1
|
Burmeister T, Bullinger L, le Coutre P. The Recurrent Atypical e8a2 BCR::ABL1 Transcript with Insertion of an Inverted 55 Base Pair ABL1 Intron 1b Sequence: A Detailed Molecular Analysis. Acta Haematol 2023; 146:413-418. [PMID: 37231781 DOI: 10.1159/000531128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Atypical BCR::ABL1 transcripts are found in approximately 2% of cases of chronic myeloid leukemia. It is important to detect them since affected patients also benefit from tyrosine kinase inhibitor therapy. In the rare e8a2 atypical BCR::ABL1 transcript, two out-of-frame exons are fused, thus, interposed nucleotides are usually found at the fusion site to restore the reading frame. In approximately half of previously reported e8a2 BCR::ABL1 cases, an inserted 55 bp sequence homologous to an inverted sequence from ABL1 intron 1b was detected. The generation of this recurrent transcript variant is not obvious. This work describes the molecular analysis of such an e8a2 BCR::ABL1 translocation from a CML patient. The genomic chromosomal breakpoint is identified, and the formation of this transcript is theoretically explained. The clinical course of the patient is reported, and recommendations are provided for the molecular analysis of future e8a2 BCR::ABL1 cases.
Collapse
MESH Headings
- Humans
- Fusion Proteins, bcr-abl/genetics
- Introns
- Base Pairing
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Sequence Inversion
Collapse
Affiliation(s)
- Thomas Burmeister
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow, Medizinische Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany
- Labor Berlin Charité - Vivantes, Berlin, Germany
| | - Lars Bullinger
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow, Medizinische Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany
| | - Philipp le Coutre
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Mitte, Medizinische Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany
| |
Collapse
|
2
|
Park S, Jun M, Park S, Park S. Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes. Int J Mol Sci 2021; 22:ijms221910485. [PMID: 34638831 PMCID: PMC8508905 DOI: 10.3390/ijms221910485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 11/18/2022] Open
Abstract
Caprifoliaceae s.l. plastid genomes (plastomes) show that one inversion and two inverted repeat boundary shifts occurred in the common ancestor of this family, after which the plastomes are generally conserved. This study reports plastome sequences of five additional species, Fedia cornucopiae, Valeriana fauriei, and Valerianella locusta from the subfamily Valerianoideae, as well as Dipsacus japonicus and Scabiosa comosa from the subfamily Dipsacoideae. Combined with the published plastomes, these plastomes provide new insights into the structural evolution of plastomes within the family. Moreover, the three plastomes from the subfamily Valerianoideae exhibited accelerated nucleotide substitution rates, particularly at synonymous sites, across the family. The patterns of accD sequence divergence in the family are dynamic with structural changes, including interruption of the conserved domain and increases in nonsynonymous substitution rates. In particular, the Valeriana accD gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the Valeriana accD gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the clpP gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded rps15, and a potential functional gene transfer to the nucleus was confirmed.
Collapse
Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Minji Jun
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea; (M.J.); (S.P.)
| | - Sunmi Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea; (M.J.); (S.P.)
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea; (M.J.); (S.P.)
- Correspondence: ; Tel.: +82-53-810-2377
| |
Collapse
|
3
|
Cope H, Barseghyan H, Bhattacharya S, Fu Y, Hoppman N, Marcou C, Walley N, Rehder C, Deak K, Alkelai A, Vilain E, Shashi V. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med 2021; 9:e1665. [PMID: 33955715 PMCID: PMC8372083 DOI: 10.1002/mgg3.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin. METHODS OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing. RESULTS OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2. CONCLUSION OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.
Collapse
Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Hayk Barseghyan
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
- Bionano Genomics IncSan DiegoCAUSA
| | | | - Yulong Fu
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
| | - Nicole Hoppman
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cherisse Marcou
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Nicole Walley
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Catherine Rehder
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Kristen Deak
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Anna Alkelai
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNYUSA
| | - Eric Vilain
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| |
Collapse
|
4
|
Liu J, Jiang M, Chen H, Liu Y, Liu C, Wu W. Comparative genome analysis revealed gene inversions, boundary expansions and contractions, and gene loss in the Stemona sessilifolia (Miq.) Miq. chloroplast genome. PLoS One 2021; 16:e0247736. [PMID: 34143785 PMCID: PMC8213164 DOI: 10.1371/journal.pone.0247736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/19/2021] [Indexed: 11/19/2022] Open
Abstract
Stemona sessilifolia (Miq.) Miq., commonly known as Baibu, is one of the most popular herbal medicines in Asia. In the Chinese Pharmacopoeia, Baibu has multiple authentic sources and there are many similar herbs sold as Baibu in herbal medicine markets. The existence of counterfeits of Baibu brings challenges to its identification. To assist in its accurate identification, we sequenced and analyzed the complete chloroplast genome of S. sessilifolia using next-generation sequencing technology. The genome was found to be 154,037 bp in length, possessing a typical quadripartite structure consisting of a pair of inverted repeats (IRs: 27,090 bp) separated by a large single copy (LSC: 81,949 bp) and a small single copy (SSC: 17,908 bp). A total of 112 unique genes were identified, including 80 protein-coding, 28 transfer RNA and four ribosomal RNA genes. In addition, 45 tandem, 27 forward, 23 palindromic and 104 simple sequence repeats were detected in the genome by repeated analysis. Compared with its counterfeits (Asparagus officinalis and Carludovica palmata) we found that IR expansion and SSC contraction events of S. sessilifolia resulted in two copies of the rpl22 gene in the IR regions and a partial duplication of the ndhF gene in the SSC region. An approximately 3-kb-long inversion was also identified in the LSC region, leading to the petA and cemA genes being presented in the complementary strand of the chloroplast DNA molecule. Comparative analysis revealed some highly variable regions, including trnF-GAA_ndhJ, atpB_rbcL, rps15_ycf1, trnG-UCC_trnR-UCU, ndhF_rpl32, accD_psaI, rps2_rpoC2, trnS-GCU_trnG-UCC, trnT-UGU_trnL-UAA and rps16_trnQ-UUG. Finally, gene loss events were investigated in the context of phylogenetic relationships. In summary, the complete plastome of S. sessilifolia will provide valuable information for the distinction between Baibu and its counterfeits and assist in elucidating the evolution of S. sessilifolia.
