1
|
Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024; 41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.
Collapse
Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Sophie Maiwald
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | | | - Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Beatrice Weber
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Austria
| |
Collapse
|
2
|
Kindelay SM, Maggert KA. Under the magnifying glass: The ups and downs of rDNA copy number. Semin Cell Dev Biol 2023; 136:38-48. [PMID: 35595601 PMCID: PMC9976841 DOI: 10.1016/j.semcdb.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/27/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022]
Abstract
The ribosomal DNA (rDNA) in Drosophila is found as two additive clusters of individual 35 S cistrons. The multiplicity of rDNA is essential to assure proper translational demands, but the nature of the tandem arrays expose them to copy number variation within and between populations. Here, we discuss means by which a cell responds to insufficient rDNA copy number, including a historical view of rDNA magnification whose mechanism was inferred some 35 years ago. Recent work has revealed that multiple conditions may also result in rDNA loss, in response to which rDNA magnification may have evolved. We discuss potential models for the mechanism of magnification, and evaluate possible consequences of rDNA copy number variation.
Collapse
Affiliation(s)
- Selina M Kindelay
- Genetics Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85724, USA
| | - Keith A Maggert
- Genetics Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ 85724, USA.
| |
Collapse
|
3
|
Fefelova EA, Pleshakova IM, Mikhaleva EA, Pirogov SA, Poltorachenko V, Abramov Y, Romashin D, Shatskikh A, Blokh R, Gvozdev V, Klenov M. Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon. Nucleic Acids Res 2022; 50:867-884. [PMID: 35037046 PMCID: PMC8789037 DOI: 10.1093/nar/gkab1276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/21/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic genomes harbor hundreds of rRNA genes, many of which are transcriptionally silent. However, little is known about selective regulation of individual rDNA units. In Drosophila melanogaster, some rDNA repeats contain insertions of the R2 retrotransposon, which is capable to be transcribed only as part of pre-rRNA molecules. rDNA units with R2 insertions are usually inactivated, although R2 expression may be beneficial in cells with decreased rDNA copy number. Here we found that R2-inserted rDNA units are enriched with HP1a and H3K9me3 repressive mark, whereas disruption of the heterochromatin components slightly affects their silencing in ovarian germ cells. Surprisingly, we observed a dramatic upregulation of R2-inserted rRNA genes in ovaries lacking Udd (Under-developed) or other subunits (TAF1b and TAF1c-like) of the SL1-like complex, which is homologues to mammalian Selective factor 1 (SL1) involved in rDNA transcription initiation. Derepression of rRNA genes with R2 insertions was accompanied by a reduction of H3K9me3 and HP1a enrichment. We suggest that the impairment of the SL1-like complex affects a mechanism of selective activation of intact rDNA units which competes with heterochromatin formation. We also propose that R2 derepression may serve as an adaptive response to compromised rRNA synthesis.
Collapse
Affiliation(s)
- Elena A Fefelova
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena 91125, USA
| | - Irina M Pleshakova
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
- Laboratory for Neurobiology of Memory, P.K. Anokhin Institute of Normal Physiology, Moscow 125315, Russia
| | - Elena A Mikhaleva
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Sergei A Pirogov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Valentin A Poltorachenko
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Yuri A Abramov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Daniil D Romashin
- Laboratory of Precision Biosystems, V. N. Orekhovich Institute of Biomedical Chemistry, 10 Pogodinskaya St., Moscow 119121, Russia
| | - Aleksei S Shatskikh
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Roman S Blokh
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
- Department of Functional Genomics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, Moscow 119334, Russia
| | - Vladimir A Gvozdev
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| | - Mikhail S Klenov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Moscow 123182, Russia
| |
Collapse
|
4
|
Luo Y, Fefelova E, Ninova M, Chen YCA, Aravin AA. Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster. eLife 2020; 9:e52416. [PMID: 33164748 PMCID: PMC7676866 DOI: 10.7554/elife.52416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/06/2020] [Indexed: 11/17/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are essential components of the ribosome and are among the most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA genes seems to be active, while others are transcriptionally silent. We found that individual rDNA genes have high level of cell-to-cell heterogeneity in their expression in Drosophila melanogaster. Insertion of heterologous sequences into rDNA leads to repression associated with reduced expression in individual cells and decreased number of cells expressing rDNA with insertions. We found that SUMO (Small Ubiquitin-like Modifier) and SUMO ligase Ubc9 are required for efficient repression of interrupted rDNA units and variable expression of intact rDNA. Disruption of the SUMO pathway abolishes discrimination of interrupted and intact rDNAs and removes cell-to-cell heterogeneity leading to uniformly high expression of individual rDNA in single cells. Our results suggest that the SUMO pathway is responsible for both repression of interrupted units and control of intact rDNA expression.
