dimorphism containing a somatic macronucleus (MAC) and a germline micronucleus (MIC). The presence in the same cell compartment of two nuclei with distinctly different structural and functional properties provides an ideal model system to explore mechanisms of genome maintenance. Although methods for the isolation of MIC have been available for many years, cross-contamination and DNA degradation remain unresolved. Here, we describe a reliable and quick method to isolate MIC with high purity and DNA integrity in T. thermophila. Different factors are examined to optimize the MIC purification. The MAC contamination ratio in purified MIC is about 0.19% and DNA integrity of purified MIC is maintained. We also establish a more accurate method to detect the contamination rate of nuclei including microscopic observation and PCR detection. This study will facilitate further epigenetic research in Tetrahymena.
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22
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Weiner AKM, Katz LA. Epigenetics as Driver of Adaptation and Diversification in Microbial Eukaryotes. Front Genet 2021; 12:642220. [PMID: 33796133 PMCID: PMC8007921 DOI: 10.3389/fgene.2021.642220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
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23
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Sawka-Gądek N, Potekhin A, Singh DP, Grevtseva I, Arnaiz O, Penel S, Sperling L, Tarcz S, Duret L, Nekrasova I, Meyer E. Evolutionary Plasticity of Mating-Type Determination Mechanisms in Paramecium aurelia Sibling Species. Genome Biol Evol 2021; 13:evaa258. [PMID: 33313646 PMCID: PMC7900874 DOI: 10.1093/gbe/evaa258] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
The Paramecium aurelia complex, a group of morphologically similar but sexually incompatible sibling species, is a unique example of the evolutionary plasticity of mating-type systems. Each species has two mating types, O (Odd) and E (Even). Although O and E types are homologous in all species, three different modes of determination and inheritance have been described: genetic determination by Mendelian alleles, stochastic developmental determination, and maternally inherited developmental determination. Previous work in three species of the latter kind has revealed the key roles of the E-specific transmembrane protein mtA and its highly specific transcription factor mtB: type O clones are produced by maternally inherited genome rearrangements that inactivate either mtA or mtB during development. Here we show, through transcriptome analyses in five additional species representing the three determination systems, that mtA expression specifies type E in all cases. We further show that the Mendelian system depends on functional and nonfunctional mtA alleles, and identify novel developmental rearrangements in mtA and mtB which now explain all cases of maternally inherited mating-type determination. Epistasis between these genes likely evolved from less specific interactions between paralogs in the P. aurelia common ancestor, after a whole-genome duplication, but the mtB gene was subsequently lost in three P. aurelia species which appear to have returned to an ancestral regulation mechanism. These results suggest a model accounting for evolutionary transitions between determination systems, and highlight the diversity of molecular solutions explored among sibling species to maintain an essential mating-type polymorphism in cell populations.
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Affiliation(s)
- Natalia Sawka-Gądek
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Deepankar Pratap Singh
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Inessa Grevtseva
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olivier Arnaiz
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Simon Penel
- CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Villeurbanne, France
| | - Linda Sperling
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sebastian Tarcz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Laurent Duret
- CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Villeurbanne, France
| | - Irina Nekrasova
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Eric Meyer
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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24
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Xu J, Zhao X, Mao F, Basrur V, Ueberheide B, Chait BT, Allis CD, Taverna SD, Gao S, Wang W, Liu Y. A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies. Nucleic Acids Res 2021; 49:5407-5425. [PMID: 33412588 PMCID: PMC8191774 DOI: 10.1093/nar/gkaa1262] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023] Open
Abstract
Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, in the protist Tetrahymena thermophila, the EZL1 (E(z)-like 1) complex, with components conserved in metazoan Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The EZL1 complex is required for histone H3 K27 and K9 methylation, heterochromatin formation, transposable element control, and programmed genome rearrangement. The EZL1 complex interacts with EMA1, a helicase required for RNA interference (RNAi). This interaction is implicated in co-transcriptional recruitment of the EZL1 complex. Binding of H3K27 and H3K9 methylation by PDD1-another PcG protein interacting with the EZL1 complex-reinforces its chromatin association. The EZL1 complex is an integral part of Polycomb bodies, which exhibit dynamic distribution in Tetrahymena development: Their dispersion is driven by chromatin association, while their coalescence by PDD1, likely via phase separation. Our results provide a molecular mechanism connecting RNAi and Polycomb repression, which coordinately regulate nuclear bodies and reorganize the genome.