Collapse
Affiliation(s)
- Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Yu Liu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Wuwei Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| |
Collapse
|
5
|
Badet T, Fouché S, Hartmann FE, Zala M, Croll D. Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen. Nat Commun 2021; 12:3551. [PMID: 34112792 PMCID: PMC8192914 DOI: 10.1038/s41467-021-23862-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere genome assemblies of a fungal pathogen of wheat to establish a nucleotide-level map of structural variation. We show that the recent emergence of pesticide resistance has been disproportionally driven by rearrangements. We use machine learning to train a model on structural variation events based on 30 chromosomal sequence features. We show that base composition and gene density are the major determinants of structural variation. Retrotransposons explain most inversion, indel and duplication events. We apply our model to Arabidopsis thaliana and show that our approach extends to more complex genomes. Finally, we analyze complete genomes of haploid offspring in a four-generation pedigree. Meiotic crossover locations are enriched for new rearrangements consistent with crossovers being mutational hotspots. The model trained on species-wide structural variation accurately predicts the position of >74% of newly generated variants along the pedigree. The predictive power highlights causality between specific sequence features and the induction of chromosomal rearrangements. Our work demonstrates that training sequence-derived models can accurately identify regions of intrinsic DNA instability in eukaryotic genomes.
Collapse
Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Simone Fouché
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Marcello Zala
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
| |
Collapse
|
6
|
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 2021; 372:eabf7117. [PMID: 33632895 PMCID: PMC8026704 DOI: 10.1126/science.abf7117] [Citation(s) in RCA: 270] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.
Collapse
Affiliation(s)
- Peter Ebert
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Bernardo Rodriguez-Martin
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Jana Ebler
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Rebecca Serra Mari
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA 92121, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Jiadong Lin
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yu Chen
- Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jingwen Ren
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin Santamarina
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Wolfram Höps
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Hufsah Ashraf
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Nelson T Chuang
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | | | | | | | | | | | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Junjie Chen
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Chong Li
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron M Wenger
- Pacific Biosciences of California, Menlo Park, CA 94025, USA
| | - Maryam Ghareghani
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123 Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123 Saarbrücken, Germany
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Allison A Regier
- Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Haley J Abel
- Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Ira M Hall
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Zepeng Mu
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xinghua Shi
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | | | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Zechen Chong
- Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | | | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Scott E Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
- Department of Graduate Studies-Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, South Korea
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tobias Marschall
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
7
|
Loveland JL, Giraldo-Deck LM, Lank DB, Goymann W, Gahr M, Küpper C. Functional differences in the hypothalamic-pituitary-gonadal axis are associated with alternative reproductive tactics based on an inversion polymorphism. Horm Behav 2021; 127:104877. [PMID: 33186586 DOI: 10.1016/j.yhbeh.2020.104877] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023]
Abstract
The evolution of social behavior depends on genetic changes, yet, how genomic variation manifests itself in behavioral diversity is still largely unresolved. Chromosomal inversions can play a pivotal role in producing distinct behavioral phenotypes, in particular, when inversion genes are functionally associated with hormone synthesis and signaling. Male ruffs exhibit alternative reproductive tactics (ARTs) with an autosomal inversion determining two alternative morphs with clear behavioral and hormonal differences from the ancestral morph. We investigated hormonal and transcriptomic differences in the pituitary and gonads. Using a GnRH challenge, we found that the ability to synthesize testosterone in inversion carriers is severely constrained, whereas the synthesis of androstenedione, a testosterone precursor, is not. Inversion morphs were able to produce a transient increase in androstenedione following the GnRH injection, supporting the view that pituitary sensitivity to GnRH is comparable to that of the ancestral morph. We then performed gene expression analyses in a second set of untreated birds and found no evidence of alterations to pituitary sensitivity, gonadotropin production or gonad sensitivity to luteinizing hormone or follicle-stimulating hormone across morphs. Inversion morphs also showed reduced progesterone receptor expression in the pituitary. Strikingly, in the gonads, inversion morphs over-expressed STAR, a gene that is located outside of the inversion and responsible for providing the cholesterol substrate required for the synthesis of sex hormones. In conclusion, our results suggest that the gonads determine morph-specific differences in hormonal regulation.
Collapse
MESH Headings
- Androstenedione/metabolism
- Animals
- Charadriiformes/genetics
- Charadriiformes/physiology
- Follicle Stimulating Hormone, beta Subunit/genetics
- Follicle Stimulating Hormone, beta Subunit/metabolism
- Gene Expression/drug effects
- Gonadal Steroid Hormones/biosynthesis
- Gonadotropin-Releasing Hormone/pharmacology
- Gonads/drug effects
- Gonads/metabolism
- Gonads/physiology
- Hypothalamo-Hypophyseal System/drug effects
- Hypothalamo-Hypophyseal System/metabolism
- Hypothalamo-Hypophyseal System/physiology
- Male
- Pituitary Gland/drug effects
- Pituitary Gland/metabolism
- Polymorphism, Genetic
- Receptors, FSH/genetics
- Receptors, FSH/metabolism
- Receptors, LH/genetics
- Receptors, LH/metabolism
- Receptors, LHRH/genetics
- Receptors, LHRH/metabolism
- Reproduction/drug effects
- Reproduction/genetics
- Sequence Inversion
- Sexual Behavior, Animal/drug effects
- Sexual Behavior, Animal/physiology
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Testosterone/metabolism
Collapse
Affiliation(s)
- J L Loveland
- Behavioural Genetics and Evolutionary Ecology Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
| | - L M Giraldo-Deck
- Behavioural Genetics and Evolutionary Ecology Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - D B Lank
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - W Goymann
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - M Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - C Küpper
- Behavioural Genetics and Evolutionary Ecology Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| |
Collapse
|
8
|
Schwartz C, Lenderts B, Feigenbutz L, Barone P, Llaca V, Fengler K, Svitashev S. CRISPR-Cas9-mediated 75.5-Mb inversion in maize. Nat Plants 2020; 6:1427-1431. [PMID: 33299151 DOI: 10.1038/s41477-020-00817-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/04/2020] [Indexed: 05/11/2023]
Abstract
CRISPR-Cas is a powerful double-strand-break technology with wide-ranging applications from gene discovery to commercial product development. Thus far, this tool has been almost exclusively used for gene knockouts and deletions, with a few examples of gene edits and targeted gene insertions. Here, we demonstrate the application of CRISPR-Cas9 technology to mediate targeted 75.5-Mb pericentric inversion in chromosome 2 in one of the elite maize inbred lines from Corteva Agriscience. This inversion unlocks a large chromosomal region containing substantial genetic variance for recombination, thus providing opportunities for the development of new maize varieties with improved phenotypes.
Collapse
|
9
|
Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang XQ, Angessa TT, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston LB, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers KJ, Langridge P, Waugh R, Pozniak CJ, Scholz U, Mayer KFX, Spannagl M, Li C, Mascher M, Stein N. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 2020; 588:284-289. [PMID: 33239781 PMCID: PMC7759462 DOI: 10.1038/s41586-020-2947-8] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
Collapse
Affiliation(s)
- Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Venkata Suresh Bonthala
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nadia Kamal
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Lang
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Tefera T Angessa
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Camilla Hill
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Penghao Wang
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Lori B Boston
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | | | - Jerry Jenkins
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Dongdong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Chunchao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jane Grimwood
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kenneth J Chalmers
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chengdao Li
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia.
