601
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Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. PLANTA 2019; 250:23-40. [PMID: 30993403 DOI: 10.1007/s00425-019-03166-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
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Affiliation(s)
- Jinna Hou
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Dandan Lu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Baoquan Li
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sufang An
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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602
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Wang S, Zhang C, Hasson D, Desai A, SenBanerjee S, Magnani E, Ukomadu C, Lujambio A, Bernstein E, Sadler KC. Epigenetic Compensation Promotes Liver Regeneration. Dev Cell 2019; 50:43-56.e6. [PMID: 31231040 PMCID: PMC6615735 DOI: 10.1016/j.devcel.2019.05.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Two major functions of the epigenome are to regulate gene expression and to suppress transposons. It is unclear how these functions are balanced during physiological challenges requiring tissue regeneration, where exquisite coordination of gene expression is essential. Transcriptomic analysis of seven time points following partial hepatectomy identified the epigenetic regulator UHRF1, which is essential for DNA methylation, as dynamically expressed during liver regeneration in mice. UHRF1 deletion in hepatocytes (Uhrf1HepKO) caused genome-wide DNA hypomethylation but, surprisingly, had no measurable effect on gene or transposon expression or liver homeostasis. Partial hepatectomy of Uhrf1HepKO livers resulted in early and sustained activation of proregenerative genes and enhanced liver regeneration. This was attributed to redistribution of H3K27me3 from promoters to transposons, effectively silencing them and, consequently, alleviating repression of liver regeneration genes, priming them for expression in Uhrf1HepKO livers. Thus, epigenetic compensation safeguards the genome against transposon activation, indirectly affecting gene regulation.
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Affiliation(s)
- Shuang Wang
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anal Desai
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sucharita SenBanerjee
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; College of Arts and Sciences, Wentworth Institute of Technology, 504 Parker St., Boston, MA 02115, USA
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Chinweike Ukomadu
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kirsten C Sadler
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates.
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603
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Convergent Co-option of the Retroviral gag Gene during the Early Evolution of Mammals. J Virol 2019; 93:JVI.00542-19. [PMID: 31068420 DOI: 10.1128/jvi.00542-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/30/2019] [Indexed: 12/30/2022] Open
Abstract
Endogenous retroviruses, records of past retroviral infections, are ubiquitous in vertebrate genomes. On occasion, vertebrate hosts have co-opted retroviral genes for their own biological functions. Here, we perform a phylogenomic survey of retroviral gag gene homologs within vertebrate genomes and identify two ancient co-opted retroviral gag genes, designated wucaishi1 (wcs1) and wucaishi2 (wcs2), in mammals. Conserved synteny and evolutionary analyses suggest that the wcs1 and wcs2 co-options occurred before the origin of modern placental mammals (∼100 million years ago) and before the origin of modern marsupials (∼80 million years ago), respectively. We found that the wcs genes were lost or pseudogenized multiple times during the evolutionary course of mammals. While the wcs1 gene is mainly subject to negative selection in placental mammals (except in Perissodactyla), the wcs2 gene underwent positive selection in marsupials. Moreover, analyses of transcriptome-sequencing (RNA-seq) data suggest that the wcs1 and the wcs2 genes are expressed in a wide range of tissues. The convergent wcs co-option in mammals implies the retroviral gag gene might have been repurposed more frequently than previously thought.IMPORTANCE Retroviruses occasionally can infect host germ lines, forming endogenous retroviruses. Vertebrates, in turn, recruited retroviral genes for their own biological functions, a process formally known as co-option or exaptation. To date, co-opted retroviral gag genes have rarely been reported. In this study, we identified two co-opted retroviral gag genes, designated wucaishi1 (wcs1) and wucaishi2 (wcs2), in mammals. The co-option of wcs1 and wcs2 occurred before the origin of modern placentals and before the origin of modern marsupials, respectively. Our study indicates that retroviral gag gene co-option might have occurred more frequently than previously thought during the evolutionary course of vertebrates.
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604
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Chisolm DA, Cheng W, Colburn SA, Silva-Sanchez A, Meza-Perez S, Randall TD, Weinmann AS. Defining Genetic Variation in Widely Used Congenic and Backcrossed Mouse Models Reveals Varied Regulation of Genes Important for Immune Responses. Immunity 2019; 51:155-168.e5. [PMID: 31248780 DOI: 10.1016/j.immuni.2019.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/24/2019] [Accepted: 05/15/2019] [Indexed: 12/27/2022]
Abstract
Genetic variation influences how the genome is interpreted in individuals and in mouse strains used to model immune responses. We developed approaches to utilize next-generation sequencing datasets to identify sequence variation in genes and enhancer elements in congenic and backcross mouse models. We defined genetic variation in the widely used B6-CD45.2 and B6.SJL-CD45.1 congenic model, identifying substantial differences in SJL genetic content retained in B6.SJL-CD45.1 strains on the basis of the vendor source of the mice. Genes encoding PD-1, CD62L, Bcl-2, cathepsin E, and Cxcr4 were within SJL genetic content in at least one vendor source of B6.SJL-CD45.1 mice. SJL genetic content affected enhancer elements, gene regulation, protein expression, and amino acid content in CD4+ T helper 1 cells, and mice infected with influenza showed reduced expression of Cxcr4 on B6.SJL-CD45.1 T follicular helper cells. These findings provide information on experimental variables and aid in creating approaches that account for genetic variables.
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Affiliation(s)
- Danielle A Chisolm
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wayne Cheng
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shelby A Colburn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Selene Meza-Perez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Troy D Randall
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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605
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Ma B, Xin Y, Kuang L, He N. Distribution and Characteristics of Transposable Elements in the Mulberry Genome. THE PLANT GENOME 2019; 12:180094. [PMID: 31290922 DOI: 10.3835/plantgenome2018.12.0094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mulberry ( C. K. Schneid) leaves have been used as the food for the domesticated silkworm, , for more than 5000 yr, and the mulberry-silkworm relationship is one of the best-known and oldest models of plant defense-insect adaptation. The availability of a genome assembly of mulberry provides us with an opportunity to mine the characteristics and distribution of transposable elements (TEs) in this species and to examine their relationship to genes and gene expression. In this study, a significantly correlated inverse relationship between the percentage coverage of genes and TEs was observed. The TE-rich regions appeared to have a lower percentage of putatively expressed genes. Distribution patterns between different TE superfamilies were detected in the mulberry genome. The elements (the TE making up the greatest proportion of the mulberry genome) were significantly overrepresented within genes in the mulberry genome, and they may have a dominant influence on evolution of the mulberry genome. Approximately 96.93% (330/344) of the TE-containing genes assigned to pathways were assigned to metabolism-related pathways. The TE-related alternative splicing events accounted for 7.58% (402/5,302) of all alternative splicing types in the mulberry genome, suggesting that TEs are one of the driving forces in the formation of the alternatively spliced genes. The results will be valuable in improving our understanding of the important roles of TEs in mulberry genome evolution.