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Affiliation(s)
| | | | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Proteomics Resource Facility, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatrix Ueberheide
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the Rockefeller University, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY 10065, USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences and the Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shan Gao
- Correspondence may also be addressed to Shan Gao.
| | - Wei Wang
- Correspondence may also be addressed to Wei Wang.
| | - Yifan Liu
- To whom correspondence should be addressed. Tel: +1 323 865 3852;
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25
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Abstract
Over the last few decades, an increasing number of vertebrate taxa have been identified that undergo programmed genome rearrangement, or programmed DNA loss, during development. In these organisms, the genome of germ cells is often reproducibly different from the genome of all other cells within the body. Although we clearly have not identified all vertebrate taxa that undergo programmed genome loss, the list of species known to undergo loss now represents ∼10% of vertebrate species, including several basally diverging lineages. Recent studies have shed new light on the targets and mechanisms of DNA loss and their association with canonical modes of DNA silencing. Ultimately, expansion of these studies into a larger collection of taxa will aid in reconstructing patterns of shared/independent ancestry of programmed DNA loss in the vertebrate lineage, as well as more recent evolutionary events that have shaped the structure and content of eliminated DNA.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
| | | | - Cody Saraceno
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
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26
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Ricci F, Luporini P, Alimenti C, Vallesi A. Functional chimeric genes in ciliates: An instructive case from Euplotes raikovi. Gene 2020; 767:145186. [PMID: 32998045 DOI: 10.1016/j.gene.2020.145186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/09/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
In ciliates, with every sexual event the transcriptionally active genes of the sub-chromosomic somatic genome that resides in the cell macronucleus are lost. They are de novo assembled starting from 'Macronuclear Destined Sequences' that arise from the fragmentation of transcriptionally silent DNA sequences of the germline chromosomic genome enclosed in the cell micronucleus. The RNA-mediated epigenetic mechanism that drives the assembly of these sequences is subject to errors which result in the formation of chimeric genes. Studying a gene family that in Euplotes raikovi controls the synthesis of protein signal pheromones responsible for a self/not-self recognition mechanism, we identified the chimeric structure of an 851-bp macronuclear gene previously known to specify soluble and membrane-bound pheromone molecules through an intron-splicing mechanism. This chimeric gene, designated mac-er-1*, conserved the native pheromone-gene structure throughout its coding and 3' regions. Instead, its 5' region is completely unrelated to the pheromone gene structure at the level of a 360-bp sequence, which derives from the assembly with a MDS destined to compound a 2417-bp gene encoding a 696-amino acid protein with unknown function. This mac-er-1* gene characterization provides further evidence that ciliates rely on functional chimeric genes that originate in non-programmed phenomena of somatic MDS recombination to increase the species genetic variability independently of gene reshuffling phenomena of the germline genome.
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Affiliation(s)
- Francesca Ricci
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Pierangelo Luporini
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Claudio Alimenti
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
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27
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Wang Y, Jiang Y, Liu Y, Li Y, Katz LA, Gao F, Yan Y. Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research. Microorganisms 2020; 8:E316. [PMID: 32106521 PMCID: PMC7142639 DOI: 10.3390/microorganisms8030316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/21/2023] Open
Abstract
While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 104 to 8.1 × 105; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.