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| |
Collapse
|
10
|
Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat Biotechnol 2020; 38:343-354. [PMID: 31873213 PMCID: PMC7612647 DOI: 10.1038/s41587-019-0366-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
Structural variation (SV), involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic SVs in single cells has been challenging, with copy-number-neutral and complex variants typically escaping detection. Here we describe single-cell tri-channel processing (scTRIP), a computational framework that integrates read depth, template strand and haplotype phase to comprehensively discover SVs in individual cells. We surveyed SV landscapes of 565 single cells, including transformed epithelial cells and patient-derived leukemic samples, to discover abundant SV classes, including inversions, translocations and complex DNA rearrangements. Analysis of the leukemic samples revealed four times more somatic SVs than cytogenetic karyotyping, submicroscopic copy-number alterations, oncogenic copy-neutral rearrangements and a subclonal chromothripsis event. Advancing current methods, single-cell tri-channel processing can directly measure SV mutational processes in individual cells, such as breakage-fusion-bridge cycles, facilitating studies of clonal evolution, genetic mosaicism and SV formation mechanisms, which could improve disease classification for precision medicine.
Collapse
Affiliation(s)
- Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Sascha Meiers
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maryam Ghareghani
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Hyobin Jeong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Tobias Rausch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Joachim B Kunz
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Silvia Jenni
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Davide Bolognini
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Gabriel M C Longo
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Benjamin Raeder
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Venla Kinanen
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jürgen Zimmermann
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Balca R Mardin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- BioMed X Innovation Center, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
- Max Planck Institute for Informatics, Saarbrücken, Germany.
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.
| |
Collapse
|
11
|
Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CYL, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT. Construction and comparison of three reference-quality genome assemblies for soybean. Plant J 2019; 100:1066-1082. [PMID: 31433882 DOI: 10.1111/tpj.14500] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 05/15/2023]
Abstract
We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
Collapse
Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, 65101, MO, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Longhui Ren
- Interdepartmental Genetics Program, Iowa State University, Ames, 50011, IA, USA
| | - Jerry Jenkins
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Claire Y-L Chung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ting-Fung Chan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Christopher G Daum
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Christopher Plott
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | | | | | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, Ames, 50011, IA, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Haifei Hu
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Yuxuan Yuan
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Qijian Song
- Soybean Genomics and Improvement Lab, US Department of Agriculture - Agricultural Research Service, Beltsville, 20705, MD, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, MN, USA
| | - David M Goodstein
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Gary Stacey
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
| | - Jeremy Schmutz
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Jane Grimwood
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| |
Collapse
|
12
|
BeltCappellino A, Majerciak V, Lobanov A, Lack J, Cam M, Zheng ZM. CRISPR/Cas9-Mediated Knockout and In Situ Inversion of the ORF57 Gene from All Copies of the Kaposi's Sarcoma-Associated Herpesvirus Genome in BCBL-1 Cells. J Virol 2019; 93:e00628-19. [PMID: 31413125 PMCID: PMC6803266 DOI: 10.1128/jvi.00628-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV)-transformed primary effusion lymphoma cell lines contain ∼70 to 150 copies of episomal KSHV genomes per cell and have been widely used for studying the mechanisms of KSHV latency and lytic reactivation. Here, we report the first complete knockout (KO) of viral ORF57 gene from all ∼100 copies of KSHV genome per cell in BCBL-1 cells. This was achieved by a modified CRISPR/Cas9 technology to simultaneously express two guide RNAs (gRNAs) and Cas9 from a single expression vector in transfected cells in combination with multiple rounds of cell selection and single-cell cloning. CRISPR/Cas9-mediated genome engineering induces the targeted gene deletion and inversion in situ We found the inverted ORF57 gene in the targeted site in the KSHV genome in one of two characterized single cell clones. Knockout of ORF57 from the KSHV genome led to viral genome instability, thereby reducing viral genome copies and expression of viral lytic genes in BCBL-1-derived single-cell clones. The modified CRISPR/Cas9 technology was very efficient in knocking out the ORF57 gene in iSLK/Bac16 and HEK293/Bac36 cells, where each cell contains only a few copies of the KSHV genome. The ORF57 KO genome was stable in iSLK/Bac16 cells, and, upon lytic induction, was partially rescued by ectopic ORF57 to express viral lytic gene ORF59 and produce infectious virions. Together, the technology developed in this study has paved the way to express two separate gRNAs and the Cas9 enzyme simultaneously in the same cell and could be efficiently applied to any genetic alterations from various genomes, including those in extreme high copy numbers.IMPORTANCE This study provides the first evidence that CRISPR/Cas9 technology can be applied to knock out the ORF57 gene from all ∼100 copies of the KSHV genome in primary effusion lymphoma (PEL) cells by coexpressing two guide RNAs (gRNAs) and Cas9 from a single expression vector in combination with single-cell cloning. The gene knockout efficiency in this system was evaluated rapidly using a direct cell PCR screening. The current CRISPR/Cas9 technology also mediated ORF57 inversion in situ in the targeted site of the KSHV genome. The successful rescue of viral lytic gene expression and infectious virion production from the ORF57 knockout (KO) genome further reiterates the essential role of ORF57 in KSHV infection and multiplication. This modified technology should be useful for knocking out any viral genes from a genome to dissect functions of individual viral genes in the context of the virus genome and to understand their contributions to viral genetics and the virus life cycle.
Collapse
Affiliation(s)
- Andrew BeltCappellino
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Justin Lack
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| |
Collapse
|
13
|
Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Pérez-Jurado L, González JR. scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS Genet 2019; 15:e1008203. [PMID: 31269027 PMCID: PMC6608898 DOI: 10.1371/journal.pgen.1008203] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/17/2019] [Indexed: 02/02/2023] Open
Abstract
Polymorphic inversions contribute to adaptation and phenotypic variation. However, large multi-centric association studies of inversions remain challenging. We present scoreInvHap, a method to genotype inversions from SNP data for genome-wide association studies (GWASs), overcoming important limitations of current methods and outperforming them in accuracy and applicability. scoreInvHap calls individual inversion-genotypes from a similarity score to the SNPs of experimentally validated references. It can be used on different sources of SNP data, including those with low SNP coverage such as exome sequencing, and is easily adaptable to genotype new inversions, either in humans or in other species. We present 20 human inversions that can be reliably and easily genotyped with scoreInvHap to discover their role in complex human traits, and illustrate a first genome-wide association study of experimentally-validated human inversions. scoreInvHap is implemented in R and it is freely available from Bioconductor. Chromosomal inversions are structural variants consisting on an orientation change of a chromosome segment. Inversions have been linked to some phenotypic differences between individuals and to genetic divergence. However, their overall contribution to complex diseases is largely underdetermined as there are no high-throughput methods to call inversion-genotypes in large cohort studies. Here, we propose a new method, scoreInvHap, to call individual inversion genotypes from their haplotype similarity. We show that scoreInvHap has a high performance when analyzing heterogeneous sources of SNP data. Our current implementation contains 20 human inversions that can be readily genotyped in existing GWAS datasets. We exemplify the utility of scoreInvHap by running the first-genome wide association of experimentally validated inversions and a multi-centric inversion association study. All in all, scoreInvHap can substantially contribute to increase our knowledge of the role of chromosomal inversions in complex diseases by re-analyzing data from existing genetic association studies.
