1
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Affiliation(s)
- María E. Elguero
- Facultad de Farmacia y Bioquímica, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Clara B. Nudel
- Facultad de Farmacia y Bioquímica, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro D. Nusblat
- Facultad de Farmacia y Bioquímica, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
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2
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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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3
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McDaniel SL, Zweifel E, Harris PKW, Yao MC, Cole ES, Chalker DL. DRH1, a p68-related RNA helicase gene, is required for chromosome breakage in Tetrahymena. Biol Open 2016; 5:1790-1798. [PMID: 27793833 PMCID: PMC5200911 DOI: 10.1242/bio.021576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The p68 DEAD box helicases comprise a widely conserved protein family involved in a large range of biological processes including transcription, splicing and translation. The genome of the ciliate Tetrahymena thermophile encodes two p68-like helicases, Drh1p and Lia2p. We show that DRH1 is essential for growth and completion of development. In growing cells, Drh1p is excluded from the nucleus and accumulates near cortical basal bodies. In contrast, during sexual reproduction, this protein localizes to meiotic micronuclei, initially in punctate foci in regions where centromeres and telomeres are known to reside and later in post-zygotic differentiating somatic macronuclei. Differentiation of the macronuclear genome involves extensive DNA rearrangements including fragmentation of the five pairs of germline-derived chromosomes into 180 chromosomal sub-fragments that are stabilized by de novo telomere deletion. In addition, thousands of internal eliminated sequences (IESs) are excised from loci dispersed throughout the genome. Strains with DRH1 deleted from the germline nuclei, which do not express the protein during post-zygotic development, fail to fragment the developing macronuclear chromosomes. IES excision still occurs in the absence of DRH1 zygotic expression; thus, Drh1p is the first protein found to be specifically required for chromosome breakage but not DNA elimination. Summary: The p68-related Drh1protein is essential for both growth and development of the ciliate Tetrahymena thermophila. It localizes to meiotic nuclei and is required for chromosome breakage of developing somatic chromosomes.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Erica Zweifel
- Biology Department, St. Olaf College, 1520 St. Olaf Avenue, Northfield, MN 55057, USA
| | - Peter K W Harris
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Meng-Chao Yao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Eric S Cole
- Biology Department, St. Olaf College, 1520 St. Olaf Avenue, Northfield, MN 55057, USA
| | - Douglas L Chalker
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA
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4
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Carle CM, Zaher HS, Chalker DL. A Parallel G Quadruplex-Binding Protein Regulates the Boundaries of DNA Elimination Events of Tetrahymena thermophila. PLoS Genet 2016; 12:e1005842. [PMID: 26950070 PMCID: PMC4780704 DOI: 10.1371/journal.pgen.1005842] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/12/2016] [Indexed: 11/19/2022] Open
Abstract
Guanine (G)-rich DNA readily forms four-stranded quadruplexes in vitro, but evidence for their participation in genome regulation is limited. We have identified a quadruplex-binding protein, Lia3, that controls the boundaries of germline-limited, internal eliminated sequences (IESs) of Tetrahymena thermophila. Differentiation of this ciliate's somatic genome requires excision of thousands of IESs, targeted for removal by small-RNA-directed heterochromatin formation. In cells lacking LIA3 (ΔLIA3), the excision of IESs bounded by specific G-rich polypurine tracts was impaired and imprecise, whereas the removal of IESs without such controlling sequences was unaffected. We found that oligonucleotides containing these polypurine tracts formed parallel G-quadruplex structures that are specifically bound by Lia3. The discovery that Lia3 binds G-quadruplex DNA and controls the accuracy of DNA elimination at loci with specific G-tracts uncovers an unrecognized potential of quadruplex structures to regulate chromosome organization.
