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Wolter F, Schindele P, Beying N, Scheben A, Puchta H. Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. THE PLANT CELL 2021; 33:3454-3469. [PMID: 34375428 PMCID: PMC8566284 DOI: 10.1093/plcell/koab204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/04/2021] [Indexed: 05/03/2023]
Abstract
In nature, single-strand breaks (SSBs) in DNA occur more frequently (by orders of magnitude) than double-strand breaks (DSBs). SSBs induced by the CRISPR/Cas9 nickase at a distance of 50-100 bp on opposite strands are highly mutagenic, leading to insertions/deletions (InDels), with insertions mainly occurring as direct tandem duplications. As short tandem repeats are overrepresented in plant genomes, this mechanism seems to be important for genome evolution. We investigated the distance at which paired 5'-overhanging SSBs are mutagenic and which DNA repair pathways are essential for insertion formation in Arabidopsis thaliana. We were able to detect InDel formation up to a distance of 250 bp, although with much reduced efficiency. Surprisingly, the loss of the classical nonhomologous end joining (NHEJ) pathway factors KU70 or DNA ligase 4 completely abolished tandem repeat formation. The microhomology-mediated NHEJ factor POLQ was required only for patch-like insertions, which are well-known from DSB repair as templated insertions from ectopic sites. As SSBs can also be repaired using homology, we furthermore asked whether the classical homologous recombination (HR) pathway is involved in this process in plants. The fact that RAD54 is not required for homology-mediated SSB repair demonstrates that the mechanisms for DSB- and SSB-induced HR differ in plants.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Natalja Beying
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Author for correspondence:
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2
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Beying N, Schmidt C, Pacher M, Houben A, Puchta H. CRISPR-Cas9-mediated induction of heritable chromosomal translocations in Arabidopsis. NATURE PLANTS 2020; 6:638-645. [PMID: 32451449 DOI: 10.1038/s41477-020-0663-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/14/2020] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) technology has been applied in plant breeding mainly on genes for improving single or multiple traits1-4. Here we show that this technology can also be used to restructure plant chromosomes. Using the Cas9 nuclease from Staphylococcus aureus5, we were able to induce reciprocal translocations in the Mbp range between heterologous chromosomes in Arabidopsis thaliana. Of note, translocation frequency was about five times more efficient in the absence of the classical non-homologous end-joining pathway. Using egg-cell-specific expression of the Cas9 nuclease and consecutive bulk screening, we were able to isolate heritable events and establish lines homozygous for the translocation, reaching frequencies up to 2.5% for individual lines. Using molecular and cytological analysis, we confirmed that the chromosome-arm exchanges we obtained between chromosomes 1 and 2 and between chromosomes 1 and 5 of Arabidopsis were conservative and reciprocal. The induction of chromosomal translocations enables mimicking of genome evolution or modification of chromosomes in a directed manner, fixing or breaking genetic linkages between traits on different chromosomes. Controlled restructuring of plant genomes has the potential to transform plant breeding.
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Affiliation(s)
- Natalja Beying
- Botanical Institute-Molecular Biology and Biochemistry of Plants, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Carla Schmidt
- Botanical Institute-Molecular Biology and Biochemistry of Plants, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Pacher
- Botanical Institute-Molecular Biology and Biochemistry of Plants, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Seeland, Germany
| | - Holger Puchta
- Botanical Institute-Molecular Biology and Biochemistry of Plants, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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3
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Mielich K, Shtifman-Segal E, Golz JC, Zeng G, Wang Y, Berman J, Kunze R. Maize Transposable Elements Ac/ Ds as Insertion Mutagenesis Tools in Candida albicans. G3 (BETHESDA, MD.) 2018; 8:1139-1145. [PMID: 29378819 PMCID: PMC5873905 DOI: 10.1534/g3.117.300388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
In nonmodel systems, genetic research is often limited by the lack of techniques for the generation and identification of gene mutations. One approach to overcome this bottleneck is the application of transposons for gene tagging. We have established a two-element transposon tagging system, based on the transposable elements Activator (Ac)/Dissociation (Ds) from maize, for in vivo insertion mutagenesis in the fungal human pathogen Candida albicans A nonautonomous Ds transposon carrying a selectable marker was constructed into the ADE2 promoter on chromosome 3 and a codon usage-adapted Ac transposase gene was inserted into the neutral NEUT5L locus on chromosome 5. In C. albicans cells expressing the transposase, the Ds element efficiently excised and reintegrated elsewhere in the genome, which makes the Ac/Ds transposons promising tools for saturating insertion mutagenesis in clinical strains of C. albicans.
