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Karakülah G, Suner A. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics 2017; 109:336-340. [DOI: 10.1016/j.ygeno.2017.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/29/2017] [Accepted: 05/31/2017] [Indexed: 02/01/2023]
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152
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Dong Y, Huang Z, Kuang Q, Wen Z, Liu Z, Li Y, Yang Y, Li M. Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes. BMC Genomics 2017; 18:666. [PMID: 28851270 PMCID: PMC5576108 DOI: 10.1186/s12864-017-4078-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes. In addition, TEs can influence the expression of nearby genes. The temporal and spatial influences of TEs remain unclear yet. RESULTS To evaluate the TEs transcription patterns, we profiled their transcript levels in 11 organs for both sexes across four developmental stages of rat. The results show that most short interspersed elements (SINEs) are commonly expressed in all conditions, which are also the major TE types with commonly expression patterns. In contrast, long terminal repeats (LTRs) are more likely to exhibit specific expression patterns. The expression tendency of TEs and genes are similar in most cases. For example, few specific genes and TEs are in the liver, muscle and heart. However, TEs perform superior over genes on classing organ, which imply their higher organ specificity than genes. By associating the TEs with the closest genes in genome, we find their expression levels are correlated, independent of their distance in some cases. CONCLUSIONS TEs sex-dependently associate with nearest genes. A gene would be associated with more than one TE. Our works can help to functionally annotate the genome and further understand the role of TEs in gene regulation.
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Affiliation(s)
- Yongcheng Dong
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Ziyan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qifan Kuang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Zhibin Liu
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yi Yang
- College of Life Science, Sichuan University, Chengdu, 610064, China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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153
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Vicient CM, Casacuberta JM. Impact of transposable elements on polyploid plant genomes. ANNALS OF BOTANY 2017; 120:195-207. [PMID: 28854566 PMCID: PMC5737689 DOI: 10.1093/aob/mcx078] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. SCOPE This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization. CONCLUSIONS TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes.
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Affiliation(s)
- Carlos M. Vicient
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
- For correspondence. E-mail
| | - Josep M. Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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154
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Lee YCG, Karpen GH. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. eLife 2017; 6. [PMID: 28695823 PMCID: PMC5505702 DOI: 10.7554/elife.25762] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are widespread genomic parasites, and their evolution has remained a critical question in evolutionary genomics. Here, we study the relatively unexplored epigenetic impacts of TEs and provide the first genome-wide quantification of such effects in D. melanogaster and D. simulans. Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs. Interestingly, the lower TE content in D. simulans compared to D. melanogaster correlates with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. Our study demonstrates that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the evolution of TEs both within and between species. DOI:http://dx.doi.org/10.7554/eLife.25762.001 The DNA inside an organism encodes all the instructions needed for the organism to develop and work properly. Organisms carefully organize and maintain their DNA (collectively known as the genome) so that the genetic information remains intact and the cell can understand the instructions. However, there are some pieces of DNA that are capable of moving around the genome. For example, pieces known as transposable elements can make new copies of themselves and jump into new locations in the genome. Most transposons do not appear to have any important roles, and in fact they are usually harmful to organisms. Despite this, transposons are present in the genomes of almost all species. The number of transposons in a genome varies greatly between individuals and species, but it is not clear why this is the case. Organisms have evolved ways to limit the damage caused by transposons. For example, many cells package regions of DNA containing transposons into a tightly packed structure known as heterochromatin. However, this type of DNA packaging sometimes spreads to neighboring sections of DNA. This is a problem because cells are not usually able to read the information contained within heterochromatin. This means that transposons can prevent some instructions from being produced when they should be. Lee and Karpen used fruit flies to investigate to what extent transposons harm organisms by changing the way DNA is packaged, and whether this influences how transposons evolve. The experiments show that that more than half of the transposons in fruit flies cause neighboring sections of DNA to be packaged into heterochromatin. This can negatively impact up to 20% of genes in the genome. As a result, transposons that have harmful effects on DNA packaging are more likely to be lost from the fly population during evolution than transposons that do not have harmful effects. Fruit fly species containing transposons that tend to package more neighboring sections of DNA into heterochromatin generally have fewer transposons than genomes containing less harmful transposons. The findings of Lee and Karpen provide new insight as to why the numbers of transposons vary among organisms. The next challenge is to find out whether transposons that alter how DNA is packaged are also common in primates and other animals. DOI:http://dx.doi.org/10.7554/eLife.25762.002