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Affiliation(s)
- Christine M. Carle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Douglas L. Chalker
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
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5
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Noto T, Kataoka K, Suhren JH, Hayashi A, Woolcock KJ, Gorovsky MA, Mochizuki K. Small-RNA-Mediated Genome-wide trans-Recognition Network in Tetrahymena DNA Elimination. Mol Cell 2015; 59:229-42. [PMID: 26095658 PMCID: PMC4518040 DOI: 10.1016/j.molcel.2015.05.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/06/2015] [Accepted: 05/15/2015] [Indexed: 12/27/2022]
Abstract
Small RNAs are used to silence transposable elements (TEs) in many eukaryotes, which use diverse evolutionary solutions to identify TEs. In ciliated protozoans, small-RNA-mediated comparison of the germline and somatic genomes underlies identification of TE-related sequences, which are then eliminated from the soma. Here, we describe an additional mechanism of small-RNA-mediated identification of TE-related sequences in the ciliate Tetrahymena. We show that a limited set of internal eliminated sequences (IESs) containing potentially active TEs produces a class of small RNAs that recognize not only the IESs from which they are derived, but also other IESs in trans. This trans recognition triggers the expression of yet another class of small RNAs that identify other IESs. Therefore, TE-related sequences in Tetrahymena are robustly targeted for elimination by a genome-wide trans-recognition network accompanied by a chain reaction of small RNA production. Two types of siRNAs (scnRNAs) are expressed in Tetrahymena sexual reproduction Early-scnRNAs are produced from Type-A IESs containing potentially active transposons Early-scnRNAs trans-recognize Type-B IESs and trigger late-scnRNA production in cis Late-scnRNA production forms trans-recognition network for robust IES elimination
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Affiliation(s)
- Tomoko Noto
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Kensuke Kataoka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Jan H Suhren
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Azusa Hayashi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Katrina J Woolcock
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Martin A Gorovsky
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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LIA4 encodes a chromoshadow domain protein required for genomewide DNA rearrangements in Tetrahymena thermophila. EUKARYOTIC CELL 2014; 13:1300-11. [PMID: 25084866 DOI: 10.1128/ec.00125-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Extensive DNA elimination occurs as part of macronuclear differentiation during Tetrahymena sexual reproduction. The identification of sequences to excise is guided by a specialized RNA interference (RNAi) machinery that targets the methylation of histone H3 lysine 9 (K9) and K27 on chromatin associated with these internal eliminated sequences (IESs). This modified chromatin is reorganized into heterochromatic subnuclear foci, which is a hallmark of their subsequent elimination. Here, we demonstrate that Lia4, a chromoshadow domain-containing protein, is an essential component in this DNA elimination pathway. LIA4 knockout (ΔLIA4) lines fail to excise IESs from their developing somatic genome and arrest at a late stage of conjugation. Lia4 acts after RNAi-guided heterochromatin formation, as both H3K9 and H3K27 methylation are established. Nevertheless, without LIA4, these cells fail to form the heterochromatic foci associated with DNA rearrangement, and Lia4 accumulates in the foci, indicating that Lia4 plays a key role in their structure. These data indicate a critical role for Lia4 in organizing the nucleus during Tetrahymena macronuclear differentiation.
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7
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Catania F, McGrath CL, Doak TG, Lynch M. Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. Genome Biol Evol 2013; 5:1200-11. [PMID: 23737328 PMCID: PMC3698930 DOI: 10.1093/gbe/evt087] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Despite playing a crucial role in germline-soma differentiation, the evolutionary significance of developmentally regulated genome rearrangements (DRGRs) has received scant attention. An example of DRGR is DNA splicing, a process that removes segments of DNA interrupting genic and/or intergenic sequences. Perhaps, best known for shaping immune-system genes in vertebrates, DNA splicing plays a central role in the life of ciliated protozoa, where thousands of germline DNA segments are eliminated after sexual reproduction to regenerate a functional somatic genome. Here, we identify and chronicle the properties of 5,286 sequences that putatively undergo DNA splicing (i.e., internal eliminated sequences [IESs]) across the genomes of three closely related species of the ciliate Paramecium (P. tetraurelia, P. biaurelia, and P. sexaurelia). The study reveals that these putative IESs share several physical characteristics. Although our results are consistent with excision events being largely conserved between species, episodes of differential IES retention/excision occur, may have a recent origin, and frequently involve coding regions. Our findings indicate interconversion between somatic--often coding--DNA sequences and noncoding IESs, and provide insights into the role of DNA splicing in creating potentially functional genetic innovation.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Germany