Collapse
Affiliation(s)
- Yicheng Luo
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Elena Fefelova
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Institute of Molecular Genetics, Russian Academy of SciencesMoscowRussian Federation
| | - Maria Ninova
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Yung-Chia Ariel Chen
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| |
Collapse
|
5
|
Bughio F, Maggert KA. The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance. Chromosome Res 2018; 27:19-30. [PMID: 30511202 DOI: 10.1007/s10577-018-9591-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly fascinating genetics of the highly transcribed repeat DNA structure at that locus.
Collapse
Affiliation(s)
- Farah Bughio
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA
- University of Arizona Cancer Center, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Keith A Maggert
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA.
- University of Arizona Cancer Center, University of Arizona College of Medicine, Tucson, AZ, USA.
| |
Collapse
|
6
|
Kojima KK. LINEs Contribute to the Origins of Middle Bodies of SINEs besides 3' Tails. Genome Biol Evol 2018; 10:370-379. [PMID: 29325122 PMCID: PMC5786205 DOI: 10.1093/gbe/evy008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 01/06/2023] Open
Abstract
Short interspersed elements (SINEs), which are nonautonomous transposable elements, require the transposition machinery of long interspersed elements (LINEs) to mobilize. SINEs are composed of two or more independently originating parts. The 5′ region is called the “head” and is derived mainly from small RNAs, and the 3′ region (“tail”) originates from the 3′ region of LINEs and is responsible for being recognized by counterpart LINE proteins. The origin of the middle “body” of SINEs is enigmatic, although significant sequence similarities among SINEs from very diverse species have been observed. Here, a systematic analysis of the similarities among SINEs and LINEs deposited on Repbase, a comprehensive database of eukaryotic repeat sequences was performed. Three primary findings are described: 1) The 5′ regions of only two clades of LINEs, RTE and Vingi, were revealed to have contributed to the middle parts of SINEs; 2) The linkage of the 5′ and 3′ parts of LINEs can be lost due to occasional tail exchange of SINEs; and 3) The previously proposed Ceph-domain was revealed to be a fusion of a CORE-domain and a 5′ part of RTE clade of LINE. Based on these findings, a hypothesis that the 5′ parts of bipartite nonautonomous LINEs, which possess only the 5′ and 3′ regions of the original LINEs, can contribute to the undefined middle part of SINEs is proposed.
Collapse
Affiliation(s)
- Kenji K Kojima
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.,Genetic Information Research Institute, Mountain View, California
| |
Collapse
|
7
|
Abstract
R2 elements are sequence specific non-LTR retrotransposons that exclusively insert in the 28S rRNA genes of animals. R2s encode an endonuclease that cleaves the insertion site and a reverse transcriptase that uses the cleaved DNA to prime reverse transcription of the R2 transcript, a process termed target primed reverse transcription. Additional unusual properties of the reverse transcriptase as well as DNA and RNA binding domains of the R2 encoded protein have been characterized. R2 expression is through co-transcription with the 28S gene and self-cleavage by a ribozyme encoded at the R2 5' end. Studies in laboratory stocks and natural populations of Drosophila suggest that R2 expression is tied to the distribution of R2-inserted units within the rDNA locus. Most individuals have no R2 expression because only a small fraction of their rRNA genes need to be active, and a contiguous region of the locus free of R2 insertions can be selected for activation. However, if the R2-free region is not large enough to produce sufficient rRNA, flanking units - including those inserted with R2 - must be activated. Finally, R2 copies rapidly turnover within the rDNA locus, yet R2 has been vertically maintained in animal lineages for hundreds of millions of years. The key to this stability is R2's ability to remain dormant in rDNA units outside the transcribed regions for generations until the stochastic nature of the crossovers that drive the concerted evolution of the rDNA locus inevitably reshuffle the inserted and uninserted units, resulting in transcription of the R2-inserted units.