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Affiliation(s)
- Yuh Chwen G Lee
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
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155
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156
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Xu S, Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, Baldwin IT. Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proc Natl Acad Sci U S A 2017; 114:6133-6138. [PMID: 28536194 PMCID: PMC5468653 DOI: 10.1073/pnas.1700073114] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis. The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinamide adenine dinucleotide (NAD) pathways. In contrast to the duplication of the polyamine pathway that is shared among several solanaceous genera producing polyamine-derived tropane alkaloids, we found that lineage-specific duplications within the NAD pathway and the evolution of root-specific expression of the duplicated Solanaceae-specific ethylene response factor that activates the expression of all nicotine biosynthetic genes resulted in the innovative and efficient production of nicotine in the genus Nicotiana Transcription factor binding motifs derived from TEs may have contributed to the coexpression of nicotine biosynthetic pathway genes and coordinated the metabolic flux. Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.
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Affiliation(s)
- Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Thomas Brockmöller
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Aura Navarro-Quezada
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Klaus Gase
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Zhihao Ling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Christoph Kreitzer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Mario Stanke
- Institute for Mathematics and Computer Science, Universität Greifswald, 17489 Greifswald, Germany
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Eric Lyons
- School of Plant Sciences, BIO5 Institute, CyVerse, University of Arizona, Tucson, AZ 85721
| | - Priyanka Pandey
- National Institute of Biomedical Genomics, Kalyani, 741251 West Bengal, India
| | - Shree P Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, 700064 West Bengal, India
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany;
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
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157
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Abstract
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.
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158
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Wang D, Qu Z, Yang L, Zhang Q, Liu ZH, Do T, Adelson DL, Wang ZY, Searle I, Zhu JK. Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:133-146. [PMID: 28106309 PMCID: PMC5514416 DOI: 10.1111/tpj.13481] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/01/2017] [Accepted: 01/05/2017] [Indexed: 05/20/2023]
Abstract
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these noncoding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA-sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. We validated the expression of these TE-lincRNAs by strand-specific RT-PCR and also demonstrated tissue-specific transcription and stress-induced TE-lincRNAs either after salt, abscisic acid (ABA) or cold treatments. For Arabidopsis TE-lincRNA11195, mutants had reduced sensitivity to ABA as demonstrated by longer roots and higher shoot biomass when compared to wild-type. Finally, by altering the chromatin state in the Arabidopsis chromatin remodelling mutant ddm1, unique lincRNAs including TE-lincRNAs were generated from the preceding untranscribed regions and interestingly inherited in a wild-type background in subsequent generations. Our findings not only demonstrate that TE-associated lincRNAs play important roles in plant abiotic stress responses but lincRNAs and TE-lincRNAs might act as an adaptive reservoir in eukaryotes.
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Affiliation(s)
- Dong Wang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhipeng Qu
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingzhu Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhi-Hong Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Trung Do
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - David L. Adelson
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Zhen-Yu Wang
- Hainan Key laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, China
| | - Iain Searle
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- For correspondence: or
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- For correspondence: or
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159
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Song X, Cao X. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:111-118. [PMID: 28273484 DOI: 10.1016/j.pbi.2017.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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160
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Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet 2017; 18:292-308. [PMID: 28286338 DOI: 10.1038/nrg.2017.7] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposable elements and retroviruses are found in most genomes, can be pathogenic and are widely used as gene-delivery and functional genomics tools. Exploring whether these genetic elements target specific genomic sites for integration and how this preference is achieved is crucial to our understanding of genome evolution, somatic genome plasticity in cancer and ageing, host-parasite interactions and genome engineering applications. High-throughput profiling of integration sites by next-generation sequencing, combined with large-scale genomic data mining and cellular or biochemical approaches, has revealed that the insertions are usually non-random. The DNA sequence, chromatin and nuclear context, and cellular proteins cooperate in guiding integration in eukaryotic genomes, leading to a remarkable diversity of insertion site distribution and evolutionary strategies.