Collapse
Affiliation(s)
- Carlos Ruiz-Arenas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alejandro Cáceres
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Marcos López-Sánchez
- Genetics Unit, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Ignacio Tolosana
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Luis Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- SA Clinical Genetics, Women's and Children's Hospital & University of Adelaide, Adelaide, South Australia Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia Australia
| | - Juan R. González
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- * E-mail:
| |
Collapse
|
14
|
Abstract
Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
Collapse
Affiliation(s)
| | - Amanda L Grusz
- Department of Biology, University of Minnesota Duluth
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
| | - Paul G Wolf
- Department of Biology, Utah State University
| | - Jeffrey P Mower
- Department of Agronomy, Center for Plant Science Innovation, University of Nebraska
| | | | | | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
| |
Collapse
|
15
|
Shou J, Li J, Liu Y, Wu Q. Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion. Mol Cell 2018; 71:498-509.e4. [PMID: 30033371 DOI: 10.1016/j.molcel.2018.06.021] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/22/2018] [Accepted: 06/13/2018] [Indexed: 01/21/2023]
Abstract
Chromosomal rearrangements including large DNA-fragment inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate genome structural variations and developmental gene regulation, but little is known about the underlying mechanisms. Here, we report that disrupting CtIP or FANCD2, which have roles in alternative non-homologous end joining, enhances precise DNA-fragment deletion. By analyzing the inserted nucleotides at the junctions of DNA-fragment editing of deletions, inversions, and duplications and characterizing the cleaved products, we find that Cas9 endonucleolytically cleaves the noncomplementary strand with a flexible scissile profile upstream of the -3 position of the PAM site in vivo and in vitro, generating double-strand break ends with 5' overhangs of 1-3 nucleotides. Moreover, we find that engineered Cas9 nucleases have distinct cleavage profiles. Finally, Cas9-mediated nucleotide insertions are nonrandom and are equal to the combined sequences upstream of both PAM sites with predicted frequencies. Thus, precise and predictable DNA-fragment editing could be achieved by perturbing DNA repair genes and using appropriate PAM configurations.
Collapse
Affiliation(s)
- Jia Shou
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Jinhuan Li
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Yingbin Liu
- Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Qiang Wu
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China.
| |
Collapse
|
16
|
Huang YC, Dang VD, Chang NC, Wang J. Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene. Proc Biol Sci 2018; 285:20180221. [PMID: 29769360 PMCID: PMC5966598 DOI: 10.1098/rspb.2018.0221] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta, two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a greater than 9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele. So, how did the inversion increase in frequency? To address these questions, we cloned one extreme breakpoint in the fire ant supergene. In doing so, we found a second large (greater than 800 Kb) rearrangement. Furthermore, we determined the temporal order of the two big inversions based on the translocation pattern of a third small fragment. Because the S. invicta supergene lacks evolutionary strata, our finding of multiple inversions may support an introgression model of the supergene. Finally, we showed that one of the inversions swapped the promoter of a breakpoint-adjacent gene, which might have conferred a selective advantage relative to the non-inverted allele. Our findings provide a rare example of gene alterations arising directly from an inversion event.
Collapse
Affiliation(s)
- Yu-Ching Huang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Viet Dai Dang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
- Biodiversity Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, Republic of China
- Department of Zoology, Southern Institute of Ecology, Hochiminh, Vietnam
| | - Ni-Chen Chang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - John Wang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
| |
Collapse
|
17
|
Chen R, Lau YL, Yang W. Detecting Small Inversions Using SRinversion. Methods Mol Biol 2018; 1833:107-114. [PMID: 30039367 DOI: 10.1007/978-1-4939-8666-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rapid development of next generation sequencing (NGS) technology has substantially improved our ability to detect genomic variations. However, unlike other variations, such as point mutations, insertions, and deletions, which can be identified in high sensitivities and specificities based on NGS reads, most of inversions, especially those shorter than 1 kb, remain difficult to detect. Here we introduce a new framework, SRinversion, which was developed specifically for detection of inversions shorter than 1 kb by splitting and realigning poorly mapped or unmapped reads of the NGS data.
Collapse
Affiliation(s)
- Ruoyan Chen
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| |
Collapse
|
18
|
Hudecova I, Jiang P, Davies J, Lo YMD, Kadir RA, Chiu RWK. Noninvasive detection of F8 int22h-related inversions and sequence variants in maternal plasma of hemophilia carriers. Blood 2017; 130:340-347. [PMID: 28490568 PMCID: PMC5532756 DOI: 10.1182/blood-2016-12-755017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/19/2017] [Indexed: 12/15/2022] Open
Abstract
Direct detection of F8 and F9 sequence variants in maternal plasma of hemophilia carriers has been demonstrated by microfluidics digital PCR. Noninvasive prenatal assessment of the most clinically relevant group of sequence variants among patients with hemophilia, namely, those involving int22h-related inversions disrupting the F8 gene, poses additional challenges because of its molecular complexity. We investigated the use of droplet digital PCR (ddPCR) and targeted massively parallel sequencing (MPS) for maternal plasma DNA analysis to noninvasively determine fetal mutational status in pregnancies at risk for hemophilia. We designed family-specific ddPCR assays to detect causative sequence variants scattered across the F8 and F9 genes. A haplotype-based approach coupled with targeted MPS was applied to deduce fetal genotype by capturing a 7.6-Mb region spanning the F8 gene in carriers with int22h-related inversions. The ddPCR analysis correctly determined fetal hemophilia status in 15 at-risk pregnancies in samples obtained from 8 to 42 weeks of gestation. There were 3 unclassified samples, but no misclassification. Detailed fetal haplotype maps of the F8 gene region involving int22h-related inversions obtained through targeted MPS enabled correct diagnoses of fetal mutational status in 3 hemophilia families. Our data suggest it is feasible to apply targeted MPS to interrogate maternally inherited F8 int22h-related inversions, whereas ddPCR represents an affordable approach for the identification of F8 and F9 sequence variants in maternal plasma. These advancements may bring benefits for the pregnancy management for carriers of hemophilia sequence variants; in particular, the common F8 int22h-related inversions, associated with the most severe clinical phenotype.