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Affiliation(s)
- Kevin Mielich
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
| | - Ella Shtifman-Segal
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Julia C Golz
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
| | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673, Singapore
| | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673, Singapore
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
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4
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Abstract
The mechanistic understanding of how DNA double-strand breaks (DSB) are repaired is rapidly advancing in part due to the advent of inducible site-specific break model systems as well as the employment of next-generation sequencing (NGS) technologies to sequence repair junctions at high depth. Unfortunately, the sheer volume of data produced by these methods makes it difficult to analyze the structure of repair junctions manually or with other general-purpose software. Here, we describe methods to produce amplicon libraries of DSB repair junctions for sequencing, to map the sequencing reads, and then to use a robust, custom python script, Hi-FiBR, to analyze the sequence structure of mapped reads. The Hi-FiBR analysis processes large data sets quickly and provides information such as number and type of repair events, size of deletion, size of insertion and inserted sequence, microhomology usage, and whether mismatches are due to sequencing error or biological effect. The analysis also corrects for common alignment errors generated by sequencing read mapping tools, allowing high-throughput analysis of DSB break repair fidelity to be accurately conducted regardless of which suite of NGS analysis software is available.
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5
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Histone H2AX and the small RNA pathway modulate both non-homologous end-joining and homologous recombination in plants. Mutat Res 2015; 783:9-14. [PMID: 26687994 DOI: 10.1016/j.mrfmmm.2015.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/05/2015] [Accepted: 12/01/2015] [Indexed: 11/21/2022]
Abstract
Using a zinc finger nuclease (ZFN) that creates a site-specific DNA double-strand break (DSB) at the endogenous ADH1 locus, we provide genetic evidence that histone H2AX and DSB-induced small RNAs modulate DNA repair by both non-homologous end-joining (NHEJ) and homologous recombination (HR) in the model plant Arabidopsis thaliana.
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Furukawa T, Angelis KJ, Britt AB. Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene. FRONTIERS IN PLANT SCIENCE 2015; 6:357. [PMID: 26074930 PMCID: PMC4444747 DOI: 10.3389/fpls.2015.00357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 05/05/2015] [Indexed: 05/20/2023]
Abstract
The DNA double-strand break (DSB) is a critical type of damage, and can be induced by both endogenous sources (e.g., errors of oxidative metabolism, transposable elements, programmed meiotic breaks, or perturbation of the DNA replication fork) and exogenous sources (e.g., ionizing radiation or radiomimetic chemicals). Although higher plants, like mammals, are thought to preferentially repair DSBs via nonhomologous end joining (NHEJ), much remains unclear about plant DSB repair pathways. Our reverse genetic approach suggests that DNA polymerase λ is involved in DSB repair in Arabidopsis. The Arabidopsis T-DNA insertion mutant (atpolλ-1) displayed sensitivity to both gamma-irradiation and treatment with radiomimetic reagents, but not to other DNA damaging treatments. The atpolλ-1 mutant showed a moderate sensitivity to DSBs, while Arabidopsis Ku70 and DNA ligase 4 mutants (atku70-3 and atlig4-2), both of which play critical roles in NHEJ, exhibited a hypersensitivity to these treatments. The atpolλ-1/atlig4-2 double mutant exhibited a higher sensitivity to DSBs than each single mutant, but the atku70/atpolλ-1 showed similar sensitivity to the atku70-3 mutant. We showed that transcription of the DNA ligase 1, DNA ligase 6, and Wee1 genes was quickly induced by BLM in several NHEJ deficient mutants in contrast to wild-type. Finally, the T-DNA transformation efficiency dropped in NHEJ deficient mutants and the lowest transformation efficiency was scored in the atpolλ-1/atlig4-2 double mutant. These results imply that AtPolλ is involved in both DSB repair and DNA damage response pathway.