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161
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Translational repression by a miniature inverted-repeat transposable element in the 3' untranslated region. Nat Commun 2017; 8:14651. [PMID: 28256530 PMCID: PMC5338036 DOI: 10.1038/ncomms14651] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/18/2017] [Indexed: 12/18/2022] Open
Abstract
Transposable elements constitute a substantial portion of eukaryotic genomes and contribute to genomic variation, function, and evolution. Miniature inverted-repeat transposable elements (MITEs), as DNA transposons, are widely distributed in plant and animal genomes. Previous studies have suggested that retrotransposons act as translational regulators; however, it remains unknown how host mRNAs are influenced by DNA transposons. Here we report a translational repression mechanism mediated by a stowaway-like MITE (sMITE) embedded in the 3'-untranslated region (3'-UTR) of Ghd2, a member of the CCT (CONSTANS [CO], CO-LIKE and TIMING OF CAB1) gene family in rice. Ghd2 regulates important agronomic traits, including grain number, plant height and heading date. Interestingly, the translational repression of Ghd2 by the sMITE mainly relies on Dicer-like 3a (OsDCL3a). Furthermore, other MITEs in the 3'-UTRs of different rice genes exhibit a similar effect on translational repression, thus suggesting that MITEs may exert a general regulatory function at the translational level.
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162
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Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 2017; 13:e1006630. [PMID: 28212378 PMCID: PMC5338827 DOI: 10.1371/journal.pgen.1006630] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
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163
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Zhou MB, Hu H, Miskey C, Lazarow K, Ivics Z, Kunze R, Yang G, Izsvák Z, Tang DQ. Transposition of the bamboo Mariner-like element Ppmar1 in yeast. Mol Phylogenet Evol 2017; 109:367-374. [PMID: 28189615 DOI: 10.1016/j.ympev.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
The moso bamboo genome contains the two structurally intact and thus potentially functional mariner-like elements Ppmar1 and Ppmar2. Both elements contain perfect terminal inverted repeats (TIRs) and a full-length intact transposase gene. Here we investigated whether Ppmar1 is functional in yeast (Saccharomyces cerevisiae). We have designed a two-component system consisting of a transposase expression cassette and a non-autonomous transposon on two separate plasmids. We demonstrate that the Ppmar1 transposase Pptpase1 catalyses excision of the non-autonomous Ppmar1NA element from the plasmid and reintegration at TA dinucleotide sequences in the yeast chromosomes. In addition, we generated 14 hyperactive Ppmar1 transposase variants by systematic single amino acid substitutions. The most active transposase variant, S171A, induces 10-fold more frequent Ppmar1NA excisions in yeast than the wild type transposase. The Ppmar1 transposon is a promising tool for insertion mutagenesis in moso bamboo and may be used in other plants as an alternative to the established transposon tagging systems.
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Affiliation(s)
- Ming-Bing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Hui Hu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Csaba Miskey
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Katina Lazarow
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Guojun Yang
- Department of Biology, University of Toronto, Mississauga, ON, Canada
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany.
| | - Ding-Qin Tang
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China.
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164
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Kalinka A, Achrem M, Poter P. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L. PeerJ 2017; 5:e2889. [PMID: 28149679 PMCID: PMC5267573 DOI: 10.7717/peerj.2889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/08/2016] [Indexed: 01/05/2023] Open
Abstract
Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.