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Affiliation(s)
- Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yongqiang Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yuan Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA;
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA;
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28
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Ninova M, Fejes Tóth K, Aravin AA. The control of gene expression and cell identity by H3K9 trimethylation. Development 2019; 146:dev181180. [PMID: 31540910 PMCID: PMC6803365 DOI: 10.1242/dev.181180] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone 3 lysine 9 trimethylation (H3K9me3) is a conserved histone modification that is best known for its role in constitutive heterochromatin formation and the repression of repetitive DNA elements. More recently, it has become evident that H3K9me3 is also deposited at certain loci in a tissue-specific manner and plays important roles in regulating cell identity. Notably, H3K9me3 can repress genes encoding silencing factors, pointing to a fundamental principle of repressive chromatin auto-regulation. Interestingly, recent studies have shown that H3K9me3 deposition requires protein SUMOylation in different contexts, suggesting that the SUMO pathway functions as an important module in gene silencing and heterochromatin formation. In this Review, we discuss the role of H3K9me3 in gene regulation in various systems and the molecular mechanisms that guide the silencing machinery to target loci.
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
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Abstract
DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done elucidating the role of 5-methylcytosine over the past several decades, only recently has it been recognized that N(6)-methyladenine (N6-mA) is present in quantifiable and biologically active levels in the DNA of eukaryotic cells. Unlike prokaryotes which utilize N6-mA to recognize "self" from "foreign" DNA, eukaryotes have been found to use N6-mA in varying ways, from regulating transposable elements to gene regulation in response to hypoxia and stress. In this review, we examine the current state of the N6-mA in research field, and the current understanding of the biochemical mechanisms which deposit and remove N6-mA from the eukaryotic genome.
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Affiliation(s)
- Myles H Alderman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Andrew Z Xiao
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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30
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Tian M, Mochizuki K, Loidl J. Non-coding RNA Transcription in Tetrahymena Meiotic Nuclei Requires Dedicated Mediator Complex-Associated Proteins. Curr Biol 2019; 29:2359-2370.e5. [PMID: 31280995 DOI: 10.1016/j.cub.2019.05.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/24/2019] [Accepted: 05/15/2019] [Indexed: 12/22/2022]
Abstract
To preserve genome integrity, eukaryotic cells use small RNA-directed mechanisms to repress transposable elements (TEs). Paradoxically, in order to silence TEs, precursors of the small RNAs must be transcribed from TEs. However, it is still poorly understood how these precursors are transcribed from TEs under silenced conditions. In the otherwise transcriptionally silent germline micronucleus (MIC) of Tetrahymena, a burst of non-coding RNA (ncRNA) transcription occurs during meiosis. The transcripts are processed into small RNAs that serve to identify TE-related sequences for elimination. The Mediator complex (Med) has an evolutionarily conserved role for transcription by bridging gene-specific transcription factors and RNA polymerase II. Here, we report that three Med-associated factors, Emit1, Emit2, and Rib1, are required for the biogenesis of small ncRNAs. Med localizes to the MIC only during meiosis, and both Med localization and MIC ncRNA transcription require Emit1 and Emit2. In the MIC, Med occupies TE-rich pericentromeric and telomeric regions in a Rib1-dependent manner. Rib1 is dispensable for ncRNA transcription but is required for the accumulation of double-stranded ncRNAs. Nuclear and sub-nuclear localization of the three Med-associated proteins is interdependent. Hence, Emit1 and Emit2 act coordinately to import Med into the MIC, and Rib1 recruits Med to specific chromosomal locations to quantitatively or qualitatively promote the biogenesis of functional ncRNA. Our results underscore that the transcription machinery can be regulated by a set of specialized Med-associated proteins to temporally transcribe TE-related sequences from a silent genome for small RNA biogenesis and genome defense.
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Affiliation(s)
- Miao Tian
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of Montpellier, 34090 Montpellier, France
| | - Josef Loidl
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
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31
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Diversification of small RNA amplification mechanisms for targeting transposon-related sequences in ciliates. Proc Natl Acad Sci U S A 2019; 116:14639-14644. [PMID: 31262823 DOI: 10.1073/pnas.1903491116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The silencing of repetitive transposable elements (TEs) is ensured by signal amplification of the initial small RNA trigger, which occurs at distinct steps of TE silencing in different eukaryotes. How such a variety of secondary small RNA biogenesis mechanisms has evolved has not been thoroughly elucidated. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after the excision of IESs. In this study, we show that in another ciliate, Tetrahymena, secondary small RNAs accumulate at least a few hours before their derived IESs are excised. We also demonstrate that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike in Paramecium, small RNA amplification occurs before IES excision in Tetrahymena This study reveals the remarkable diversity of secondary small RNA biogenesis mechanisms, even among ciliates with similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.