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Affiliation(s)
- Tomoyuki Furukawa
- Department of Plant Biology, University of California at DavisDavis, CA, USA
| | - Karel J. Angelis
- DNA Repair Lab, Institute of Experimental Botany of the Academy of Sciences of the Czech RepublicPraha, Czech Republic
| | - Anne B. Britt
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- *Correspondence: Anne B. Britt, Department of Plant Biology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair. Proc Natl Acad Sci U S A 2014; 111:6684-9. [PMID: 24760826 DOI: 10.1073/pnas.1321854111] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The insertion of DNA into a genome can result in the duplication and dispersal of functional sequences through the genome. In addition, a deeper understanding of insertion mechanisms will inform methods of genetic engineering and plant transformation. Exploiting structural variations in numerous rice accessions, we have inferred and analyzed intermediate length (10-1,000 bp) insertions in plants. Insertions in this size class were found to be approximately equal in frequency to deletions, and compound insertion-deletions comprised only 0.1% of all events. Our findings indicate that, as observed in humans, tandem or partially tandem duplications are the dominant form of insertion (48%), although short duplications from ectopic donors account for a sizable fraction of insertions in rice (38%). Many nontandem duplications contain insertions from nearby DNA (within 200 bp) and can contain multiple donor sources--some distant--in single events. Although replication slippage is a plausible explanation for tandem duplications, the end homology required in such a model is most often absent and rarely is >5 bp. However, end homology is commonly longer than expected by chance. Such findings lead us to favor a model of patch-mediated double-strand-break creation followed by nonhomologous end-joining. Additionally, a striking bias toward 31-bp partially tandem duplications suggests that errors in nucleotide excision repair may be resolved via a similar, but distinct, pathway. In summary, the analysis of recent insertions in rice suggests multiple underappreciated causes of structural variation in eukaryotes.
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8
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Bétermier M, Bertrand P, Lopez BS. Is non-homologous end-joining really an inherently error-prone process? PLoS Genet 2014; 10:e1004086. [PMID: 24453986 PMCID: PMC3894167 DOI: 10.1371/journal.pgen.1004086] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA double-strand breaks (DSBs) are harmful lesions leading to genomic instability or diversity. Non-homologous end-joining (NHEJ) is a prominent DSB repair pathway, which has long been considered to be error-prone. However, recent data have pointed to the intrinsic precision of NHEJ. Three reasons can account for the apparent fallibility of NHEJ: 1) the existence of a highly error-prone alternative end-joining process; 2) the adaptability of canonical C-NHEJ (Ku- and Xrcc4/ligase IV-dependent) to imperfect complementary ends; and 3) the requirement to first process chemically incompatible DNA ends that cannot be ligated directly. Thus, C-NHEJ is conservative but adaptable, and the accuracy of the repair is dictated by the structure of the DNA ends rather than by the C-NHEJ machinery. We present data from different organisms that describe the conservative/versatile properties of C-NHEJ. The advantages of the adaptability/versatility of C-NHEJ are discussed for the development of the immune repertoire and the resistance to ionizing radiation, especially at low doses, and for targeted genome manipulation.