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606
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Brind'Amour J, Mager DL. Reality check for transposon enhancers. eLife 2019; 8:47900. [PMID: 31148541 PMCID: PMC6544458 DOI: 10.7554/elife.47900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022] Open
Abstract
Hundreds of retrovirus-like sequences have features that suggest they might be gene enhancers, but only a small fraction displays gene-regulating activity in experiments on mouse stem cells.
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Affiliation(s)
- Julie Brind'Amour
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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607
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Bourgeois Y, Boissinot S. On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements. Genes (Basel) 2019; 10:genes10060419. [PMID: 31151307 PMCID: PMC6627506 DOI: 10.3390/genes10060419] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/05/2019] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Transposable elements (TEs) play an important role in shaping genomic organization and structure, and may cause dramatic changes in phenotypes. Despite the genetic load they may impose on their host and their importance in microevolutionary processes such as adaptation and speciation, the number of population genetics studies focused on TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review the current knowledge about the dynamics of transposable elements at recent evolutionary time scales, and discuss the mechanisms that condition their abundance and frequency. We first discuss non-adaptive mechanisms such as purifying selection and the variable rates of transposition and elimination, and then focus on positive and balancing selection, to finally conclude on the potential role of TEs in causing genomic incompatibilities and eventually speciation. We also suggest possible ways to better model TEs dynamics in a population genomics context by incorporating recent advances in TEs into the rich information provided by SNPs about the demography, selection, and intrinsic properties of genomes.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, P.O. 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Stéphane Boissinot
- New York University Abu Dhabi, P.O. 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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608
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Rubenstein DR, Ågren JA, Carbone L, Elde NC, Hoekstra HE, Kapheim KM, Keller L, Moreau CS, Toth AL, Yeaman S, Hofmann HA. Coevolution of Genome Architecture and Social Behavior. Trends Ecol Evol 2019; 34:844-855. [PMID: 31130318 DOI: 10.1016/j.tree.2019.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 01/02/2023]
Abstract
Although social behavior can have a strong genetic component, it can also result in selection on genome structure and function, thereby influencing the evolution of the genome itself. Here we explore the bidirectional links between social behavior and genome architecture by considering variation in social and/or mating behavior among populations (social polymorphisms) and across closely related species. We propose that social behavior can influence genome architecture via associated demographic changes due to social living. We establish guidelines to exploit emerging whole-genome sequences using analytical approaches that examine genome structure and function at different levels (regulatory vs structural variation) from the perspective of both molecular biology and population genetics in an ecological context.
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Affiliation(s)
- Dustin R Rubenstein
- Columbia University, Department of Ecology, Evolution, and Environmental Biology and Center for Integrative Animal Behavior, New York, NY 10027, USA.
| | - J Arvid Ågren
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138, USA
| | - Lucia Carbone
- Oregon Health & Science University, Department of Medicine, KCVI, Portland, OR 97239, USA; Oregon National Primate Research Center, Division of Genetics, Beaverton, OR 97006, USA
| | - Nels C Elde
- University of Utah School of Medicine, Department of Human Genetics, Salt Lake City, UT 84112, USA
| | - Hopi E Hoekstra
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138, USA; Harvard University, Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Cambridge, MA 02138, USA
| | - Karen M Kapheim
- Utah State University, Department of Biology, Logan, UT 84322, USA
| | - Laurent Keller
- University of Lausanne, Department of Ecology and Evolution, Biophore, UNIL, 1015 Lausanne, Switzerland
| | - Corrie S Moreau
- Cornell University, Departments of Entomology and Ecology and Evolutionary Biology, Ithaca, NY 14850, USA
| | - Amy L Toth
- Iowa State University, Department of Ecology, Evolution, and Organismal Biology and Department of Entomology, Ames, IA 50011, USA
| | - Sam Yeaman
- University of Calgary, Department of Biological Sciences, Calgary, AB T2N 1N4, Canada
| | - Hans A Hofmann
- The University of Texas at Austin, Department of Integrative Biology and Institute for Cellular and Molecular Biology, 2415 Speedway C-0990, Austin, TX 78712, USA.
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609
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Zhao W, Tan J, Zhu T, Ou J, Li Y, Shen L, Wu H, Han L, Liu Y, Jia X, Bai T, Li H, Ke X, Zhao J, Zou X, Hu Z, Guo H, Xia K. Rare inherited missense variants of POGZ associate with autism risk and disrupt neuronal development. J Genet Genomics 2019; 46:247-257. [PMID: 31196716 DOI: 10.1016/j.jgg.2019.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 03/22/2019] [Accepted: 04/02/2019] [Indexed: 11/16/2022]
Abstract
Excess de novo likely gene-disruptive and missense variants within dozens of genes have been identified in autism spectrum disorder (ASD) and other neurodevelopmental disorders. However, many rare inherited missense variants of these high-risk genes have not been thoroughly evaluated. In this study, we analyzed the rare missense variant burden of POGZ in a large cohort of ASD patients from the Autism Clinical and Genetic Resources in China (ACGC) and further dissected the functional effect of disease-associated missense variants on neuronal development. Our results showed a significant burden of rare missense variants in ASD patients compared to the control population (P = 4.6 × 10-5, OR = 3.96), and missense variants in ASD patients showed more severe predicted functional outcomes than those in controls. Furthermore, by leveraging published large-scale sequencing data of neurodevelopmental disorders (NDDs) and sporadic case reports, we identified 8 de novo missense variants of POGZ in NDD patients. Functional analysis revealed that two inherited, but not de novo, missense variants influenced the cellular localization of POGZ and failed to rescue the defects in neurite and dendritic spine development caused by Pogz knockdown in cultured mouse primary cortical neurons. Significantly, L1CAM, an autism candidate risk gene, is differentially expressed in POGZ deficient cell lines. Reduced expression of L1cam was able to partially rescue the neurite length defects caused by Pogz knockdown. Our study showed the important roles of rare inherited missense variants of POGZ in ASD risk and neuronal development and identified the potential downstream targets of POGZ, which are important for further molecular mechanism studies.