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32
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Zhao X, Xiong J, Mao F, Sheng Y, Chen X, Feng L, Dui W, Yang W, Kapusta A, Feschotte C, Coyne RS, Miao W, Gao S, Liu Y. RNAi-dependent Polycomb repression controls transposable elements in Tetrahymena. Genes Dev 2019; 33:348-364. [PMID: 30808657 PMCID: PMC6411011 DOI: 10.1101/gad.320796.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/02/2019] [Indexed: 12/30/2022]
Abstract
In this study, Zhao et al. show that in the protozoan Tetrahymena thermophila, germline-specific internally eliminated sequences (IESs) become transcriptionally activated in mutants deficient in the RNAi-dependent Polycomb repression pathway. Their findings suggest that the interplay between RNAi and Polycomb repression is a widely conserved phenomenon whose ancestral role is epigenetic silencing of TEs. RNAi and Polycomb repression play evolutionarily conserved and often coordinated roles in transcriptional silencing. Here, we show that, in the protozoan Tetrahymena thermophila, germline-specific internally eliminated sequences (IESs)—many related to transposable elements (TEs)—become transcriptionally activated in mutants deficient in the RNAi-dependent Polycomb repression pathway. Germline TE mobilization also dramatically increases in these mutants. The transition from noncoding RNA (ncRNA) to mRNA production accompanies transcriptional activation of TE-related sequences and vice versa for transcriptional silencing. The balance between ncRNA and mRNA production is potentially affected by cotranscriptional processing as well as RNAi and Polycomb repression. We posit that interplay between RNAi and Polycomb repression is a widely conserved phenomenon, whose ancestral role is epigenetic silencing of TEs.
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Affiliation(s)
- Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yalan Sheng
- Institute of Evolution and 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
| | - Xiao Chen
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lifang Feng
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Robert S Coyne
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shan Gao
- Institute of Evolution and 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
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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33
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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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34
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Noto T, Mochizuki K. Whats, hows and whys of programmed DNA elimination in Tetrahymena. Open Biol 2018; 7:rsob.170172. [PMID: 29021213 PMCID: PMC5666084 DOI: 10.1098/rsob.170172] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/12/2017] [Indexed: 12/20/2022] Open
Abstract
Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in Tetrahymena thermophila removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in cis by the small RNA-mediated genome comparison of the MIC to the MAC. Other IESs are targeted for elimination in trans by the same small RNAs through repetitive sequences. Furthermore, the small RNA–heterochromatin feedback loop ensures robust DNA elimination. Here, we review an updated picture of the DNA elimination mechanism, discuss the physiological and evolutionary roles of DNA elimination, and outline the key questions that remain unanswered.
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Affiliation(s)
- Tomoko Noto
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Kazufumi Mochizuki
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
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35
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Noto T, Mochizuki K. Small RNA-Mediated trans-Nuclear and trans-Element Communications in Tetrahymena DNA Elimination. Curr Biol 2018; 28:1938-1949.e5. [DOI: 10.1016/j.cub.2018.04.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 10/14/2022]
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36
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37
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Qiu GH, Huang C, Zheng X, Yang X. The protective function of noncoding DNA in genome defense of eukaryotic male germ cells. Epigenomics 2018; 10:499-517. [PMID: 29616594 DOI: 10.2217/epi-2017-0103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Peripheral and abundant noncoding DNA has been hypothesized to protect the genome and the central protein-coding sequences against DNA damage in somatic genome. In the cytosol, invading exogenous nucleic acids may first be deactivated by small RNAs encoded by noncoding DNA via mechanisms similar to the prokaryotic CRISPR-Cas system. In the nucleus, the radicals generated by radiation in the cytosol, radiation energy and invading exogenous nucleic acids are absorbed, blocked and/or reduced by peripheral heterochromatin, and damaged DNA in heterochromatin is removed and excluded from the nucleus to the cytoplasm through nuclear pore complexes. To further strengthen the hypothesis, this review summarizes the experimental evidence supporting the protective function of noncoding DNA in the genome of male germ cells. Based on these data, this review provides evidence supporting the protective role of noncoding DNA in the genome defense of sperm genome through similar mechanisms to those of the somatic genome.