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Affiliation(s)
- Mireille Bétermier
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette, France
- CNRS, Centre de Recherches de Gif-sur-Yvette, FRC3115, Gif-sur-Yvette, France
- Université Paris-Sud, Département de Biologie, Orsay, France
| | - Pascale Bertrand
- CEA, DSV, Institut de Radiobiologie Moléculaire et Cellulaire, Laboratoire Réparation et Vieillissement, Fontenay-aux-Roses, France
- UMR 8200 CNRS, Villejuif, France
| | - Bernard S. Lopez
- Université Paris-Sud, Département de Biologie, Orsay, France
- UMR 8200 CNRS, Villejuif, France
- Institut de Cancérologie, Gustave Roussy, Villejuif, France
- * E-mail:
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9
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Huefner ND, Yoshiyama K, Friesner JD, Conklin PA, Britt AB. Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2014; 5:206. [PMID: 24904606 PMCID: PMC4033213 DOI: 10.3389/fpls.2014.00206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
Low linear energy transfer (LET) gamma rays and high LET HZE (high atomic weight, high energy) particles act as powerful mutagens in both plants and animals. DNA damage generated by HZE particles is more densely clustered than that generated by gamma rays. To understand the genetic requirements for resistance to high versus low LET radiation, a series of Arabidopsis thaliana mutants were exposed to either 1GeV Fe nuclei or gamma radiation. A comparison of effects on the germination and subsequent growth of seedlings led us to conclude that the relative biological effectiveness (RBE) of the two types of radiation (HZE versus gamma) are roughly 3:1. Similarly, in wild-type lines, loss of somatic heterozygosity was induced at an RBE of about a 2:1 (HZE versus gamma). Checkpoint and repair defects, as expected, enhanced sensitivity to both agents. The "replication fork" checkpoint, governed by ATR, played a slightly more important role in resistance to HZE-induced mutagenesis than in resistance to gamma induced mutagenesis.
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Affiliation(s)
- Neil D. Huefner
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
| | - Kaoru Yoshiyama
- Department of Plant Biology, University of California at DavisDavis, CA, USA
| | - Joanna D. Friesner
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
| | - Phillip A. Conklin
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
| | - Anne B. Britt
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
- *Correspondence: Anne B. Britt, Department of Plant Biology, University of California at Davis, 1002 Life Sciences, One Shields Avenue, Davis, CA 95616, USA e-mail:
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10
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Munari FM, Guecheva TN, Bonatto D, Henriques JAP. New features on Pso2 protein family in DNA interstrand cross-link repair and in the maintenance of genomic integrity in Saccharomyces cerevisiae. Fungal Genet Biol 2013; 60:122-32. [PMID: 24076078 DOI: 10.1016/j.fgb.2013.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/11/2013] [Accepted: 09/15/2013] [Indexed: 11/27/2022]
Abstract
Pso2 protein, a member of the highly conserved metallo-β-lactamase (MBL) super family of nucleases, plays a central role in interstrand crosslink repair (ICL) in yeast. Pso2 protein is the founder member of a distinct group within the MBL superfamily, called β-CASP family. Three mammalian orthologs of this protein that act on DNA were identified: SNM1A, SNM1B/Apollo and SNM1C/Artemis. Yeast Pso2 and all three mammalian orthologs proteins have been shown to possess nuclease activity. Besides Pso2, ICL repair involves proteins of several DNA repair pathways. Over the last years, new homologs for human proteins have been identified in yeast. In this review, we will focus on studies clarifying the function of Pso2 protein during ICL repair in yeast, emphasizing the contribution of Brazilian research groups in this topic. New sub-pathways in the mechanisms of ICL repair, such as recently identified conserved Fanconi Anemia pathway in yeast as well as a contribution of non-homologous end joining are discussed.