Collapse
|
8
|
Mukha DV, Pasyukova EG, Kapelinskaya TV, Kagramanova AS. Endonuclease domain of the Drosophila melanogaster R2 non-LTR retrotransposon and related retroelements: a new model for transposition. Front Genet 2013; 4:63. [PMID: 23637706 PMCID: PMC3636483 DOI: 10.3389/fgene.2013.00063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 04/05/2013] [Indexed: 01/25/2023] Open
Abstract
The molecular mechanisms of the transposition of non-long terminal repeat (non-LTR) retrotransposons are not well understood; the key questions of how the 3′-ends of cDNA copies integrate and how site-specific integration occurs remain unresolved. Integration depends on properties of the endonuclease (EN) domain of retrotransposons. Using the EN domain of the Drosophila R2 retrotransposon as a model for other, closely related non-LTR retrotransposons, we investigated the EN domain and found that it resembles archaeal Holliday-junction resolvases. We suggest that these non-LTR retrotransposons are co-transcribed with the host transcript. Combined with the proposed resolvase activity of the EN domain, this model yields a novel mechanism for site-specific retrotransposition within this class of retrotransposons, with resolution proceeding via a Holliday junction intermediate.
Collapse
Affiliation(s)
- Dmitry V Mukha
- Vavilov Institute of General Genetics, Russian Academy of Sciences Moscow, Russia
| | | | | | | |
Collapse
|
9
|
Abstract
The rDNA genes are transcribed by RNA polymerase I to make structural RNAs for ribosomes. Hundreds of rDNA genes are typically arranged in an array that spans megabase pairs of DNA. These arrays are the major sites of transcription in growing cells, accounting for as much as 50% of RNA synthesis. The repetitive rDNA arrays are thought to use heterochromatic gene silencing as a mechanism for metabolic regulation, since repeated sequences nucleate heterochromatin formation in eukaryotes. Drosophila melanogaster carries an rDNA array on the X chromosome and on the Y chromosome, and genetic analysis has suggested that both are transcribed. However, using a chromatin-marking assay, we find that the entire X chromosome rDNA array is normally silenced in D. melanogaster males, while the Y chromosome rDNA array is dominant and expressed. This resembles "nucleolar dominance," a phenomenon that occurs in interspecific hybrids where an rDNA array from one parental species is silenced, and that from the other parent is preferentially transcribed. Interspecies nucleolar dominance is thought to result from incompatibilities between species-specific transcription factors and the rDNA promoters in the hybrid, but our results show that nucleolar dominance is a normal feature of rDNA regulation. Nucleolar dominance within D. melanogaster is only partially dependent on known components of heterochromatic gene silencing, implying that a distinctive chromatin regulatory system may act at rDNA genes. Finally, we isolate variant Y chromosomes that allow X chromosome array expression and suggest that the large-scale organization of rDNA arrays contribute to nucleolar dominance. This is the first example of allelic inactivation in D. melanogaster.