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8
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Mutations in Pdd1 reveal distinct requirements for its chromodomain and chromoshadow domain in directing histone methylation and heterochromatin elimination. EUKARYOTIC CELL 2013; 13:190-201. [PMID: 24297443 DOI: 10.1128/ec.00219-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pdd1, a specialized HP1-like protein, is required for genome-wide DNA rearrangements that restructure a previously silent germ line genome into an active somatic genome during macronuclear differentiation of Tetrahymena thermophila. We deleted or otherwise mutated conserved regions of the protein to investigate how its different domains promote the excision of thousands of internal eliminated sequences (IESs). Previous studies revealed that Pdd1 contributes to recognition of IES loci after they are targeted by small-RNA-guided methylation of histone H3 on lysine 27 (H3K27), subsequently aids the establishment of H3K9 methylation, and recruits proteins that lead to excision. The phenotypes we observed for different Pdd1 alleles showed that each of the two chromodomains and the chromoshadow domain (CSD) have distinct contributions during somatic genome differentiation. Chromodomain 1 (CD1) is essential for conjugation as either its deletion or the substitution of two key aromatic amino acid residues (the W97A W100A mutant) is lethal. These mutations caused mislocalization of a cyan fluorescent protein (CFP)-tagged protein, prevented the establishment of histone H3 dimethylated on K9 (H3K9me2), and abolished IES excision. Nevertheless, the requirement for CD1 could be bypassed by recruiting Pdd1 directly to an IES by addition of a specific DNA binding domain. Chromodomain 2 (CD2) was necessary for producing viable progeny, but low levels of H3K9me2 and IES excision still occurred. A mutation in the chromoshadow domain (CSD) prevented Pdd1 focus formation but still permitted ∼17% of conjugants to produce viable progeny. However, this mutant was unable to stimulate excision when recruited to an ectopic IES, indicating that this domain is important for recruitment of excision factors.
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10
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Mochizuki K. Developmentally programmed, RNA-directed genome rearrangement in Tetrahymena. Dev Growth Differ 2011; 54:108-19. [PMID: 22103557 DOI: 10.1111/j.1440-169x.2011.01305.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Developmentally programmed genome rearrangement has been observed in a variety of eukaryotes from vertebrates to worms to protists, and it provides an interesting exception to the general rule of the constancy of the genome. DNA elimination in the ciliated protozoan Tetrahymena is one of the most well-characterized programmed genome rearrangement events. DNA elimination in the newly formed macronucleus of Tetrahymena is epigenetically regulated by the DNA sequence of the parental macronucleus. Dicer-produced, Piwi-associated small RNAs mediate this epigenetic regulation, probably through a whole-genome comparison of the germline micronucleus to the somatic macronucleus. However, a correlation between small RNAs and programmed genome rearrangement could not be detected in the worm Ascaris suum. Therefore, different types of eukaryotes may have developed unique solutions to perform genome rearrangement.
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Affiliation(s)
- Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
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11
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Chalker DL, Yao MC. DNA elimination in ciliates: transposon domestication and genome surveillance. Annu Rev Genet 2011; 45:227-46. [PMID: 21910632 DOI: 10.1146/annurev-genet-110410-132432] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ciliated protozoa extensively remodel their somatic genomes during nuclear development, fragmenting their chromosomes and removing large numbers of internal eliminated sequences (IESs). The sequences eliminated are unique and repetitive DNAs, including transposons. Recent studies have identified transposase proteins that appear to have been domesticated and are used by these cells to eliminate DNA not wanted in the somatic macronucleus. This DNA elimination process is guided by meiotically produced small RNAs, generated in the germline nucleus, that recognize homologous sequences leading to their removal. These scan RNAs are found in complexes with PIWI proteins. Before they search the developing genome for IESs to eliminate, they scan the parental somatic nucleus and are removed from the pool if they match homologous sequences in that previously reorganized genome. In Tetrahymena, the scan RNAs target heterochromatin modifications to mark IESs for elimination. This DNA elimination pathway in ciliates shares extensive similarity with piRNA-mediated silencing of metazoans and highlights the remarkable ability of homologous RNAs to shape developing genomes.