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Affiliation(s)
- Guo-Hua Qiu
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology; Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province University; College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Cuiqin Huang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology; Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province University; College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xintian Zheng
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology; Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province University; College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xiaoyan Yang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology; Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province University; College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
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38
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Jose AM. Replicating and Cycling Stores of Information Perpetuate Life. Bioessays 2018; 40:e1700161. [PMID: 29493806 PMCID: PMC7303024 DOI: 10.1002/bies.201700161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Indexed: 12/12/2022]
Abstract
Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. See also the video abstract here: https://youtu.be/IdWEL-T6TPU.
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Affiliation(s)
- Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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39
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Minkina O, Hunter CP. Intergenerational Transmission of Gene Regulatory Information in Caenorhabditis elegans. Trends Genet 2017; 34:54-64. [PMID: 29103876 DOI: 10.1016/j.tig.2017.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/28/2017] [Accepted: 09/29/2017] [Indexed: 01/12/2023]
Abstract
Epigenetic mechanisms can stably maintain gene expression states even after the initiating conditions have changed. Often epigenetic information is transmitted only to daughter cells, but evidence is emerging, in both vertebrate and invertebrate systems, for transgenerational epigenetic inheritance (TEI), the transmission of epigenetic gene regulatory information across generations. Each new description of TEI helps uncover the properties, molecular mechanisms and biological roles for TEI. The nematode Caenorhabditis elegans has been particularly instrumental in the effort to understand TEI, as multiple environmental and genetic triggers can initiate an epigenetic signal that can alter the expression of both transgenes and endogenous loci. Here, we review recent studies of TEI in C. elegans.
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Affiliation(s)
- Olga Minkina
- Department of Biology, New York University, New York, New York 10003, USA
| | - Craig P Hunter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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40
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Feng L, Wang G, Hamilton EP, Xiong J, Yan G, Chen K, Chen X, Dui W, Plemens A, Khadr L, Dhanekula A, Juma M, Dang HQ, Kapler GM, Orias E, Miao W, Liu Y. A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement. Nucleic Acids Res 2017; 45:9481-9502. [PMID: 28934495 PMCID: PMC5766162 DOI: 10.1093/nar/gkx652] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/15/2017] [Indexed: 12/20/2022] Open
Abstract
Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation. Large NMC contain genes implicated in development-specific roles. One such gene encodes the domesticated piggyBac transposase TPB6, required for heterochromatin-dependent precise excision of IES residing within exons of functionally important genes. These conserved exonic IES determine alternative transcription products in the developing macronucleus; some even contain free-standing genes. Examples of precise loss of some exonic IES in the micronucleus and retention of others in the macronucleus of related species suggest an evolutionary analogy to introns. Our results reveal that germline-limited sequences can encode genes with specific expression patterns and development-related functions, which may be a recurring theme in eukaryotic organisms experiencing programmed genome rearrangement during germline to soma differentiation.