Collapse
|
10
|
Eickbush DG, Eickbush TH. R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements. Mob DNA 2012; 3:10. [PMID: 22621441 PMCID: PMC3414825 DOI: 10.1186/1759-8753-3-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 05/23/2012] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND R2 is a non-long terminal repeat (non-LTR) retrotransposable element that inserts site specifically into the 28S genes of the ribosomal (r)RNA gene loci. Encoded at the 5' end is a ribozyme that generates the precise 5' end by self-cleavage of a 28S gene cotranscript. Sequences at the 3' end are necessary for the R2 protein to bind RNA and initiate the target primed reverse transcription (TPRT) reaction. These minimal RNA requirements suggested that if recombination/DNA repair conjoined the 5' and 3' ends of R2, the result would be a non-autonomous element that could survive as long as autonomous R2 elements supplied the TPRT activity. RESULTS A PCR-based survey of 39 Drosophila species aided by genomic sequences from 12 of these species revealed two types of non-autonomous elements. We call these elements SIDEs (for 'Short Internally Deleted Elements'). The first consisted of a 5' ribozyme and a 3' end of an R2 element as predicted. Variation at the 5' junctions of the R2 SIDE copies was typical for R2 insertions suggesting their propagation by TPRT. The second class of SIDE contained sequences from R1 elements, another non-LTR retrotransposon that inserts into rRNA gene loci. These insertions had an R2 ribozyme immediately upstream of R1 3' end sequences. These hybrid SIDEs were inserted at the R1 site with 14 bp target site duplications typical of R1 insertions suggesting they used the R1 machinery for retrotransposition. Finally, the survey revealed examples of U12 small nuclear (sn)RNA and tRNA sequences at the 5' end of R2 elements suggesting the R2 reverse transcriptase can template jump from the R2 transcript to a second RNA during TPRT. CONCLUSIONS The R2 SIDE and R2/R1 hybrid SIDEs are rare examples of non-autonomous retrotransposons in the Drosophila genome. Associated non-autonomous elements and in vivo template jumps are two additional characteristics R2 shares with other non-LTR retrotransposons such as mammalian L1s. Analysis of the hybrid SIDEs provides supporting evidence that R1 elements, like R2 elements, recognize their 3' untranslated region (UTR) sequences and, thus, belong to the stringent class of non-LTR elements.
Collapse
Affiliation(s)
- Danna G Eickbush
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
| | | |
Collapse
|
11
|
Cabral-de-Mello DC, Cabrero J, López-León MD, Camacho JPM. Evolutionary dynamics of 5S rDNA location in acridid grasshoppers and its relationship with H3 histone gene and 45S rDNA location. Genetica 2011; 139:921-31. [PMID: 21755328 DOI: 10.1007/s10709-011-9596-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 07/01/2011] [Indexed: 10/18/2022]
|
12
|
Stage DE, Eickbush TH. Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila. Genome Biol 2009; 10:R49. [PMID: 19416522 PMCID: PMC2718515 DOI: 10.1186/gb-2009-10-5-r49] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/27/2009] [Accepted: 05/05/2009] [Indexed: 01/31/2023] Open
Abstract
Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons. Background Most arthropods contain R1 and R2 retrotransposons that specifically insert into the 28S rRNA genes. Here, the sequencing reads from 12 Drosophila genomes have been used to address two questions concerning these elements. First, to what extent is the evolution of these elements subject to the concerted evolution process that is responsible for sequence homogeneity among the different copies of rRNA genes? Second, how precise are the target DNA cleavages and priming of DNA synthesis used by these elements? Results Most copies of R1 and R2 in each species were found to exhibit less than 0.2% sequence divergence. However, in many species evidence was obtained for the formation of distinct sublineages of elements, particularly in the case of R1. Analysis of the hundreds of R1 and R2 junctions with the 28S gene revealed that cleavage of the first DNA strand was precise both in location and the priming of reverse transcription. Cleavage of the second DNA strand was less precise within a species, differed between species, and gave rise to variable priming mechanisms for second strand synthesis. Conclusions These findings suggest that the high sequence identity amongst R1 and R2 copies is because all copies are relatively new. However, each active element generates its own independent lineage that can eventually populate the locus. Independent lineages occur more often with R1, possibly because these elements contain their own promoter. Finally, both R1 and R2 use imprecise, rapidly evolving mechanisms to cleave the second strand and prime second strand synthesis.