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Affiliation(s)
- Wenjing Zhao
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Jieqiong Tan
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Tengfei Zhu
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Jianjun Ou
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Ying Li
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Lu Shen
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Huidan Wu
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Lin Han
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Yanling Liu
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Xiangbin Jia
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Ting Bai
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Honghui Li
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, China
| | - Xiaoyan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital Affiliated of Nanjing Medical University, Nanjing, 210029, China
| | - Jingping Zhao
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiaobing Zou
- Children Development Behavior Center of the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhengmao Hu
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Hui Guo
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China; Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, 410011, China.
| | - Kun Xia
- Center of Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China; School of Life Sciences and Technology, Xinjiang University, Ürümqi, 830046, China; CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, 200030, China.
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610
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Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes (Basel) 2019; 10:genes10050338. [PMID: 31064091 PMCID: PMC6562904 DOI: 10.3390/genes10050338] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
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Affiliation(s)
- Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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611
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Jiang JC, Upton KR. Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. Mob DNA 2019; 10:16. [PMID: 31061680 PMCID: PMC6486989 DOI: 10.1186/s13100-019-0158-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/01/2019] [Indexed: 12/22/2022] Open
Abstract
Background Transposable elements (TE) are commonly regarded as “junk DNA” with no apparent regulatory roles in the human genome. However, a growing body of evidence demonstrates that some TEs exhibit regulatory activities in a range of biological pathways and diseases, with notable examples in bile metabolism and innate immunity. TEs are typically suppressed by epigenetic modifications in healthy somatic tissues, which prevents both undesirable effects of insertional mutagenesis, and also unwanted gene activation. Interestingly, TEs are widely reported to be dysregulated in epithelial cancers, and while much attention has been paid to their effects on genome instability, relatively little has been reported on their effects on gene regulation. Here, we investigated the contribution of TEs to the transcriptional regulation in breast cancer cell lines. Results We found that a subset of TE subfamilies were enriched in oncogenic transcription factor binding sites and also harboured histone marks associated with active transcription, raising the possibility of these subfamilies playing a broad role in breast cancer transcriptional regulation. To directly assess promoter activity in triple negative breast cancer cell lines, we identified four breast cancer-associated genes with putative TE-derived promoters. TE deletion confirmed a contribution to promoter activity in all cases, and for two examples the promoter activity was almost completely contained within the TE. Conclusions Our findings demonstrate that TEs provide abundant oncogenic transcription factor binding sites in breast cancer and that individual TEs contain substantial promoter activity. Our findings provide further evidence for transcriptional regulation of human genes through TE exaptation by demonstrating the regulatory potential of TEs in multiple breast cancer cell lines. Electronic supplementary material The online version of this article (10.1186/s13100-019-0158-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiayue-Clara Jiang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - Kyle R Upton
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
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612
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Todd CD, Deniz Ö, Taylor D, Branco MR. Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells. eLife 2019; 8:e44344. [PMID: 31012843 PMCID: PMC6544436 DOI: 10.7554/elife.44344] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/20/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that they play significant roles in gene regulation. Here we tested a set of long terminal repeat TE families for roles as enhancers in mouse embryonic and trophoblast stem cells. Epigenomic and transcriptomic data suggested that a large number of TEs helped to establish tissue-specific gene expression programmes. Genetic editing of individual TEs confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a subset of TEs are important for gene regulation in early mouse development, and highlight the importance of functional experiments when evaluating gene regulatory roles of TEs.
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Affiliation(s)
- Christopher D Todd
- Blizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUnited Kingdom
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUnited Kingdom
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Darren Taylor
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Miguel R Branco
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
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613
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Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D. Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs. Cell Stem Cell 2019; 24:724-735.e5. [PMID: 31006620 PMCID: PMC6509360 DOI: 10.1016/j.stem.2019.03.012] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/04/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
Abstract
Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation. KLFs foster EGA by activating enhancers embedded in young TEs (TEENhancers) TEENhancers confer a degree of species specificity to early genome activation TEENhancers stimulate the expression of KZFPs responsible for their repression These KZFPs in turn facilitate TEENhancers’ exaptation as tissue-specific regulators
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Affiliation(s)
- Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Thorold W Theunissen
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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614
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Function and Evolution of Upstream ORFs in Eukaryotes. Trends Biochem Sci 2019; 44:782-794. [PMID: 31003826 DOI: 10.1016/j.tibs.2019.03.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 12/18/2022]
Abstract
There is growing interest in the role of translational regulation in cellular homeostasis during organismal development. Translation initiation is the rate-limiting step in mRNA translation and is central to translational regulation. Upstream open reading frames (uORFs) are regulatory elements that are prevalent in eukaryotic mRNAs. uORFs modulate the translation initiation rate of downstream coding sequences (CDSs) by sequestering ribosomes. Over the past several years, genome-wide studies have revealed the widespread regulatory functions of uORFs in different species in different biological contexts. Here, we review the current understanding of uORF-mediated translational regulation from the perspective of functional and evolutionary genomics and address remaining gaps that deserve further study.
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615
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Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L. Mager
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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616
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Sultana T, van Essen D, Siol O, Bailly-Bechet M, Philippe C, Zine El Aabidine A, Pioger L, Nigumann P, Saccani S, Andrau JC, Gilbert N, Cristofari G. The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection. Mol Cell 2019; 74:555-570.e7. [PMID: 30956044 DOI: 10.1016/j.molcel.2019.02.036] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 01/10/2023]
Abstract
L1 retrotransposons are transposable elements and major contributors of genetic variation in humans. Where L1 integrates into the genome can directly impact human evolution and disease. Here, we experimentally induced L1 retrotransposition in cells and mapped integration sites at nucleotide resolution. At local scales, L1 integration is mostly restricted by genome sequence biases and the specificity of the L1 machinery. At regional scales, L1 shows a broad capacity for integration into all chromatin states, in contrast to other known mobile genetic elements. However, integration is influenced by the replication timing of target regions, suggesting a link to host DNA replication. The distribution of new L1 integrations differs from those of preexisting L1 copies, which are significantly reshaped by natural selection. Our findings reveal that the L1 machinery has evolved to efficiently target all genomic regions and underline a predominant role for post-integrative processes on the distribution of endogenous L1 elements.