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Affiliation(s)
- Douglas L Chalker
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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12
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Mochizuki K. DNA rearrangements directed by non-coding RNAs in ciliates. WILEY INTERDISCIPLINARY REVIEWS. RNA 2010; 1:376-87. [PMID: 21956937 PMCID: PMC3746294 DOI: 10.1002/wrna.34] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA unscrambling, takes place in the newly developed macronucleus during the sexual reproduction of ciliated protozoa. Recent studies have revealed that two distant classes of ciliates use distinct types of non-coding RNAs to regulate such DNA rearrangement events. DNA elimination in Tetrahymena is regulated by small non-coding RNAs that are produced and utilized in an RNA interference (RNAi)-related process. It has been proposed that the small RNAs produced from the micronuclear genome are used to identify eliminated DNA sequences by whole-genome comparison between the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the parental macronuclear genome. These long RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. Both cases provide useful examples to study epigenetic chromatin regulation by non-coding RNAs.
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Affiliation(s)
- Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria.
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13
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Nishiyama N, Mikami K, Matsuoka A, Ochiai T, Yamauchi K. Extreme heterogeneous composition of the Paramecium caudatum macronuclear genomic DNA between hemoglobin and nucleosome assembly protein-1 genes. Genes Genet Syst 2010; 85:9-17. [PMID: 20410661 DOI: 10.1266/ggs.85.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The intergenic region between the hemoglobin (hb) and nucleosome assembly protein-1 (nap-1) genes in the Paramecium caudatum macronuclear genome was previously found to be heterogeneously composed. Cloning of this intergenic region from the macronuclear genomic DNA identified four unique DNA fragments of different sizes. Sequencing of the cloned fragments revealed extreme heterogeneity and characteristics of both internal eliminated sequence (IES) and imprecise internal deletion sequences (IIDSs) in the intergenic region. Missing sequences were an AT-rich and direct repeats existed in their boundaries. Southern blotting of the total genomic DNA and polymerase chain reaction (PCR) of the total genomic DNAs indicated that there exist a dozen DNA fragments of different sizes in this intergenic region. It is likely that the heterogeneity found in the P. caudatum macronuclear genome results from the variable removal of an intergenic region.
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Affiliation(s)
- Norihito Nishiyama
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka 422-8529, Japan
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14
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Huvos P. Varied truncation and clustering characterize some short repeats identified in micronucleus-specific DNA of Tetrahymena thermophila. Gene 2009; 448:174-9. [PMID: 19619624 DOI: 10.1016/j.gene.2009.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 07/07/2009] [Accepted: 07/12/2009] [Indexed: 10/20/2022]
Abstract
There are over 6000 internally eliminated DNA sequences (IESs) in the Tetrahymena genome that are deleted in a programmed fashion during the development of a polyploid, somatic macronucleus from a diploid germline micronucleus. Recently, based on several results, a homology and small RNA-based mechanism has been proposed for the efficient elimination of IES elements. Since the RNAi machinery is proposed to be intimately involved in silencing potentially harmful repeats such as transposons and viruses, characterization of repeats and the conditions for their developmental elimination from the somatic genome is warranted. Three short (500-600 bp) repeat families, members of which had been experimentally identified in IESs, that is, in micronucleus-specific DNA, are examined here using the Tetrahymena genome database. Members of all three families display varied degrees of truncation and are represented in macronuclear sequences. A 200 bp segment of one of the families can appear in the genome on its own, or as part of a 600 bp repeat detected experimentally, or in association with an unrelated 1 kb sequence to form a 1.2 kb repeat that is also frequently truncated. The 1 kb sequence contains a 300 bp section similar to a repeat associated with a non-long terminal repeat-like element and is often found accompanied by several more copies of this shorter repeat. These observations indicate that transposition may have had a role in the evolution of the short repeat families.
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Affiliation(s)
- Piroska Huvos
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL 62901-4413, USA.
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Duharcourt S, Lepère G, Meyer E. Developmental genome rearrangements in ciliates: a natural genomic subtraction mediated by non-coding transcripts. Trends Genet 2009; 25:344-50. [PMID: 19596481 DOI: 10.1016/j.tig.2009.05.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 05/29/2009] [Accepted: 05/29/2009] [Indexed: 11/24/2022]
Abstract
Several classes of non-protein-coding RNAs have recently been identified as epigenetic regulators of developmental genome rearrangements in ciliates, providing an interesting insight into the role of genome-wide transcription. In these unicellular eukaryotes, extensive rearrangements of the germline genome occur during the development of a new somatic macronucleus from the germline micronucleus. Rearrangement patterns are not dictated by the germline sequence, but reproduce the pre-existing rearrangements of the maternal somatic genome, implying a homology-dependent global comparison of germline and somatic genomes. We review recent evidence showing that this is achieved by a natural genomic subtraction, computed by pairing interactions between meiosis-specific, germline scnRNAs (small RNAs that resemble metazoan piRNAs) and longer non-coding transcripts from the somatic genome. We focus on current models for the RNA-based mechanisms enabling the cell to recognize the germline sequences to be eliminated from the somatic genome and to maintain an epigenetic memory of rearrangement patterns across sexual generations.