Collapse
Affiliation(s)
- Irena Hudecova
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; and
| | - Peiyong Jiang
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; and
| | - Joanna Davies
- Department of Obstetrics and Gynaecology and
- Katharine Dormandy Haemophilia and Thrombosis Center, Royal Free Hospital, London, United Kingdom
| | - Y M Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; and
| | - Rezan A Kadir
- Department of Obstetrics and Gynaecology and
- Katharine Dormandy Haemophilia and Thrombosis Center, Royal Free Hospital, London, United Kingdom
| | - Rossa W K Chiu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; and
| |
Collapse
|
19
|
Kefala A, Kotsifaki D, Providaki M, Amprazi M, Kokkinidis M. Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle. Acta Crystallogr F Struct Biol Commun 2017; 73:51-53. [PMID: 28045394 PMCID: PMC5287371 DOI: 10.1107/s2053230x16020173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/19/2016] [Indexed: 11/10/2022] Open
Abstract
Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four-α-helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and preliminary crystallographic characterization of revRM6 are reported. The protein was overexpressed in Escherichia coli, purified to homogeneity and crystallized. The crystals belonged to space group P41212, with unit-cell parameters a = b = 44.98, c = 159.74 Å, and diffracted to a resolution of 3.45 Å.
Collapse
Affiliation(s)
- Aikaterini Kefala
- Department of Biology, University of Crete, Voutes University Campus, PO Box 2208, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| | - Maria Amprazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, Voutes University Campus, PO Box 2208, 70013 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| |
Collapse
|
20
|
Kleinboelting N, Huep G, Appelhagen I, Viehoever P, Li Y, Weisshaar B. The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism. Mol Plant 2015; 8:1651-64. [PMID: 26343971 DOI: 10.1016/j.molp.2015.08.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/28/2015] [Accepted: 08/13/2015] [Indexed: 05/06/2023]
Abstract
Transformation by Agrobacterium tumefaciens, an important tool in modern plant research, involves the integration of T-DNA initially present on a plasmid in agrobacteria into the genome of plant cells. The process of attachment of the agrobacteria to plant cells and the transport of T-DNA into the cell and further to the nucleus has been well described. However, the exact mechanism of integration into the host's DNA is still unclear, although several models have been proposed. During confirmation of T-DNA insertion alleles from the GABI-Kat collection of Arabidopsis thaliana mutants, we have generated about 34,000 sequences from the junctions between inserted T-DNA and adjacent genome regions. Here, we describe the evaluation of this dataset with regard to existing models for T-DNA integration. The results suggest that integration into the plant genome is mainly mediated by the endogenous plant DNA repair machinery. The observed integration events showed characteristics highly similar to those of repair sites of double-strand breaks with respect to microhomology and deletion sizes. In addition, we describe unexpected integration events, such as large deletions and inversions at the integration site that are relevant for correct interpretation of results from T-DNA insertion mutants in reverse genetics experiments.
Collapse
Affiliation(s)
- Nils Kleinboelting
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Gunnar Huep
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Ingo Appelhagen
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Prisca Viehoever
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Yong Li
- Department of Medicine IV, University Hospital Freiburg, Berliner Allee 29, 79110 Freiburg, Germany
| | - Bernd Weisshaar
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
| |
Collapse
|
21
|
Laffitte MCN, Genois MM, Mukherjee A, Légaré D, Masson JY, Ouellette M. Formation of linear amplicons with inverted duplications in Leishmania requires the MRE11 nuclease. PLoS Genet 2014; 10:e1004805. [PMID: 25474106 PMCID: PMC4256157 DOI: 10.1371/journal.pgen.1004805] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/06/2014] [Indexed: 11/22/2022] Open
Abstract
Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment. Extrachromosomal DNA amplification is frequent in the human protozoan parasite Leishmania when challenged with drug or other stressful conditions. DNA amplicons, either circular or linear, are formed by recombination between direct or inverted repeats spread throughout the genome of the parasite. The recombinase RAD51 is involved in the formation of circular amplicons, but the mechanism by which linear amplicons are formed is still unknown in this parasite. Studies in other organisms have provided some evidence that a DNA break is required for linear amplifications, and that the DNA repair protein MRE11 can be involved in this process. In this work, we present our biochemical, cellular and molecular characterization of the Leishmania infantum MRE11 orthologue and provide evidence that this nuclease is involved in the formation of linear amplicons in Leishmania. Our results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment.
Collapse
Affiliation(s)
| | - Marie-Michelle Genois
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavillon, Oncology Axis, Quebec City, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Québec, Canada
| | - Angana Mukherjee
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
| | - Danielle Légaré
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavillon, Oncology Axis, Quebec City, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
- * E-mail:
| |
Collapse
|
22
|
Tobler R, Franssen SU, Kofler R, Orozco-terWengel P, Nolte V, Hermisson J, Schlötterer C. Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol Biol Evol 2014; 31:364-75. [PMID: 24150039 PMCID: PMC3907058 DOI: 10.1093/molbev/mst205] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Experimental evolution in combination with whole-genome sequencing (evolve and resequence [E&R]) is a promising approach to define the genotype-phenotype map and to understand adaptation in evolving populations. Many previous studies have identified a large number of putative selected sites (i.e., candidate loci), but it remains unclear to what extent these loci are genuine targets of selection or experimental noise. To address this question, we exposed the same founder population to two different selection regimes-a hot environment and a cold environment-and quantified the genomic response in each. We detected large numbers of putative selected loci in both environments, albeit with little overlap between the two sets of candidates, indicating that most resulted from habitat-specific selection. By quantifying changes across multiple independent biological replicates, we demonstrate that most of the candidate SNPs were false positives that were linked to selected sites over distances much larger than the typical linkage disequilibrium range of Drosophila melanogaster. We show that many of these mid- to long-range associations were attributable to large segregating inversions and confirm by computer simulations that such patterns could be readily replicated when strong selection acts on rare haplotypes. In light of our findings, we outline recommendations to improve the performance of future Drosophila E&R studies which include using species with negligible inversion loads, such as D. mauritiana and D. simulans, instead of D. melanogaster.