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Affiliation(s)
- Lifang Feng
- 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.,School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guanxiong Yan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao Chen
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amber Plemens
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lara Khadr
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arjune Dhanekula
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mina Juma
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hung Quang Dang
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Geoffrey M Kapler
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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41
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Orias E, Singh DP, Meyer E. Genetics and Epigenetics of Mating Type Determination in Paramecium and Tetrahymena. Annu Rev Microbiol 2017; 71:133-156. [PMID: 28715961 DOI: 10.1146/annurev-micro-090816-093342] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
While sex is an ancient and highly conserved eukaryotic invention, self-incompatibility systems such as mating types or sexes appear to be derived limitations that show considerable evolutionary plasticity. Within a single class of ciliates, Paramecium and Tetrahymena species have long been known to present a wide variety of mating type numbers and modes of inheritance, but only recently have the genes involved been identified. Although similar transmembrane proteins mediate self/nonself recognition in both ciliates, the mechanisms of mating type determination differ widely, ranging from Mendelian systems to developmental nuclear differentiation, either stochastic or maternally inherited. The non-Mendelian systems rely on programmed editing of the germline genome that occurs during differentiation of the somatic nucleus, and they have co-opted different DNA recombination mechanisms-some previously unknown. Here we review the recent molecular advances and some remaining unsolved questions and discuss the possible implications of these diverse mechanisms for inbreeding/outbreeding balance regulation.
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Affiliation(s)
- Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93105;
| | - Deepankar Pratap Singh
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, PSL Research University, F-75005 Paris, France; .,Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
| | - Eric Meyer
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, PSL Research University, F-75005 Paris, France;
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42
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Arnaiz O, Van Dijk E, Bétermier M, Lhuillier-Akakpo M, de Vanssay A, Duharcourt S, Sallet E, Gouzy J, Sperling L. Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. BMC Genomics 2017; 18:483. [PMID: 28651633 PMCID: PMC5485702 DOI: 10.1186/s12864-017-3887-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/21/2017] [Indexed: 12/22/2022] Open
Abstract
Background The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. Results We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. Conclusions We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3′ and 5′ UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis regulatory motifs). The P. tetraurelia improved transcriptome resource, gene annotations for P. tetraurelia, P. biaurelia, P. sexaurelia and P. caudatum, and Paramecium-trained EuGene configuration are available through ParameciumDB (http://paramecium.i2bc.paris-saclay.fr). TrUC software is freely distributed under a GNU GPL v3 licence (https://github.com/oarnaiz/TrUC). Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3887-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France
| | - Erwin Van Dijk
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France
| | - Mireille Bétermier
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France
| | - Maoussi Lhuillier-Akakpo
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France.,Current address: IRCM, CEA, INSERM UMR 967, Université Paris Diderot, Université Paris-Saclay, 92265, Fontenay-aux-Roses CEDEX, France
| | - Augustin de Vanssay
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Sandra Duharcourt
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France.
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43
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Pilling OA, Rogers AJ, Gulla-Devaney B, Katz LA. Insights into transgenerational epigenetics from studies of ciliates. Eur J Protistol 2017; 61:366-375. [PMID: 28689743 DOI: 10.1016/j.ejop.2017.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/06/2017] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Abstract
Epigenetics, a term with many meanings, can be broadly defined as the study of dynamic states of the genome. Ciliates, a clade of unicellular eukaryotes, can teach us about the intersection of epigenetics and evolution due to the advantages of working with cultivable ciliate lineages, plus their tendency to express extreme phenotypes such as heritable doublet morphology. Moreover, ciliates provide a powerful model for studying epigenetics given the presence of dimorphic nuclei - a somatic macronucleus and germline micronucleus - within each cell. Here, we exemplify the power of studying ciliates to learn about epigenetic phenomena. We highlight "classical" examples from morphology and physiology including cortical inheritance, mating type determination, and serotype expression. In addition, we detail molecular studies of epigenetic phenomena, including: DNA elimination; alternative processing and unscrambling; and copy number determination. Based on the implications of these studies, we discuss epigenetics as a possible functional mechanism for rapid speciation in ciliates.
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Affiliation(s)
- Olivia A Pilling
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Anna J Rogers
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | | | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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Tetrahymena as a Unicellular Model Eukaryote: Genetic and Genomic Tools. Genetics 2017; 203:649-65. [PMID: 27270699 DOI: 10.1534/genetics.114.169748] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/08/2016] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena's utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice.