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Affiliation(s)
- Tania Sultana
- Université Côte d'Azur, Inserm, CNRS, IRCAN, Nice, France
| | | | - Oliver Siol
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | | | | | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Léo Pioger
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Pilvi Nigumann
- Université Côte d'Azur, Inserm, CNRS, IRCAN, Nice, France
| | - Simona Saccani
- Université Côte d'Azur, Inserm, CNRS, IRCAN, Nice, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Nicolas Gilbert
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France; Institut de Médecine Régénératrice et de Biothérapie, Inserm U1183, CHU Montpellier, Montpellier, France
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617
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Saika H, Mori A, Endo M, Toki S. Targeted deletion of rice retrotransposon Tos17 via CRISPR/Cas9. PLANT CELL REPORTS 2019; 38:455-458. [PMID: 30465094 DOI: 10.1007/s00299-018-2357-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/14/2018] [Indexed: 06/09/2023]
Abstract
A successful example of transposon deletion via CRISPR/Cas9-mediated genome editing suggests a novel alternative approach to plant breeding. Transposition of transposable elements (TEs) can affect adjacent genes, leading to changes in genetic traits. Expression levels and patterns, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus can be affected. Artificial modification of loci adjacent to TEs, or TEs themselves, by genome editing could mimic the translocation of TEs that occurs in nature, suggesting that it might be possible to produce novel plants by modification of TEs via genome editing. To our knowledge, there are no reports thus far of modification of TEs by genome editing in plants. In this study, we performed targeted deletion of the Tos17 retrotransposon, which is flanked at both ends by long terminal repeat (LTR) sequences, via genome editing in rice. We succeeded in targeted mutagenesis of the LTR, and targeted deletion between LTRs, in calli transformed with CRISPR/Cas9 vectors for the Tos17 LTR. Moreover, we also successfully obtained regenerated plants derived from transformed calli and plants homozygous for lacking Tos17 in the next generation. Taken together, our results demonstrate successful deletion of the Tos17 retrotransposon from the rice genome by targeted mutagenesis using CRISPR/Cas9. We believe that this strategy could be applied to other TEs in many plant species, providing a rapid breeding technology as an alternative means to re-activate expression of agronomically important genes that have been inactivated by TE insertion, especially in plants such as fruit trees, in which it is difficult to maintain parental agronomical traits by cross-breeding due to high heterozygosity.
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Affiliation(s)
- Hiroaki Saika
- Plant Genome Engineering Research Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
| | - Akiko Mori
- Plant Genome Engineering Research Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Yokohama, Kanagawa, 244-0813, Japan
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618
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Jang HS, Shah NM, Du AY, Dailey ZZ, Pehrsson EC, Godoy PM, Zhang D, Li D, Xing X, Kim S, O'Donnell D, Gordon JI, Wang T. Transposable elements drive widespread expression of oncogenes in human cancers. Nat Genet 2019; 51:611-617. [PMID: 30926969 PMCID: PMC6443099 DOI: 10.1038/s41588-019-0373-3] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 02/12/2019] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) are an abundant and rich genetic resource of regulatory sequences1-3. Cryptic regulatory elements within TEs can be epigenetically reactivated in cancer to influence oncogenesis in a process termed onco-exaptation4. However, the prevalence and impact of TE onco-exaptation events across cancer types are poorly characterized. Here, we analyzed 7,769 tumors and 625 normal datasets from 15 cancer types, identifying 129 TE cryptic promoter-activation events involving 106 oncogenes across 3,864 tumors. Furthermore, we interrogated the AluJb-LIN28B candidate: the genetic deletion of the TE eliminated oncogene expression, while dynamic DNA methylation modulated promoter activity, illustrating the necessity and sufficiency of a TE for oncogene activation. Collectively, our results characterize the global profile of TE onco-exaptation and highlight this prevalent phenomenon as an important mechanism for promiscuous oncogene activation and ultimately tumorigenesis.
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Affiliation(s)
- Hyo Sik Jang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Alan Y Du
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Zea Z Dailey
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Paula M Godoy
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - David Zhang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Sungsu Kim
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disease, Washington University School of Medicine, St Louis, MO, USA
| | - David O'Donnell
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey I Gordon
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
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619
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Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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620
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Abstract
Among the multitude of papers published yearly in scientific journals, precious few publications may be worth looking back in half a century to appreciate the significance of the discoveries that would later become common knowledge and get a chance to shape a field or several adjacent fields. Here, Kimura's fundamental concept of neutral mutation-random drift, which was published 50 years ago, is re-examined in light of its pervasive influence on comparative genomics and, more specifically, on the contribution of transposable elements to eukaryotic genome evolution.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA
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621
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Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation. Clin Ther 2019; 41:675-698. [PMID: 30910331 DOI: 10.1016/j.clinthera.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease. METHODS A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool. FINDINGS Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection. IMPLICATIONS Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences ("junk repetitive DNA"), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.
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622
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Bodea GO, McKelvey EGZ, Faulkner GJ. Retrotransposon-induced mosaicism in the neural genome. Open Biol 2019; 8:rsob.180074. [PMID: 30021882 PMCID: PMC6070720 DOI: 10.1098/rsob.180074] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.
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Affiliation(s)
- Gabriela O Bodea
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eleanor G Z McKelvey
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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623
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Abstract
Committing to a differentiation pathway means leaving alternative pathways behind. Adoue et al. (2019) report that the H3K9-methyltrasferase Setdb1 plays a role in inhibiting the Th1 program in committed Th2 cells, and mechanistically, its role might relate to the selective targeting of endogenous retroviruses adjacent to Th1 enhancers.
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Affiliation(s)
- Tonya J Webb
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA.
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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624
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Centromere Repeats: Hidden Gems of the Genome. Genes (Basel) 2019; 10:genes10030223. [PMID: 30884847 PMCID: PMC6471113 DOI: 10.3390/genes10030223] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.
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625
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Abstract
The mechanisms underlying rapid adaptation to changing environments in species with reduced genetic variation, referred to as the “genetic paradox of invasion,” are unknown. We report that transposable elements (TEs) are highly enriched in the gene promoter regions of Capsella rubella compared with its outcrossing sister species Capsella grandiflora. We also show that a number of polymorphic TEs in C. rubella are associated with changes in gene expression. Frequent TE insertions at FLOWERING LOCUS C of C. rubella affect flowering-time variation, an important life history trait correlated with fitness. These results indicate that TE insertions drive rapid phenotypic variation, which could potentially help adapting to novel environments in species with limited genetic variation. Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.