Collapse
Affiliation(s)
- Ray Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Joachim Hermisson
- Mathematics and Biosciences Group, Department of Mathematics, University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Vienna, Austria
| | | |
Collapse
|
23
|
Martínez-Fundichely A, Casillas S, Egea R, Ràmia M, Barbadilla A, Pantano L, Puig M, Cáceres M. InvFEST, a database integrating information of polymorphic inversions in the human genome. Nucleic Acids Res 2014; 42:D1027-32. [PMID: 24253300 PMCID: PMC3965118 DOI: 10.1093/nar/gkt1122] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/18/2013] [Accepted: 10/24/2013] [Indexed: 12/27/2022] Open
Abstract
The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant human polymorphic inversions. Due to the complexity of this type of changes and the underlying high false-positive discovery rate, it is necessary to integrate all the available data to get a reliable estimate of the real number of inversions. InvFEST automatically merges predictions into different inversions, refines the breakpoint locations, and finds associations with genes and segmental duplications. In addition, it includes data on experimental validation, population frequency, functional effects and evolutionary history. All this information is readily accessible through a complete and user-friendly web report for each inversion. In its current version, InvFEST combines information from 34 different studies and contains 1092 candidate inversions, which are categorized based on internal scores and manual curation. Therefore, InvFEST aims to represent the most reliable set of human inversions and become a central repository to share information, guide future studies and contribute to the analysis of the functional and evolutionary impact of inversions on the human genome.
Collapse
Affiliation(s)
- Alexander Martínez-Fundichely
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Sònia Casillas
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Raquel Egea
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miquel Ràmia
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio Barbadilla
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lorena Pantano
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
24
|
Logacheva MD, Schelkunov MI, Nuraliev MS, Samigullin TH, Penin AA. The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements. Genome Biol Evol 2014; 6:238-46. [PMID: 24398375 PMCID: PMC3914687 DOI: 10.1093/gbe/evu001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 12/31/2022] Open
Abstract
Plastid genomes of nonphotosynthetic plants represent a perfect model for studying evolution under relaxed selection pressure. However, the information on their sequences is still limited. We sequenced and assembled plastid genome of Petrosavia stellaris, a rare mycoheterotrophic monocot plant. After orchids, Petrosavia represents only the second family of nonphotosynthetic monocots to have its plastid genome examined. Several unusual features were found: retention of the ATP synthase genes and rbcL gene; extensive gene order rearrangement despite a relative lack of repeat sequences; an unusually short inverted repeat region that excludes most of the rDNA operon; and a lack of evidence for accelerated sequence evolution. Plastome of photosynthetic relative of P. stellaris, Japonolirion osense, has standard gene order and does not have the predisposition to inversions. Thus, the rearrangements in the P. stellaris plastome are the most likely associated with transition to heterotrophic way of life.
Collapse
Affiliation(s)
- Maria D. Logacheva
- M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail I. Schelkunov
- M.V. Lomonosov Moscow State University, Moscow, Russia
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maxim S. Nuraliev
- M.V. Lomonosov Moscow State University, Moscow, Russia
- Joint Russian–Vietnamese Tropical Scientific and Technological Center, Cau Giay, Hanoi, Vietnam
| | | | - Aleksey A. Penin
- M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
25
|
Citterio CE, Rossetti LC, Souchon PF, Morales C, Thouvard-Viprey M, Salmon-Musial AS, Mauran PLA, Doco-Fenzy M, González-Sarmiento R, Rivolta CM, De Brasi CD, Targovnik HM. Novel mutational mechanism in the thyroglobulin gene: imperfect DNA inversion as a cause for hereditary hypothyroidism. Mol Cell Endocrinol 2013; 381:220-9. [PMID: 23933148 DOI: 10.1016/j.mce.2013.07.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 07/21/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
The objective of this study was to perform genetic analysis in three brothers of Turkish origin born from consanguineus parents and affected by congenital hypothyroidism, goiter and low levels of serum TG. The combination of sequencing of DNA, PCR mapping, quantitative real-time PCR, inverse-PCR (I-PCR), multiplex PCR and bioinformatics analysis were used in order to detect TG mutations. We demonstrated that the three affected siblings are homozygous for a DNA inversion of 16,962bp in the TG gene associated with two deleted regions at both sides of the inversion limits. The inversion region includes the first 9bp of exon 48, 1015bp of intron 47, 191bp of exon 47, 1523bp of intron 46, 135bp of exon 46 and the last 14,089bp of intron 45. The proximal deletion corresponds to 27bp of TG intron 45, while the distal deletion spans the last 230bp of TG exon 48 and the first 588bp of intergenic region downstream TG end. The parents were heterozygous carriers of the complex rearrangement. In conclusion, a novel large imperfect DNA inversion within the TG gene was identified by the strategy of I-PCR. This aberration was not detectable by normal sequencing of the exons and exon/intron boundaries. Remarkably, the finding represents the first description of a TG deficiency disease caused by a DNA inversion.
Collapse
Affiliation(s)
- Cintia E Citterio
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética y Biología Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Sanna V, Ceglia C, Tarsitano M, Lombardo B, Coppola A, Zarrilli F, Castaldo G, Di Minno G. Aberrant F8 gene intron 1 inversion with concomitant duplication and deletion in a severe hemophilia A patient from Southern Italy. J Thromb Haemost 2013; 11:195-7. [PMID: 23140572 DOI: 10.1111/jth.12061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V Sanna
- CEINGE-Biotecnologie Avanzate, Naples Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Enyeart PJ, Chirieleison SM, Dao MN, Perutka J, Quandt EM, Yao J, Whitt JT, Keatinge-Clay AT, Lambowitz AM, Ellington AD. Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol Syst Biol 2013; 9:685. [PMID: 24002656 PMCID: PMC3792343 DOI: 10.1038/msb.2013.41] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/23/2013] [Indexed: 12/21/2022] Open
Abstract
Efficient bacterial genetic engineering approaches with broad-host applicability are rare. We combine two systems, mobile group II introns ('targetrons') and Cre/lox, which function efficiently in many different organisms, into a versatile platform we call GETR (Genome Editing via Targetrons and Recombinases). The introns deliver lox sites to specific genomic loci, enabling genomic manipulations. Efficiency is enhanced by adding flexibility to the RNA hairpins formed by the lox sites. We use the system for insertions, deletions, inversions, and one-step cut-and-paste operations. We demonstrate insertion of a 12-kb polyketide synthase operon into the lacZ gene of Escherichia coli, multiple simultaneous and sequential deletions of up to 120 kb in E. coli and Staphylococcus aureus, inversions of up to 1.2 Mb in E. coli and Bacillus subtilis, and one-step cut-and-pastes for translocating 120 kb of genomic sequence to a site 1.5 Mb away. We also demonstrate the simultaneous delivery of lox sites into multiple loci in the Shewanella oneidensis genome. No selectable markers need to be placed in the genome, and the efficiency of Cre-mediated manipulations typically approaches 100%.