Collapse
Affiliation(s)
- Deborah E Stage
- Biology Department, University of Rochester, Rochester NY 14627-0211, USA.
| | | |
Collapse
|
13
|
The R2 mobile element of Rhynchosciara americana: molecular, cytological and dynamic aspects. Chromosome Res 2009; 17:455-67. [PMID: 19350401 DOI: 10.1007/s10577-009-9038-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 03/03/2009] [Accepted: 03/03/2009] [Indexed: 10/20/2022]
Abstract
Ribosomal RNA genes are encoded by large units clustered (18S, 5S, and 28S) in the nucleolar organizer region in several organisms. Sometimes additional insertions are present in the coding region for the 28S rDNA. These insertions are specific non-long terminal repeat retrotransposons that have very restricted integration targets within the genome. The retrotransposon present in the genome of Rhynchosciara americana, RaR2, was isolated by the screening of a genomic library. Sequence analysis showed the presence of conserved regions, such as a reverse transcriptase domain and a zinc finger motif in the amino terminal region. The insertion site was highly conserved in R. americana and a phylogenetic analysis showed that this element belongs to the R2 clade. The chromosomal localization confirmed that the RaR2 mobile element was inserted into a specific site in the rDNA gene. The expression level of RaR2 in salivary glands during larval development was determined by quantitative RT-PCR, and the increase of relative expression in the 3P of the fourth instar larval could be related to intense gene activity characteristic of this stage. 5'-Truncated elements were identified in different DNA samples. Additionally, in three other Rhynchosciara species, the R2 element was present as a full-length element.
Collapse
|
14
|
Glass SK, Moszczynska A, Crease TJ. The effect of transposon Pokey insertions on sequence variation in the 28S rRNA gene of Daphnia pulex. Genome 2009; 51:988-1000. [PMID: 19088812 DOI: 10.1139/g08-092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The goal of this study was to determine the impact of breeding system and the presence of the transposon Pokey on intraindividual variation in 28S rRNA genes. We PCR-amplified, cloned, and sequenced 1000 nucleotides downstream of the Pokey insertion site in genes with and without insertions from 10 obligately and 10 cyclically parthenogenetic isolates of Daphnia pulex. Variation among genes with Pokey insertions was higher than variation among genes without insertions in both cyclic and obligate isolates. Although the differences were not quite significant (p = 0.06 in both cases), the results suggest that Pokey insertions are likely to inhibit the homogenization of their host genes to some extent. We also observed that the complement of 28S rRNA alleles differed between genes with and without inserts in some isolates, suggesting that a particular inserted gene can persist for substantial periods of time and even spread within the rDNA array, despite the fact that insertions are deleterious. This apparently contradictory pattern can be explained if homogenization of rRNA genes occurs primarily by gene conversion, but copies with Pokey inserts can occasionally increase in frequency within arrays owing to unequal crossing over events that do not originate in the inserted genes themselves.
Collapse
Affiliation(s)
- Shiona K Glass
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1 Canada
| | | | | |
Collapse
|
15
|
Zhou J, Eickbush TH. The pattern of R2 retrotransposon activity in natural populations of Drosophila simulans reflects the dynamic nature of the rDNA locus. PLoS Genet 2009; 5:e1000386. [PMID: 19229317 PMCID: PMC2637433 DOI: 10.1371/journal.pgen.1000386] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 01/20/2009] [Indexed: 11/18/2022] Open
Abstract
The pattern and frequency of insertions that enable transposable elements to remain active in a population are poorly understood. The retrotransposable element R2 exclusively inserts into the 28S rRNA genes where it establishes long-term, stable relationships with its animal hosts. Previous studies with laboratory stocks of Drosophila simulans have suggested that control over R2 retrotransposition resides within the rDNA loci. In this report, we sampled 180 rDNA loci of animals collected from two natural populations of D. simulans. The two populations were found to have similar patterns of R2 activity. About half of the rDNA loci supported no or very low levels of R2 transcripts with no evidence of R2 retrotransposition. The remaining half of the rDNA loci had levels of R2 transcripts that varied in a continuous manner over almost a 100-fold range and did support new retrotransposition events. Structural analysis of the rDNA loci in 18 lines that spanned the range of R2 transcript levels in these populations revealed that R2 number and rDNA locus size varied 2-fold; however, R2 activity was not readily correlated with either of these parameters. Instead R2 activity was best correlated with the distribution of elements within the rDNA locus. Loci with no activity had larger contiguous blocks of rDNA units free of R2-insertions. These data suggest a model in which frequent recombination within the rDNA locus continually redistributes R2-inserted units resulting in changing levels of R2 activity within individual loci and persistent R2 activity within the population.