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626
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Petri R, Brattås PL, Sharma Y, Jönsson ME, Pircs K, Bengzon J, Jakobsson J. LINE-2 transposable elements are a source of functional human microRNAs and target sites. PLoS Genet 2019; 15:e1008036. [PMID: 30865625 PMCID: PMC6433296 DOI: 10.1371/journal.pgen.1008036] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/25/2019] [Accepted: 02/20/2019] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are dynamically expressed at high levels in multiple human tissues, but the function of TE-derived transcripts remains largely unknown. In this study, we identify numerous TE-derived microRNAs (miRNAs) by conducting Argonaute2 RNA immunoprecipitation followed by small RNA sequencing (AGO2 RIP-seq) on human brain tissue. Many of these miRNAs originated from LINE-2 (L2) elements, which entered the human genome around 100–300 million years ago. L2-miRNAs derived from the 3’ end of the L2 consensus sequence and thus shared very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3’UTR. In line with this, many protein-coding genes carried fragments of L2-derived sequences in their 3’UTR: these sequences served as target sites for L2-miRNAs. L2-miRNAs and their targets were generally ubiquitously expressed at low levels in multiple human tissues, suggesting a role for this network in buffering transcriptional levels of housekeeping genes. In addition, we also found evidence that this network is perturbed in glioblastoma. In summary, our findings uncover a TE-based post-transcriptional network that shapes transcriptional regulation in human cells. Transposable elements (TEs) are repetitive sequences, that have contributed to the landscaping of the genome by jumping into new positions and amplifying in number. TEs have been suggested to play a role in gene regulation, but it remains poorly understood how they contribute to this process. In this study, we show that in various human tissues, an ancient class of TEs give rise to small non-coding RNAs, called microRNAs (miRNAs), that are important regulators of gene expression. The same class of TEs also serves as target sites for these TE-derived miRNAs when they are part of protein-coding transcripts. We also provide evidence that TE-derived miRNAs and target sites may play a role in human disease, as they are dysregulated in aggressive brain tumors. Altogether, our study provides novel insight into how TEs acting as miRNAs play a role in gene regulation in both, healthy and diseased human tissues.
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Affiliation(s)
- Rebecca Petri
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Per Ludvik Brattås
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Marie E. Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Johan Bengzon
- Department of Clinical Sciences, Division of Neurosurgery, Lund Stem Cell Center, Lund University and Region Skåne, Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
- * E-mail:
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627
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Marin P, Genitoni J, Barloy D, Maury S, Gibert P, Ghalambor CK, Vieira C. Biological invasion: The influence of the hidden side of the (epi)genome. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13317] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pierre Marin
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
| | - Julien Genitoni
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRA Rennes France
- LBLGC EA 1207 INRA, Université d'Orléans, USC 1328 Orléans France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRA Rennes France
| | - Stéphane Maury
- LBLGC EA 1207 INRA, Université d'Orléans, USC 1328 Orléans France
| | - Patricia Gibert
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
| | - Cameron K. Ghalambor
- Department of Biology and Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
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628
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Salvucci E. The human-microbiome superorganism and its modulation to restore health. Int J Food Sci Nutr 2019; 70:781-795. [DOI: 10.1080/09637486.2019.1580682] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- E. Salvucci
- Instituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC-CONICET-UNC), Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales; Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba
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629
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Mage RG, Esteves PJ, Rader C. Rabbit models of human diseases for diagnostics and therapeutics development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:99-104. [PMID: 30339876 PMCID: PMC6364550 DOI: 10.1016/j.dci.2018.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 05/03/2023]
Abstract
This review presents some examples of studies using the European rabbit (Oryctolagus cuniculus) that have led to, and continue to, contribute to advancement of understanding of human diseases as well as therapeutics development. In addition, we tabulate FDA-approved rabbit polyclonal and rabbit monoclonal antibodies (mAbs) that are used for diagnostic applications, as well as an overview of some "humanized" or otherwise altered rabbit mAbs that are in initial phase I, II, or advanced to phase III clinical trials. Information about endogenous retriviruses learned from studies of rabbits and other members of the order Lagomorpha are summarized as this knowledge now applies to new therapeutics being developed for several human diseases including Multiple Sclerosis, Type 1 Diabetes and Cancer.
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Affiliation(s)
- Rose G Mage
- Laboratory of Immune System Biology, NIAID, NIH, Bldg 10 11N311, 10 Center Drive, Bethesda, MD, 20892-1892, USA.
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
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630
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Babaian A, Thompson IR, Lever J, Gagnier L, Karimi MM, Mager DL. LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq. Bioinformatics 2019; 35:3839-3841. [DOI: 10.1093/bioinformatics/btz130] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/14/2019] [Accepted: 02/19/2019] [Indexed: 12/28/2022] Open
Abstract
Abstract
Summary
Transposable elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-derived transcriptional initiation contributes to the transcriptome has been marred by computational and methodological deficiencies. We developed LIONS for the analysis of RNA-seq data to specifically detect and quantify TE-initiated transcripts.
Availability and implementation
Source code, container, test data and instruction manual are freely available at www.github.com/ababaian/LIONS.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Artem Babaian
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - I Richard Thompson
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Jake Lever
- University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Liane Gagnier
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
| | - Mohammad M Karimi
- MRC London Institute of Medical Sciences, Imperial College, London, UK
| | - Dixie L Mager
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
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631
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Renault S, Genty M, Gabori A, Boisneau C, Esnault C, Dugé de Bernonville T, Augé-Gouillou C. The epigenetic regulation of HsMar1, a human DNA transposon. BMC Genet 2019; 20:17. [PMID: 30764754 PMCID: PMC6375154 DOI: 10.1186/s12863-019-0719-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of these elements, the hypothesis has emerged that their regulation can coordinate a regulatory network of genes. Herein, we investigated whether transposition regulation of HsMar1, a human DNA transposon, differs in presence or absence of endogenous HsMar1 copies. In the case where HsMar1 transposition is regulated, the number of repetitive DNA sequences issued by HsMar1 and distributed in the human genome makes HsMar1 a good candidate to regulate neighboring gene expression by epigenetic mechanisms. RESULTS A recombinant active HsMar1 copy was inserted in HeLa (human) and CHO (hamster) cells and its genomic excision monitored. We show that HsMar1 excision is blocked in HeLa cells, whereas CHO cells are competent to promote HsMar1 excision. We demonstrate that de novo HsMar1 insertions in HeLa cells (human) undergo rapid silencing by cytosine methylation and apposition of H3K9me3 marks, whereas de novo HsMar1 insertions in CHO cells (hamster) are not repressed and enriched in H3K4me3 modifications. The overall analysis of HsMar1 endogenous copies in HeLa cells indicates that neither full-length endogenous inactive copies nor their Inverted Terminal Repeats seem to be specifically silenced, and are, in contrast, devoid of epigenetic marks. Finally, the setmar gene, derived from HsMar1, presents H3K4me3 modifications as expected for a human housekeeping gene. CONCLUSIONS Our work highlights that de novo and old HsMar1 are not similarly regulated by epigenetic mechanisms. Old HsMar1 are generally detected as lacking epigenetic marks, irrespective their localisation relative to the genes. Considering the putative existence of a network associating HsMar1 old copies and SETMAR, two non-mutually exclusive hypotheses are proposed: active and inactive HsMar1 copies are not similarly regulated or/and regulations concern only few loci (and few genes) that cannot be detected at the whole genome level.