Collapse
Affiliation(s)
- Peter J Enyeart
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Steven M Chirieleison
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Mai N Dao
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Jiri Perutka
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
| | - Erik M Quandt
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Jacob T Whitt
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Adrian T Keatinge-Clay
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
| | - Alan M Lambowitz
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
28
|
Hayes M, Pyon YS, Li J. A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data. PLoS One 2012; 7:e52881. [PMID: 23300804 PMCID: PMC3531386 DOI: 10.1371/journal.pone.0052881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/22/2012] [Indexed: 01/08/2023] Open
Abstract
Structural variation (SV) has been reported to be associated with numerous diseases such as cancer. With the advent of next generation sequencing (NGS) technologies, various types of SV can be potentially identified. We propose a model based clustering approach utilizing a set of features defined for each type of SV events. Our method, termed SVMiner, not only provides a probability score for each candidate, but also predicts the heterozygosity of genomic deletions. Extensive experiments on genome-wide deep sequencing data have demonstrated that SVMiner is robust against the variability of a single cluster feature, and it significantly outperforms several commonly used SV detection programs. SVMiner can be downloaded from http://cbc.case.edu/svminer/.
Collapse
Affiliation(s)
- Matthew Hayes
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Yoon Soo Pyon
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jing Li
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
| |
Collapse
|
29
|
Fujita J, Miyawaki Y, Suzuki A, Maki A, Okuyama E, Murata M, Takagi A, Murate T, Suzuki N, Matsushita T, Saito H, Kojima T. A possible mechanism for Inv22-related F8 large deletions in severe hemophilia A patients with high responding factor VIII inhibitors. J Thromb Haemost 2012; 10:2099-107. [PMID: 22906111 DOI: 10.1111/j.1538-7836.2012.04897.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Intron 22 inversion (Inv22) of the coagulation factor (F)VIII gene (F8) is a frequent cause of severe hemophilia A. In addition to Inv22, a variety of F8 mutations (1492 unique mutations) causing hemophilia A have been reported, of which 171 involve deletions of over 50 bp (HAMSTeRs database; http://hadb.org.uk/). However, only 10% of these large deletions have been fully characterized at the nucleotide level. PATIENTS AND METHODS We investigated gene abnormalities in three unrelated severe hemophilia A patients with high titer FVIII inhibitors. They had previously been shown to carry large deletions of the F8, but the precise gene abnormalities remain to be elucidated. RESULTS Inverse shifting-PCR (IS-PCR) Inv22 diagnostic tests revealed that these patients carried either type I or II Inv22. However, they showed a wild-type (WT) pattern in the IS-PCR Inv22 complementary tests. We further analyzed their X chromosomes to account for the puzzling results, and found that they had different centromeric breakpoints in the Inv22 X chromosomes, adjacent to the palindromic regions containing int22h-2 or -3, and their spacer region, respectively. The connections appeared to be shifted towards the telomere of the WT F8 Xq28, resulting in a new telomere with an additional intact int22h copy. CONCLUSIONS These gene rearrangements might result from double-strand breaks in the most distal regions of the long arms of the Inv22 X chromosomes, followed by DNA restorations using the WT F8 Xq28 by non-homologous end joining or break-induced replication; thus leading to large F8 deletions in severe hemophilia A patients.
Collapse
Affiliation(s)
- J Fujita
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Mandalos N, Saridaki M, Harper JL, Kotsoni A, Yang P, Economides AN, Remboutsika E. Application of a novel strategy of engineering conditional alleles to a single exon gene, Sox2. PLoS One 2012; 7:e45768. [PMID: 23029233 PMCID: PMC3459942 DOI: 10.1371/journal.pone.0045768] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 08/20/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Conditional by Inversion (COIN) method for engineering conditional alleles relies on an invertible optimized gene trap-like element, the COIN module, for imparting conditionality. The COIN module contains an optimized 3' splice site-polyadenylation signal pair, but is inserted antisense to the target gene and therefore does not alter transcription, until it is inverted by Cre recombinase. In order to make COIN applicable to all protein-coding genes, the COIN module has been engineered within an artificial intron, enabling insertion into an exon. METHODOLOGY/PRINCIPAL FINDINGS Therefore, theoretically, the COIN method should be applicable to single exon genes, and to test this idea we engineered a COIN allele of Sox2. This single exon gene presents additional design challenges, in that its proximal promoter and coding region are entirely contained within a CpG island, and are also spanned by an overlapping transcript, Sox2Ot, which contains mmu-miR1897. Here, we show that despite disruption of the CpG island by the COIN module intron, the COIN allele of Sox2 (Sox2(COIN)) is phenotypically wild type, and also does not interfere with expression of Sox2Ot and miR1897. Furthermore, the inverted COIN allele of Sox2, Sox2(INV) is functionally null, as homozygotes recapitulate the phenotype of Sox2(βgeo/βgeo) mice, a well-characterized Sox2 null. Lastly, the benefit of the eGFP marker embedded in the COIN allele is demonstrated as it mirrors the expression pattern of Sox2. CONCLUSIONS/SIGNIFICANCE Our results demonstrate the applicability of the COIN technology as a method of choice for targeting single exon genes.
Collapse
Affiliation(s)
- Nikolaos Mandalos
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| | - Marannia Saridaki
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| | - Jessica Lea Harper
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, United States of America
| | - Anastasia Kotsoni
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| | - Peter Yang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, United States of America
| | - Aris N. Economides
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, United States of America
| | - Eumorphia Remboutsika
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| |
Collapse
|
31
|
Somvanshi VS, Sloup RE, Crawford JM, Martin AR, Heidt AJ, Kim KS, Clardy J, Ciche TA. A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. Science 2012; 337:88-93. [PMID: 22767929 PMCID: PMC4006969 DOI: 10.1126/science.1216641] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Microbial populations stochastically generate variants with strikingly different properties, such as virulence or avirulence and antibiotic tolerance or sensitivity. Photorhabdus luminescens bacteria have a variable life history in which they alternate between pathogens to a wide variety of insects and mutualists to their specific host nematodes. Here, we show that the P. luminescens pathogenic variant (P form) switches to a smaller-cell variant (M form) to initiate mutualism in host nematode intestines. A stochastic promoter inversion causes the switch between the two distinct forms. M-form cells are much smaller (one-seventh the volume), slower growing, and less bioluminescent than P-form cells; they are also avirulent and produce fewer secondary metabolites. Observations of form switching by individual cells in nematodes revealed that the M form persisted in maternal nematode intestines, were the first cells to colonize infective juvenile (IJ) offspring, and then switched to P form in the IJ intestine, which armed these nematodes for the next cycle of insect infection.