Collapse
Affiliation(s)
- Jun Zhou
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Thomas H. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
| |
Collapse
|
16
|
Epigenetic regulation of retrotransposons within the nucleolus of Drosophila. Mol Cell Biol 2008; 28:6452-61. [PMID: 18678644 DOI: 10.1128/mcb.01015-08] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
R2 retrotransposable elements exclusively insert into a conserved region of the tandemly organized 28S rRNA genes. Despite inactivating a subset of these genes, R2 elements have persisted in the ribosomal DNA (rDNA) loci of insects for hundreds of millions of years. Controlling R2 proliferation was addressed in this study using lines of Drosophila simulans previously shown to have either active or inactive R2 retrotransposition. Lines with active retrotransposition were shown to have high R2 transcript levels, which nuclear run-on transcription experiments revealed were due to increased transcription of R2-inserted genes. Crosses between R2 active and inactive lines indicated that an important component of this transcriptional control is linked to or near the rDNA locus, with the R2 transcription level of the inactive parent being dominant. Pulsed-field gel analysis suggested that the R2 active and inactive states were determined by R2 distribution within the locus. Molecular and cytological analyses further suggested that the entire rDNA locus from the active line can be silenced in favor of the locus from the inactive line. This silencing of entire rDNA loci represents an example of the large-scale epigenetic control of transposable elements and shares features with the nucleolar dominance frequently seen in interspecies hybrids.
Collapse
|
17
|
Raskina O, Barber JC, Nevo E, Belyayev A. Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes. Cytogenet Genome Res 2008; 120:351-7. [PMID: 18504364 DOI: 10.1159/000121084] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2007] [Indexed: 11/19/2022] Open
Abstract
Chromosomal change is one of the more hotly debated potential mechanisms of speciation. It has long been argued over whether--and to what degree--changes in chromosome structure contribute to reproductive isolation and, ultimately, speciation. In this review we do not aim to completely analyze accumulated data about chromosomal speciation but wish to draw attention to several critical points of speciation-related chromosomal change, namely: (a) interrelations between chromosomal rearrangements and repetitive DNA fraction; (b) mobility of ribosomal DNA clusters; and (c) rDNA and transposable elements as perpetual generators of genome instability.
Collapse
Affiliation(s)
- O Raskina
- Institute of Evolution, University of Haifa, Israel
| | | | | | | |
Collapse
|
18
|
Johansen SD, Haugen P, Nielsen H. Expression of protein-coding genes embedded in ribosomal DNA. Biol Chem 2007; 388:679-86. [PMID: 17570819 DOI: 10.1515/bc.2007.089] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that encode reverse transcriptase-like genes, and group I introns and archaeal introns that encode homing endonuclease genes (HEGs). Although rDNA-embedded protein genes are widespread in nuclei, organelles and bacteria, there is surprisingly little information available on how these genes are expressed. Exceptions include a handful of HEGs from group I introns. Recent studies have revealed unusual and essential roles of group I and group I-like ribozymes in the endogenous expression of HEGs. Here we discuss general aspects of rDNA-embedded protein genes and focus on HEG expression from group I introns in the nucleolus.