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Affiliation(s)
- Sylvaine Renault
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
| | - Murielle Genty
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
| | - Alison Gabori
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
| | - Catherine Boisneau
- UMR CITERES CNRS 7324, Université de Tours, 35 Allée Ferdinand de Lesseps, 37200 Tours, France
| | - Charles Esnault
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
| | | | - Corinne Augé-Gouillou
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
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632
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Hassing B, Winter D, Becker Y, Mesarich CH, Eaton CJ, Scott B. Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne. PLoS One 2019; 14:e0209463. [PMID: 30759164 PMCID: PMC6374014 DOI: 10.1371/journal.pone.0209463] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby maintaining a mutualistic symbiotic interaction. Recent studies have suggested that small secreted proteins, termed effectors, play a vital role in the suppression of host defence responses. To date only a few effectors with important roles in mutualistic interactions have been described. Here we make use of the fully assembled E. festucae genome and EffectorP to generate a suite of 141 effector candidates. These were analysed with respect to their genome location and expression profiles in planta and in several symbiosis-defective mutants. We found an association between effector candidates and a class of transposable elements known as MITEs, but no correlation with other dynamic features of the E. festucae genome, such as transposable element-rich regions. Three effector candidates and a small GPI-anchored protein were chosen for functional analysis based on their high expression in planta compared to in culture and their differential regulation in symbiosis defective E. festucae mutants. All three candidate effector proteins were shown to possess a functional signal peptide and two could be detected in the extracellular medium by western blotting. Localization of the effector candidates in planta suggests that they are not translocated into the plant cell, but rather, are localized in the apoplastic space or are attached to the cell wall. Deletion and overexpression of the effector candidates, as well as the putative GPI-anchored protein, did not affect the plant growth phenotype or restrict growth of E. festucae mutants in planta. These results indicate that these proteins are either not required for the interaction at the observed life stages or that there is redundancy between effectors expressed by E. festucae.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Küehn-Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Carl H. Mesarich
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Carla J. Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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633
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Fu B, Ma H, Liu D. Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development. Int J Mol Sci 2019; 20:ijms20030790. [PMID: 30759824 PMCID: PMC6387303 DOI: 10.3390/ijms20030790] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/13/2023] Open
Abstract
Pre-implantation embryo development encompasses several key developmental events, especially the activation of zygotic genome activation (ZGA)-related genes. Endogenous retroviruses (ERVs), which are regarded as “deleterious genomic parasites”, were previously considered to be “junk DNA”. However, it is now known that ERVs, with limited conservatism across species, mediate conserved developmental processes (e.g., ZGA). Transcriptional activation of ERVs occurs during the transition from maternal control to zygotic genome control, signifying ZGA. ERVs are versatile participants in rewiring gene expression networks during epigenetic reprogramming. Particularly, a subtle balance exists between ERV activation and ERV repression in host–virus interplay, which leads to stage-specific ERV expression during pre-implantation embryo development. A large portion of somatic cell nuclear transfer (SCNT) embryos display developmental arrest and ZGA failure during pre-implantation embryo development. Furthermore, because of the close relationship between ERV activation and ZGA, exploring the regulatory mechanism underlying ERV activation may also shed more light on the enigma of SCNT embryo development in model animals.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Hong Ma
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Di Liu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
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634
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Ellison C, Bachtrog D. Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila. PLoS Biol 2019; 17:e3000094. [PMID: 30742611 PMCID: PMC6417741 DOI: 10.1371/journal.pbio.3000094] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/14/2019] [Accepted: 01/18/2019] [Indexed: 11/18/2022] Open
Abstract
The repeatability or predictability of evolution is a central question in evolutionary biology and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage-compensation male-specific lethal (MSL) complex to study the mutational paths that have led to the acquisition of hundreds of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the D. melanica and D. robusta species groups by genome sequencing and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve hundreds of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element (TE) insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes and appears to be contingent on genomic properties of that species, such as simple repeat or TE density. This establishes the "genomic environment" as an important determinant in predicting the outcome of evolutionary adaptations.
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Affiliation(s)
- Christopher Ellison
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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635
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Le Luyer J, Auffret P, Quillien V, Leclerc N, Reisser C, Vidal-Dupiol J, Ky CL. Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera. BMC Genomics 2019; 20:111. [PMID: 30727965 PMCID: PMC6366105 DOI: 10.1186/s12864-019-5443-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/09/2019] [Indexed: 01/31/2023] Open
Abstract
Background Cultured pearls are unique gems produced by living organisms, mainly molluscs of the Pinctada genus, through the biomineralization properties of pearl sac tissue. Improvement of P. margaritifera pearl quality is one of the biggest challenges that Polynesian research has faced to date. To achieve this goal, a better understanding of the complex mechanisms related to nacre and pearl formation is essential and can now be approached through the use of massive parallel sequencing technologies. The aim of this study was to use RNA-seq to compare whole transcriptome expression of pearl sacs that had producing pearls with high and low quality. For this purpose, a comprehensive reference transcriptome of P. margaritifera was built based on multi-tissue sampling (mantle, gonad, whole animal), including different living stages (juvenile, adults) and phenotypes (colour morphotypes, sex). Results Strikingly, few genes were found to be up-regulated for high quality pearls (n = 16) compared to the up-regulated genes in low quality pearls (n = 246). Biomineralization genes up-regulated in low quality pearls were specific to prismatic and prism-nacre layers. Alternative splicing was further identified in several key biomineralization genes based on a recent P. margaritifera draft genome. Conclusion This study lifts the veil on the multi-level regulation of biomineralization genes associated with pearl quality determination. Electronic supplementary material The online version of this article (10.1186/s12864-019-5443-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Le Luyer
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - P Auffret
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - V Quillien
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - N Leclerc
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - C Reisser
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - J Vidal-Dupiol
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia.,Ifremer, UMR 5244 Interactions Hôtes-Pathogènes-Environnements, Université de Montpellier, Place Eugène Bataillon CC 80, 34095, Montpellier, France
| | - C-L Ky
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia.