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Affiliation(s)
- Fernanda Mosena Munari
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
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11
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Jia Q, den Dulk-Ras A, Shen H, Hooykaas PJJ, de Pater S. Poly(ADP-ribose)polymerases are involved in microhomology mediated back-up non-homologous end joining in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2013; 82:339-51. [PMID: 23625359 DOI: 10.1007/s11103-013-0065-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/20/2013] [Indexed: 05/25/2023]
Abstract
Besides the KU-dependent classical non-homologous end-joining (C-NHEJ) pathway, an alternative NHEJ pathway first identified in mammalian systems, which is often called the back-up NHEJ (B-NHEJ) pathway, was also found in plants. In mammalian systems PARP was found to be one of the essential components in B-NHEJ. Here we investigated whether PARP1 and PARP2 were also involved in B-NHEJ in Arabidopsis. To this end Arabidopsis parp1, parp2 and parp1parp2 (p1p2) mutants were isolated and functionally characterized. The p1p2 double mutant was crossed with the C-NHEJ ku80 mutant resulting in the parp1parp2ku80 (p1p2k80) triple mutant. As expected, because of their role in single strand break repair (SSBR) and base excision repair (BER), the p1p2 and p1p2k80 mutants were shown to be sensitive to treatment with the DNA damaging agent MMS. End-joining assays in cell-free leaf protein extracts of the different mutants using linear DNA substrates with different ends reflecting a variety of double strand breaks were performed. The results showed that compatible 5'-overhangs were accurately joined in all mutants, that KU80 protected the ends preventing the formation of large deletions and that PARP proteins were involved in microhomology mediated end joining (MMEJ), one of the characteristics of B-NHEJ.
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Affiliation(s)
- Qi Jia
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
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12
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Mani SR, Juliano CE. Untangling the web: the diverse functions of the PIWI/piRNA pathway. Mol Reprod Dev 2013; 80:632-64. [PMID: 23712694 DOI: 10.1002/mrd.22195] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/13/2013] [Indexed: 12/26/2022]
Abstract
Small RNAs impact several cellular processes through gene regulation. Argonaute proteins bind small RNAs to form effector complexes that control transcriptional and post-transcriptional gene expression. PIWI proteins belong to the Argonaute protein family, and bind PIWI-interacting RNAs (piRNAs). They are highly abundant in the germline, but are also expressed in some somatic tissues. The PIWI/piRNA pathway has a role in transposon repression in Drosophila, which occurs both by epigenetic regulation and post-transcriptional degradation of transposon mRNAs. These functions are conserved, but clear differences in the extent and mechanism of transposon repression exist between species. Mutations in piwi genes lead to the upregulation of transposon mRNAs. It is hypothesized that this increased transposon mobilization leads to genomic instability and thus sterility, although no causal link has been established between transposon upregulation and genome instability. An alternative scenario could be that piwi mutations directly affect genomic instability, and thus lead to increased transposon expression. We propose that the PIWI/piRNA pathway controls genome stability in several ways: suppression of transposons, direct regulation of chromatin architecture and regulation of genes that control important biological processes related to genome stability. The PIWI/piRNA pathway also regulates at least some, if not many, protein-coding genes, which further lends support to the idea that piwi genes may have broader functions beyond transposon repression. An intriguing possibility is that the PIWI/piRNA pathway is using transposon sequences to coordinate the expression of large groups of genes to regulate cellular function.
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Affiliation(s)
- Sneha Ramesh Mani
- Yale Stem Cell Center, Yale University, New Haven, Connecticut 06520, USA
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13
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Abstract
Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.