Collapse
Affiliation(s)
- Vishal S. Somvanshi
- Department of Microbiology and Molecular Genetics and Center for Microbial Pathogenesis, Michigan State University, East Lansing, MI 48824, USA
| | - Rudolph E. Sloup
- Department of Microbiology and Molecular Genetics and Center for Microbial Pathogenesis, Michigan State University, East Lansing, MI 48824, USA
| | - Jason M. Crawford
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander R. Martin
- Department of Microbiology and Molecular Genetics and Center for Microbial Pathogenesis, Michigan State University, East Lansing, MI 48824, USA
| | - Anthony J. Heidt
- Department of Microbiology and Molecular Genetics and Center for Microbial Pathogenesis, Michigan State University, East Lansing, MI 48824, USA
| | - Kwi-suk Kim
- Department of Microbiology and Molecular Genetics and Center for Microbial Pathogenesis, Michigan State University, East Lansing, MI 48824, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Todd A. Ciche
- Department of Microbiology and Molecular Genetics and Center for Microbial Pathogenesis, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
32
|
Abstract
Gene conversion is the unidirectional transfer of genetic information between orthologous (allelic) or paralogous (nonallelic) genomic segments. Though a number of studies have examined nucleotide replacements, little is known about length difference mutations produced by gene conversion. Here, we investigate insertions and deletions produced by nonallelic gene conversion in 338 Drosophila and 10,149 primate paralogs. Using a direct phylogenetic approach, we identify 179 insertions and 614 deletions in Drosophila paralogs, and 132 insertions and 455 deletions in primate paralogs. Thus, nonallelic gene conversion is strongly deletion-biased in both lineages, with almost 3.5 times as many conversion-induced deletions as insertions. In primates, the deletion bias is considerably stronger for long indels and, in both lineages, the per-site rate of gene conversion is orders of magnitudes higher than that of ordinary mutation. Due to this high rate, deletion-biased nonallelic gene conversion plays a key role in genome size evolution, leading to the cooperative shrinkage and eventual disappearance of selectively neutral paralogs. Gene conversion is a process whereby a DNA sequence is copied from one segment of the genome (donor) to another (recipient), resulting in the replacement, insertion, or deletion of a DNA sequence in the recipient. This exchange is facilitated by the high sequence similarity of the two segments, which is due to their evolutionary relationship. Here, we study insertions and deletions produced by gene conversion between paralogs, segments related by DNA duplication events. By comparing paralog sequences in multiple species of fruit flies and primates, we find that deletions occur more than three times as frequently as insertions. We also discover that the rate of gene conversion between paralogs is quite high. The deletion bias and high rate of this process causes paralogs to shrink cooperatively and eventually be eliminated from the genome. Because of the abundance of paralogs in animal genomes, this phenomenon can lead to a significant reduction in genome size. Therefore, our finding enhances our understanding of the forces that lead to changes in genome size during evolution.
Collapse
Affiliation(s)
- Raquel Assis
- Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California Berkeley, Berkeley, California, USA.
| | | |
Collapse
|
33
|
Rossetti LC, Radic CP, Abelleyro MM, Larripa IB, De Brasi CD. Eighteen years of molecular genotyping the hemophilia inversion hotspot: from southern blot to inverse shifting-PCR. Int J Mol Sci 2011; 12:7271-85. [PMID: 22072947 PMCID: PMC3211038 DOI: 10.3390/ijms12107271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 10/08/2011] [Accepted: 10/19/2011] [Indexed: 11/16/2022] Open
Abstract
The factor VIII gene (F8) intron 22 inversion (Inv22) is a paradigmatic duplicon-mediated rearrangement, found in about one half of patients with severe hemophilia A worldwide. The identification of this prevalent cause of hemophilia was delayed for nine years after the F8 characterization in 1984. The aim of this review is to present the wide diversity of practical approaches that have been developed for genotyping the Inv22 (and related int22h rearrangements) since discovery in 1993. The sequence- Southern blot, long distance-PCR and inverse shifting-PCR-for Inv22 genotyping is an interesting example of scientific ingenuity and evolution in order to resolve challenging molecular diagnostic problems.
Collapse
Affiliation(s)
- Liliana C Rossetti
- Departamento de Genética, Instituto de Investigaciones Hematológicas, Academia Nacional de Medicina, Pacheco de Melo 3081, Ciudad de Buenos Aires (CP 1425), Argentina; E-Mails: (C.P.R.); (M.M.A.); (I.B.L.); (C.D.D.B.)
| | | | | | | | | |
Collapse
|
34
|
Gao L, Zhou Y, Wang ZW, Su YJ, Wang T. Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers. BMC Plant Biol 2011; 11:64. [PMID: 21486489 PMCID: PMC3098776 DOI: 10.1186/1471-2229-11-64] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/13/2011] [Indexed: 05/12/2023]
Abstract
BACKGROUND The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. RESULTS A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. CONCLUSIONS Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.
Collapse
Affiliation(s)
- Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yuan Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhi-Wei Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ying-Juan Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ting Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| |
Collapse
|
35
|
Abstract
Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.
Collapse
Affiliation(s)
- Alison Ling
- Université de Poitiers, CNRS UMR 6556 Ecologie, Evolution, Symbiose, Poitiers, France
| | - Richard Cordaux
- Université de Poitiers, CNRS UMR 6556 Ecologie, Evolution, Symbiose, Poitiers, France
- * E-mail:
| |
Collapse
|
36
|
Poisot E, Théodore L. [PREs, sequences conveying epigenetic memory, are conserved during evolution]. Med Sci (Paris) 2010; 26:355-8. [PMID: 20412738 DOI: 10.1051/medsci/2010264355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
37
|
Hrabák J, Zemanová A, Chudácková E. [Mobile genetic elements in the epidemiology of bacterial resistance to antibiotics]. Epidemiol Mikrobiol Imunol 2010; 59:55-66. [PMID: 20586167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The study of the role of mobile elements and mobilization of resistance genes is crucial for understanding the epidemiology of antibiotic resistance. This review summarizes recent data on the insertion sequences, transposons, integrons and plasmids that are involved in the mobilization of bacterial antibiotic resistance genes.
Collapse
Affiliation(s)
- J Hrabák
- Ustav mikrobiologie, LF UK a FN v Plzni.
| | | | | |
Collapse
|
38
|
Sawamura K, Kamiya K, Sato H, Tomimura Y, Matsuda M, Oguma Y. Evolutionary Relationships in theDrosophila ananassaeSpecies Cluster Based on Introns of Multiple Nuclear Loci. Zoolog Sci 2010; 27:303-12. [PMID: 20377348 DOI: 10.2108/zsj.27.303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kyoichi Sawamura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | | | | | | | | | | |
Collapse
|