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Affiliation(s)
- Sandra Duharcourt
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, 75005 Paris, France.
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16
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Aronica L, Bednenko J, Noto T, DeSouza LV, Siu KM, Loidl J, Pearlman RE, Gorovsky MA, Mochizuki K. Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena. Genes Dev 2008; 22:2228-41. [PMID: 18708581 PMCID: PMC2518816 DOI: 10.1101/gad.481908] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 06/25/2008] [Indexed: 12/17/2022]
Abstract
Tetrahymena eliminates micronuclear-limited sequences from the developing macronucleus during sexual reproduction. Homology between the sequences to be eliminated and approximately 28-nucleotide small RNAs (scnRNAs) associated with an Argonaute family protein Twi1p likely underlies this elimination process. However, the mechanism by which Twi1p-scnRNA complexes identify micronuclear-limited sequences is not well understood. We show that a Twi1p-associated putative RNA helicase Ema1p is required for the interaction between Twi1p and chromatin. This requirement explains the phenotypes of EMA1 KO strains, including loss of selective down-regulation of scnRNAs homologous to macronuclear-destined sequences, loss of H3K9 and K27 methylation in the developing new macronucleus, and failure to eliminate DNA. We further demonstrate that Twi1p interacts with noncoding transcripts derived from parental and developing macronuclei and this interaction is greatly reduced in the absence of Ema1p. We propose that Ema1p functions in DNA elimination by stimulating base-pairing interactions between scnRNAs and noncoding transcripts in both parental and developing new macronuclei.
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Affiliation(s)
- Lucia Aronica
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
| | - Janna Bednenko
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Tomoko Noto
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
| | - Leroi V. DeSouza
- Department of Chemistry and Center for Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
| | - K.W. Michael Siu
- Department of Chemistry and Center for Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Josef Loidl
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Ronald E. Pearlman
- Department of Biology and Center for Research in Mass Spectronomy, York University, Toronto, Ontario M3J 1P3, Canada
| | - Martin A. Gorovsky
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
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17
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Lepère G, Bétermier M, Meyer E, Duharcourt S. Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. Genes Dev 2008; 22:1501-12. [PMID: 18519642 PMCID: PMC2418586 DOI: 10.1101/gad.473008] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 03/28/2008] [Indexed: 12/22/2022]
Abstract
The germline genome of ciliates is extensively rearranged during the development of a new somatic macronucleus from the germline micronucleus, after sexual events. In Paramecium tetraurelia, single-copy internal eliminated sequences (IESs) are precisely excised from coding sequences and intergenic regions. For a subset of IESs, introduction of the IES sequence into the maternal macronucleus specifically inhibits excision of the homologous IES in the developing zygotic macronucleus, suggesting that epigenetic regulation of excision involves a global comparison of germline and somatic genomes. ScanRNAs (scnRNAs) produced during micronuclear meiosis by a developmentally regulated RNAi pathway have been proposed to mediate this transnuclear cross-talk. In this study, microinjection experiments provide direct evidence that 25-nucleotide (nt) scnRNAs promote IES excision. We further show that noncoding RNAs are produced from the somatic maternal genome, both during vegetative growth and during sexual events. Maternal inhibition of IES excision is abolished when maternal somatic transcripts containing an IES are targeted for degradation by a distinct RNAi pathway involving 23-nt siRNAs. The results strongly support a scnRNA/macronuclear RNA scanning model in which a natural genomic subtraction, occurring during meiosis between deletion-inducing scnRNAs and antagonistic transcripts from the maternal macronucleus, regulates rearrangements of the zygotic genome.
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Affiliation(s)
- Gersende Lepère
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
| | - Mireille Bétermier
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
| | - Eric Meyer
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
| | - Sandra Duharcourt
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
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