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636
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Capture of a Hyena-Specific Retroviral Envelope Gene with Placental Expression Associated in Evolution with the Unique Emergence among Carnivorans of Hemochorial Placentation in Hyaenidae. J Virol 2019; 93:JVI.01811-18. [PMID: 30463979 DOI: 10.1128/jvi.01811-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/15/2018] [Indexed: 12/30/2022] Open
Abstract
Capture of retroviral envelope genes from endogenous retroviruses has played a role in the evolution of mammals, with evidence for the involvement of these genes in the formation of the maternofetal interface of the placenta. It has been shown that the diversity of captured genes is likely to be responsible for the diversity of placental structures, ranging from poorly invasive (epitheliochorial) to highly invasive (hemochorial), with an intermediate state (endotheliochorial) as found in carnivorans. The latter recapitulate part of this evolution, with the hyena being the sole carnivoran with a hemochorial placenta. In this study, we performed RNA sequencing on hyena placental transcripts and searched for endogenous retroviral envelope genes that have been captured specifically in the Hyaenidae clade and are not found in any other carnivoran. We identified an envelope gene that is expressed in the placenta at the level of the maternofetal interface, as evidenced by in situ hybridization/immunohistochemistry. The gene entry is coincidental with the emergence of the Hyaenidae clade 30 million years ago (Mya), being found at the same genomic locus in all 4 extant hyena species. Its coding sequence has further been maintained during all of Hyaenidae evolution. It is not found in any of the 30 other carnivorans-both Felidae and Canidae-that we screened. This envelope protein does not disclose any fusogenic activity in ex vivo assays, at variance with the syncytin-Car1 gene, which is found in all carnivorans, including the hyena, in which it is still present, transcriptionally active in the placenta, and fusogenic. Together, the present results illustrate the permanent renewal of placenta-specific genes by retroviral capture and de facto provide a candidate gene for the endotheliochorial to hemochorial transition of Hyaenidae among carnivorans.IMPORTANCE The placenta is the most diverse organ among mammals, due in part to stochastic capture of retroviral envelope genes. In carnivorans, capture of syncytin-Car1 took place 80 Mya. It is fusogenic, expressed at the syncytialized placental maternofetal interface, and conserved among all carnivorans, consistent with their shared endotheliochorial placenta. Hyenas are a remarkable exception, with a highly invasive hemochorial placenta, as found in humans, where disruption of maternal blood vessels results in maternal blood bathing the syncytial maternofetal interface. In this study, we identified a retroviral envelope gene capture and exaptation that took place about 30 Mya and is coincident with the emergence of the Hyaenidae, being conserved in all extant hyena species. It is expressed at the maternofetal interface in addition to the shared syncytin-Car1 gene. This new env gene, not present in any other carnivoran, is a likely candidate to be responsible for the specific structure of the hyena placenta.
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637
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The Histone Methyltransferase SETDB1 Controls T Helper Cell Lineage Integrity by Repressing Endogenous Retroviruses. Immunity 2019; 50:629-644.e8. [PMID: 30737147 DOI: 10.1016/j.immuni.2019.01.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 02/07/2023]
Abstract
Upon activation, naive CD4+ T cells differentiate into distinct T cell subsets via processes reliant on epigenetically regulated, lineage-specific developmental programs. Here, we examined the function of the histone methyltransferase SETDB1 in T helper (Th) cell differentiation. Setdb1-/- naive CD4+ T cells exhibited exacerbated Th1 priming, and when exposed to a Th1-instructive signal, Setdb1-/- Th2 cells crossed lineage boundaries and acquired a Th1 phenotype. SETDB1 did not directly control Th1 gene promoter activity but relied instead on deposition of the repressive H3K9me3 mark at a restricted and cell-type-specific set of endogenous retroviruses (ERVs) located in the vicinity of genes involved in immune processes. Refined bioinformatic analyses suggest that these retrotransposons regulate Th1 gene cis-regulatory elements or act as Th1 gene enhancers. Thus, H3K9me3 deposition by SETDB1 ensures Th cell lineage integrity by repressing a repertoire of ERVs that have been exapted into cis-regulatory modules to shape and control the Th1 gene network.
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638
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Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genet 2019; 15:e1007900. [PMID: 30753202 PMCID: PMC6372155 DOI: 10.1371/journal.pgen.1007900] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/16/2018] [Indexed: 11/30/2022] Open
Abstract
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
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Affiliation(s)
- Gabriel E. Rech
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - María Bogaerts-Márquez
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Maite G. Barrón
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Vivien Horváth
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Sandeep Venkataram
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Josefa González
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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639
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Attig J, Ule J. Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis. Bioessays 2019; 41:e1800132. [DOI: 10.1002/bies.201800132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/14/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jan Attig
- Dr. J. Attig, Prof. J. Ule; The Francis Crick Institute; 1 Midland Road London NW1 1AT UK
| | - Jernej Ule
- Dr. J. Attig, Prof. J. Ule; The Francis Crick Institute; 1 Midland Road London NW1 1AT UK
- Prof. J. Ule; Department of Molecular Neuroscience; UCL Institute of Neurology; Queen Square London WC1N 3BG UK
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640
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641
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Carlevaro-Fita J, Polidori T, Das M, Navarro C, Zoller TI, Johnson R. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome Res 2019. [PMID: 30587508 DOI: 10.1101/gr.229922.117.freely] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
The sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs), otherwise known as RIDLs (repeat insertion domains of lncRNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localization. By using global localization data from 10 human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution and evolutionarily conserved L2b, MIRb, and MIRc elements. This is observed in multiple cell types and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localization of lncRNAs.