Collapse
Affiliation(s)
- Steinar D Johansen
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Tromsø, Norway.
| | | | | |
Collapse
|
19
|
Ye J, Eickbush TH. Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster. Mol Cell Biol 2006; 26:8781-90. [PMID: 17000772 PMCID: PMC1636831 DOI: 10.1128/mcb.01409-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
About half of the rRNA gene units (rDNA units) of Drosophila melanogaster are inserted by the retrotransposable elements R1 and R2. Because transcripts to R1 and R2 were difficult to detect on blots and electron microscopic observations of rRNA synthesis suggested that only uninserted rDNA units were transcribed, it has long been postulated that inserted rDNA units are in a repressed (inactive) chromatin structure. Studies described here suggest that inserted and uninserted units are equally accessible to DNase I and micrococcal nuclease and contain similar levels of histone H3 and H4 acetylation and H3K9 methylation. These studies have low sensitivity, because psoralen cross-linking suggested few (estimated <10%) of the rDNA units of any type are transcriptionally active. Nuclear run-on experiments revealed that R1-inserted and R2-inserted units are activated for transcription at about 1/5 and 1/10, respectively, the rate of uninserted units. Most transcription complexes of the inserted units terminate within the elements, thus explaining why previous molecular and electron microscopic methods indicated inserted units are seldom transcribed. The accumulating data suggest that all units within small regions of the rDNA loci are activated for transcription, with most control over R1 and R2 activity involving steps downstream of transcription initiation.
Collapse
Affiliation(s)
- Junqiang Ye
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | |
Collapse
|
20
|
Ye J, Pérez-González CE, Eickbush DG, Eickbush TH. Competition between R1 and R2 transposable elements in the 28S rRNA genes of insects. Cytogenet Genome Res 2005; 110:299-306. [PMID: 16093682 DOI: 10.1159/000084962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 01/13/2004] [Indexed: 11/19/2022] Open
Abstract
R1 and R2 are non-LTR retrotransposons that insert in the 28S rRNA genes of arthropods. R1 elements insert into a site that is 74 bp downstream of the R2 insertion site, thus the presence of an R2 in the same 28S gene may inhibit the expression of R1. Consistent with such a suggestion, the R1 elements of Drosophila melanogaster have a strong bias against inserting into 28S genes already containing an R2 element. R2 elements, on the other hand, are only 2-3 fold inhibited from inserting into a 28S gene already containing an R1. D. melanogaster R1 elements are unusual in that they generate a 23-bp deletion of the target site upstream of the insertion. Using in vitro assays developed to study R2 integration, we show that the presence of R1 sequences 51 bp downstream of the R2 insertion site changes the nucleosomal structure that can be formed by the R2 target site. The R2 endonuclease is inhibited from cleaving these altered nucleosomes. We suggest that R1 elements have been selected to make this large deletion of the 28S gene to block the insertion of an upstream R2 element. These findings are consistent with the model that R1 and R2 are in competition for the limited number of insertion sites available within their host's genome.
Collapse
Affiliation(s)
- J Ye
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | | | | | |
Collapse
|
21
|
Averbeck KT, Eickbush TH. Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus. Genetics 2005; 171:1837-46. [PMID: 16143606 PMCID: PMC1456108 DOI: 10.1534/genetics.105.047670] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-LTR retrotransposons R1 and R2 have persisted in rRNA gene loci (rDNA) since the origin of arthropods despite their continued elimination by the recombinational mechanisms of concerted evolution. This study evaluated the short-term evolutionary dynamics of the rDNA locus by measuring the divergence among replicate Drosophila melanogaster lines after 400 generations. The total number of rDNA units on the X chromosome of each line varied from 140 to 310, while the fraction of units inserted with R1 and R2 retrotransposons ranged from 37 to 65%. This level of variation is comparable to that found in natural population surveys. Variation in locus size and retrotransposon load was correlated with large changes in the number of uninserted and R1-inserted units, yet the numbers of R2-inserted units were relatively unchanged. Intergenic spacer (IGS) region length variants were also used to evaluate changes in the rDNA loci. All IGS length variants present in the lines showed significant increases and decreases of copy number. These studies, combined with previous data following specific R1 and R2 insertions in these lines, help to define the type and distribution, both within the locus and within the individual units, of recombinational events that give rise to the concerted evolution of the rDNA locus.