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Affiliation(s)
- Katina Lazarow
- Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, Germany
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14
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dela Paz JS, Stronghill PE, Douglas SJ, Saravia S, Hasenkampf CA, Riggs CD. Chromosome fragile sites in Arabidopsis harbor matrix attachment regions that may be associated with ancestral chromosome rearrangement events. PLoS Genet 2012; 8:e1003136. [PMID: 23284301 PMCID: PMC3527283 DOI: 10.1371/journal.pgen.1003136] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/17/2012] [Indexed: 11/18/2022] Open
Abstract
Mutations in the BREVIPEDICELLUS (BP) gene of Arabidopsis thaliana condition a pleiotropic phenotype featuring defects in internode elongation, the homeotic conversion of internode to node tissue, and downward pointing flowers and pedicels. We have characterized five mutant alleles of BP, generated by EMS, fast neutrons, x-rays, and aberrant T–DNA insertion events. Curiously, all of these mutagens resulted in large deletions that range from 140 kbp to over 900 kbp just south of the centromere of chromosome 4. The breakpoints of these mutants were identified by employing inverse PCR and DNA sequencing. The south breakpoints of all alleles cluster in BAC T12G13, while the north breakpoint locations are scattered. With the exception of a microhomology at the bp-5 breakpoint, there is no homology in the junction regions, suggesting that double-stranded breaks are repaired via non-homologous end joining. Southwestern blotting demonstrated the presence of nuclear matrix binding sites in the south breakpoint cluster (SBC), which is A/T rich and possesses a variety of repeat sequences. In situ hybridization on pachytene chromosome spreads complemented the molecular analyses and revealed heretofore unrecognized structural variation between the Columbia and Landsberg erecta genomes. Data mining was employed to localize other large deletions around the HY4 locus to the SBC region and to show that chromatin modifications in the region shift from a heterochromatic to euchromatic profile. Comparisons between the BP/HY4 regions of A. lyrata and A. thaliana revealed that several chromosome rearrangement events have occurred during the evolution of these two genomes. Collectively, the features of the region are strikingly similar to the features of characterized metazoan chromosome fragile sites, some of which are associated with karyotype evolution. Chromosome evolution involves both small-scale (e.g. single nucleotide) changes, as well as large-scale rearrangements such as inversions, translocations, and fusion events. We investigated mutations of the BREVIPEDICELLUS gene of Arabidopsis, which is a master regulator of inflorescence architecture. These mutations are not due to single nucleotide changes, but rather to large deletions, some spanning nearly one million base pairs. Molecular and biochemical analyses reveal that the chromosome breakpoints cluster in an area that is rich in repetitive elements and harbor multiple binding sites for nuclear matrix proteins. Data mining revealed intriguing correlations between the breakpoint cluster and hotspots of genetic recombination, regions of the chromosome that have undergone several rearrangement events during evolution, and changes in histone protein modifications. We propose that these unstable regions are chromosome fragile sites that assist in marking a boundary between gene-poor, transcriptionally repressed centromeric chromatin and a more relaxed chromatin domain that is gene-rich.
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Affiliation(s)
- Joelle S dela Paz
- Department of Biological Sciences and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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15
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Abstract
Activator/Dissociation (Ac/Ds) transposable elements from maize are widely used as insertional mutagenesis and gene isolation tools in plants and more recently also in medaka and zebrafish. They are particularly valuable for plant species that are transformation-recalcitrant and have long generation cycles or large genomes with low gene densities. Ac/Ds transposition frequencies vary widely, however, and in some species they are too low for large-scale mutagenesis. We discovered a hyperactive Ac transposase derivative, AcTPase(4x), that catalyzes in the yeast Saccharomyces cerevisiae 100-fold more frequent Ds excisions than the wild-type transposase, whereas the reintegration frequency of excised Ds elements is unchanged (57%). Comparable to the wild-type transposase in plants, AcTPase(4x) catalyzes Ds insertion preferentially into coding regions and to genetically linked sites, but the mutant protein apparently has lost the weak bias of the wild-type protein for insertion sites with elevated guanine-cytosine content and nonrandom protein-DNA twist. AcTPase(4x) exhibits hyperactivity also in Arabidopsis thaliana where it effects a more than sixfold increase in Ds excision relative to wild-type AcTPase and thus may be useful to facilitate Ac/Ds-based insertion mutagenesis approaches.
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