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Affiliation(s)
- Joana Carlevaro-Fita
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Taisia Polidori
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Monalisa Das
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Carmen Navarro
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain
| | - Tatjana I Zoller
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Rory Johnson
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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642
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Broecker F, Moelling K. Evolution of Immune Systems From Viruses and Transposable Elements. Front Microbiol 2019; 10:51. [PMID: 30761103 PMCID: PMC6361761 DOI: 10.3389/fmicb.2019.00051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Virus-derived sequences and transposable elements constitute a substantial portion of many cellular genomes. Recent insights reveal the intimate evolutionary relationship between these sequences and various cellular immune pathways. At the most basic level, superinfection exclusion may be considered a prototypical virus-mediated immune system that has been described in both prokaryotes and eukaryotes. More complex immune mechanisms fully or partially derived from mobile genetic elements include CRISPR-Cas of prokaryotes and the RAG1/2 system of vertebrates, which provide immunological memory of foreign genetic elements and generate antibody and T cell receptor diversity, respectively. In this review, we summarize the current knowledge on the contribution of mobile genetic elements to the evolution of cellular immune pathways. A picture is emerging in which the various cellular immune systems originate from and are spread by viruses and transposable elements. Immune systems likely evolved from simple superinfection exclusion to highly complex defense strategies.
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Affiliation(s)
- Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
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643
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Abstract
Minority subpopulations within embryonic stem cell cultures display an expanded developmental potential similar to that of early embryo blastomeres or the early inner cell mass. The ability to isolate and culture totipotent cells capable of giving rise to the entire conceptus would enhance our capacity to study early embryo development, and might enable more efficient generation of chimeric animals for research and organ production for transplantation. Here we review the biological and molecular characterization of cultured cells with developmental potential similar to totipotent blastomeres, and assess recent progress toward the capture and stabilization of the totipotent state in vitro.
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644
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Vogel E, Santos D, Mingels L, Verdonckt TW, Broeck JV. RNA Interference in Insects: Protecting Beneficials and Controlling Pests. Front Physiol 2019; 9:1912. [PMID: 30687124 PMCID: PMC6336832 DOI: 10.3389/fphys.2018.01912] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/18/2018] [Indexed: 01/01/2023] Open
Abstract
Insects constitute the largest and most diverse group of animals on Earth with an equally diverse virome. The main antiviral immune system of these animals is the post-transcriptional gene-silencing mechanism known as RNA(i) interference. Furthermore, this process can be artificially triggered via delivery of gene-specific double-stranded RNA molecules, leading to specific endogenous gene silencing. This is called RNAi technology and has important applications in several fields. In this paper, we review RNAi mechanisms in insects as well as the potential of RNAi technology to contribute to species-specific insecticidal strategies. Regarding this aspect, we cover the range of strategies considered and investigated so far, as well as their limitations and the most promising approaches to overcome them. Additionally, we discuss patterns of viral infection, specifically persistent and acute insect viral infections. In the latter case, we focus on infections affecting economically relevant species. Within this scope, we review the use of insect-specific viruses as bio-insecticides. Last, we discuss RNAi-based strategies to protect beneficial insects from harmful viral infections and their potential practical application. As a whole, this manuscript stresses the impact of insect viruses and RNAi technology in human life, highlighting clear lines of investigation within an exciting and promising field of research.
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Affiliation(s)
- Elise Vogel
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Lina Mingels
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Thomas-Wolf Verdonckt
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Jozef Vanden Broeck
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
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645
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Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol 2019; 19:11. [PMID: 30626321 PMCID: PMC6327564 DOI: 10.1186/s12862-018-1324-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. RESULTS Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. CONCLUSION While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.
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Affiliation(s)
- Malte Petersen
- University of Bonn, Bonn, Germany
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt, 60325 Germany
| | - David Armisén
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Abderrahman Khila
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg (Brsg.), 79104 Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
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646
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Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat Commun 2019; 10:24. [PMID: 30604755 PMCID: PMC6318337 DOI: 10.1038/s41467-018-07974-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
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Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Ernandes Manfroi
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Ibaraki, Japan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Emilie Debladis
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
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647
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Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nat Commun 2019; 10:34. [PMID: 30604769 PMCID: PMC6318327 DOI: 10.1038/s41467-018-08006-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 01/18/2023] Open
Abstract
The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs are increasingly recognized for their important biological functions, they are a potential danger to genomic stability and are carefully regulated by the epigenetic system. However, the full complexity of this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that TEs are suppressed by heterochromatic marks like H3K9me3, and are also labelled by all major types of chromatin modification in complex patterns, including bivalent activatory and repressive marks. We identified 29 epigenetic modifiers that significantly deregulated at least one type of TE. The loss of Setdb1, Ncor2, Rnf2, Kat5, Prmt5, Uhrf1, and Rrp8 caused widespread changes in TE expression and chromatin accessibility. These effects were context-specific, with different chromatin modifiers regulating the expression and chromatin accessibility of specific subsets of TEs. Our work reveals the complex patterns of epigenetic regulation of TEs. Transposable elements (TEs) fulfill essential but poorly understood roles in genome organization and gene expression control. Here the authors show that the regulation of TEs occurs through overlapping epigenetic mechanisms that control the expression and chromatin signatures at TEs.
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648
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Vaschetto LM, Ortiz N. The Role of Sequence Duplication in Transcriptional Regulation and Genome Evolution. Curr Genomics 2019; 20:405-408. [PMID: 32476997 PMCID: PMC7235390 DOI: 10.2174/1389202920666190320140721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 12/26/2022] Open
Abstract
Sequence duplication is nowadays recognized as an important mechanism that underlies the evolution of eukaryote genomes, being indeed one of the most powerful strategies for the generation of adaptive diversity by modulating transcriptional activity. The evolutionary novelties simultaneously associated with sequence duplication and differential gene expression can be collectively referred to as duplication-mediated transcriptional regulation. In the last years, evidence has emerged supporting the idea that sequence duplication and functionalization represent important evolutionary strategies acting at the genome level, and both coding and non-coding sequences have been found to be targets of such events. Moreover, it has been proposed that deleterious effects of sequence duplication might be potentially silenced by endogenous cell machinery (i.e., RNA interference, epigenetic repressive marks, etc). Along these lines, our aim is to highlight the role of sequence duplication on transcriptional activity and the importance of both in genome evolution.
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Affiliation(s)
- Luis M Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, (FCEFyN, UNC), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina
| | - Natalia Ortiz
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina.,Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, UNC, Córdoba, Argentina
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649
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Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B. Computational aspects underlying genome to phenome analysis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:182-198. [PMID: 30500991 PMCID: PMC6849790 DOI: 10.1111/tpj.14179] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.
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Affiliation(s)
- Anthony M. Bolger
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Hendrik Poorter
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Kathryn Dumschott
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Marie E. Bolger
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasCampus de Teatinos29071MálagaSpain
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Björn Usadel
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
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650
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Pirogov SA, Maksimenko OG, Georgiev PG. Transposable Elements in the Evolution of Gene Regulatory Networks. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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