Collapse
|
22
|
Maggert KA, Golic KG. Highly efficient sex chromosome interchanges produced by I-CreI expression in Drosophila. Genetics 2005; 171:1103-14. [PMID: 16020774 PMCID: PMC1456814 DOI: 10.1534/genetics.104.040071] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The homing endonuclease I-CreI recognizes a site in the gene encoding the 23S rRNA of Chlamydomonas reinhardtii. A very similar sequence is present in the 28S rRNA genes that are located on the X and Y chromosomes of Drosophila melanogaster. In this work we show that I-CreI expression in Drosophila is capable of causing induced DNA damage and eliciting cell cycle arrest. Expression also caused recombination between the X and Y chromosomes in the heterochromatic regions where the rDNA is located, presumably as a result of a high frequency of double-strand breaks in these regions. Approximately 20% of the offspring of males expressing I-CreI showed exceptional inheritance of X- and Y-linked markers, consistent with chromosome exchange at rDNA loci. Cytogenetic analysis confirmed the structures of many of these products. Exchange between the X and Y chromosomes can be induced in males and females to produce derivative-altered Y chromosomes, attached-XY, and attached-X chromosomes. This method has advantages over the traditional use of X rays for generating X-Y interchanges because it is very frequent and it generates predictable products.
Collapse
Affiliation(s)
- Keith A Maggert
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | | |
Collapse
|
23
|
Zhang X, Eickbush TH. Characterization of active R2 retrotransposition in the rDNA locus of Drosophila simulans. Genetics 2005; 170:195-205. [PMID: 15781697 PMCID: PMC1449725 DOI: 10.1534/genetics.104.038703] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rRNA gene (rDNA) loci of all arthropod lineages contain non-LTR retrotransposable elements that have evolved to specifically insert into the 28S rRNA genes. Extensive in vitro experiments have been conducted to investigate the mechanism of R2 retrotransposition but little is known of the insertion frequency or cellular factors that might regulate R2 activity. In this article, isofemale lines obtained from a population of Drosophila simulans were surveyed for recent R2 insertions. Within most lines, all individuals showed the same collection of R2 insertions, providing no evidence for recent R2 activity. However, in a few of the isofemale lines, virtually all individuals differed in their R2 insertion profiles. The descendants of individual pairs of flies from these "active lines" rapidly accumulated new insertions. The frequent insertion of new R2 elements was associated with the elimination of old R2 elements from the rDNA locus. The existence of lines in which R2 retrotransposes frequently and lines in which the elements appear dormant suggests that cellular mechanisms that can regulate the activity of R2 exist. Retrotransposition activity was correlated with the number of full-length R2 elements but not with the size of the rDNA locus or the number of uninserted units.
Collapse
Affiliation(s)
- Xian Zhang
- Department of Biology, University of Rochester, New York 14627, USA
| | | |
Collapse
|
24
|
Pérez-González CE, Burke WD, Eickbush TH. R1 and R2 retrotransposition and deletion in the rDNA loci on the X and Y chromosomes of Drosophila melanogaster. Genetics 2004; 165:675-85. [PMID: 14573479 PMCID: PMC1462780 DOI: 10.1093/genetics/165.2.675] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The non-LTR retrotransposons R1 and R2 insert into the 28S rRNA genes of arthropods. Comparisons among Drosophila lineages have shown that these elements are vertically inherited, while studies within species have indicated a rapid turnover of individual copies (elimination of old copies and the insertion of new copies). To better understand the turnover of R1 and R2, 200 retrotranspositions and nearly 100 eliminations have been scored in the Harwich mutation-accumulation lines of Drosophila melanogaster. Because the rDNA arrays in D. melanogaster are present on the X and Y chromosomes and no exchanges were detected in these lines, it was possible to show that R1 retrotranspositions occur predominantly in the male germ line, while R2 retrotranspositions were more evenly divided between the germ lines of both sexes. The rate of elimination of elements from the Y rDNA array was twice that of the X rDNA array with both chromosomal loci containing regions where the rate of elimination was on average eight times higher. Most R1 and R2 eliminations appear to occur by large intrachromosomal events (i.e., loop-out events) that involve multiple rDNA units. These findings are interpreted in light of the known abundance of R1 and R2 elements in the X and Y rDNA loci of D. melanogaster.
Collapse
|