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Farley BM, Collins K. Transgenerational function of Tetrahymena Piwi protein Twi8p at distinctive noncoding RNA loci. RNA (NEW YORK, N.Y.) 2017; 23:530-545. [PMID: 28053272 PMCID: PMC5340916 DOI: 10.1261/rna.060012.116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
Transgenerational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of transgenerational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of transgenerational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated transgenerational regulation to include unique noncoding RNA loci. Ciliates such as Tetrahymena have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction. We show that the nuclear-localized Tetrahymena Piwi protein Twi8p shuttles from parental to zygotic macronuclei. Genetic elimination of Twi8p has no phenotype for cells in asexual growth. On the other hand, cells lacking Twi8p arrest in sexual reproduction with zygotic nuclei that retain the germline genome structure, without the DNA elimination and fragmentation required to generate a functional macronucleus. Twi8p-bound small RNAs originate from long-noncoding RNAs with a terminal hairpin, which become detectable in the absence of Twi8p. Curiously, the loci that generate Twi8p-bound small RNAs are essential for asexual cell growth, even though Twi8 RNPs are essential only in sexual reproduction. Our findings suggest the model that Twi8 RNPs act on silent germline chromosomes to permit their conversion to expressed macronuclear chromosomes. Overall this work reveals that a Piwi protein carrying small RNAs from long-noncoding RNA loci has transgenerational function in establishing zygotic nucleus competence for gene expression.
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MESH Headings
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Chromosomes
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- Gene Rearrangement
- Genome, Protozoan
- Macronucleus/genetics
- Macronucleus/metabolism
- Micronucleus, Germline/genetics
- Micronucleus, Germline/metabolism
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Reproduction, Asexual/genetics
- Tetrahymena/genetics
- Tetrahymena/growth & development
- Tetrahymena/metabolism
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Affiliation(s)
- Brian M Farley
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3202, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3202, USA
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46
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Wang Y, Sheng Y, Liu Y, Pan B, Huang J, Warren A, Gao S. N 6 -methyladenine DNA modification in the unicellular eukaryotic organism Tetrahymena thermophila. Eur J Protistol 2017; 58:94-102. [DOI: 10.1016/j.ejop.2016.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 01/30/2023]
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Affiliation(s)
- F. Paul Doerder
- Department of Biological, Geological and Environmental Sciences; Cleveland State University; Cleveland Ohio 44115 USA
| | - Joseph Frankel
- Department of Biology; University of Iowa; Iowa City Iowa 52242 USA
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48
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In Memoriam: David L. Nanney (1925-2016): Tetrahymena Genetics Founder and Epigenetics Champion. Genetics 2016; 204:1633-1634. [PMID: 27927907 DOI: 10.1534/genetics.116.196162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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49
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Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. eLife 2016; 5. [PMID: 27892853 PMCID: PMC5182062 DOI: 10.7554/elife.19090] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/14/2016] [Indexed: 12/30/2022] Open
Abstract
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
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Affiliation(s)
- Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Piroska E Huvos
- Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, United States
| | | | - Nikhat Zafar
- J. Craig Venter Institute, Rockville, United States
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, United States
| | | | | | | | | | - Carsten Russ
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Qiandong Zeng
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Lin Fan
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Joshua Z Levin
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Terrance Shea
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sarah K Young
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Ryan Hegarty
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Riza Daza
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sharvari Gujja
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jennifer R Wortman
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Bruce W Birren
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Chad Nusbaum
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Clayton M Carey
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Tomoko Noto
- Institute of Molecular Biotechnology, Vienna, Austria
| | | | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
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50
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Abstract
Over the past 20 years, breakthrough discoveries of chromatin-modifying enzymes and associated mechanisms that alter chromatin in response to physiological or pathological signals have transformed our knowledge of epigenetics from a collection of curious biological phenomena to a functionally dissected research field. Here, we provide a personal perspective on the development of epigenetics, from its historical origins to what we define as 'the modern era of epigenetic research'. We primarily highlight key molecular mechanisms of and conceptual advances in epigenetic control that have changed our understanding of normal and perturbed development.
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Affiliation(s)
- C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York 10065, New York, USA
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg D-79108, Germany
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