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Affiliation(s)
- Anna Kalinka
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Magdalena Achrem
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Paulina Poter
- Department of Cell Biology, Faculty of Biology, University of Szczecin , Szczecin , Poland
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165
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Li S, Xia Q, Wang F, Yu X, Ma J, Kou H, Lin X, Gao X, Liu B. Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:363. [PMID: 28377781 PMCID: PMC5359294 DOI: 10.3389/fpls.2017.00363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/01/2017] [Indexed: 05/05/2023]
Abstract
DNA methylation is an integral component of the epigenetic code in most higher eukaryotes. Exploring the extent to which DNA methylation can be altered under a specific condition and its heritability is important for elucidating the biological functions of this epigenetic modification. Here, we conducted MSAP analysis of rice plants with altered phenotypes subsequent to a low-dose Nd3+YAG laser irradiation. We found that all four methylation patterns at the 5'-CCGG sites that are analyzable by MSAP showed substantial changes in the immediately treated M0 plants. Interestingly, the frequencies of hypo- and hypermethylation were of similar extents, which largely offset each other and render the total methylation levels unchanged. Further analysis revealed that the altered methylation patterns were meiotically heritable to at least the M2 generation but accompanied with further changes in each generation. The methylation changes and their heritability of the metastable epigenetic state were verified by bisulfite sequencing of portion of the retrotranspon, Tos17, an established locus for assessing DNA methylation liability in rice. Real-time PCR assay indicated that the expression of various methylation-related chromatin genes was perturbed, and a Pearson correlation analysis showed that many of these genes, especially two AGOs (AGO4-1 and AGO4-2), were significantly correlated with the methylation pattern alterations. In addition, excisions of a MITE transposon, mPing, occurred rampantly in the laser irradiated plants and their progenies. Together, our results indicate that heritable DNA methylation changes can be readily induced by low-dose laser irradiation, and which can be accompanied by transpostional activation of transposable elements.
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Affiliation(s)
- Siyuan Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal UniversityChangchun, China
- School of Life Sciences, Jilin Agricultural UniversityChangchun, China
| | - Qiong Xia
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal UniversityChangchun, China
| | - Fang Wang
- College of Oceanology & Food Science, Quanzhou Normal UniversityQuanzhou, China
- *Correspondence: Fang Wang
| | - Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal UniversityChangchun, China
| | - Jian Ma
- College of Agronomy, Jilin Agricultural UniversityChangchun, China
| | - Hongping Kou
- College of Agronomy, Jilin Agricultural UniversityChangchun, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural SciencesChangchun, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal UniversityChangchun, China
- Xiang Gao
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal UniversityChangchun, China
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166
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Epigenetic Control of Gene Expression in Maize. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 328:25-48. [DOI: 10.1016/bs.ircmb.2016.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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167
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Han MJ, Zhou QZ, Zhang HH, Tong X, Lu C, Zhang Z, Dai F. iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw148. [PMID: 28025339 PMCID: PMC5199201 DOI: 10.1093/database/baw148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 01/23/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects. Database URL: http://gene.cqu.edu.cn/iMITEdb/
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Affiliation(s)
- Min-Jin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
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168
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169
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Jiang SH, Li GY, Xiong XM. Novel miniature inverted-repeat transposable elements derived from novel CACTA transposons were discovered in the genome of the ant Camponotus floridanus. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0464-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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170
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Patra B, Kon Y, Yadav G, Sevold AW, Frumkin JP, Vallabhajosyula RR, Hintze A, Østman B, Schossau J, Bhan A, Marzolf B, Tamashiro JK, Kaur A, Baliga NS, Grayhack EJ, Adami C, Galas DJ, Raval A, Phizicky EM, Ray A. A genome wide dosage suppressor network reveals genomic robustness. Nucleic Acids Res 2016; 45:255-270. [PMID: 27899637 PMCID: PMC5224485 DOI: 10.1093/nar/gkw1148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/17/2016] [Accepted: 11/07/2016] [Indexed: 01/17/2023] Open
Abstract
Genomic robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of genomic robustness in budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs and higher diversity of functions among the co-suppressors than previously observed. Dosage suppression of essential genes encoding RNA polymerase subunits and chromosome cohesion complex suggests a surprising degree of functional plasticity of macromolecular complexes, and the existence of numerous degenerate pathways for circumventing the effects of potentially lethal mutations. These results imply that organisms and cancer are likely able to exploit the genomic robustness properties, due the persistence of cryptic gene and pathway functions, to generate variation and adapt to selective pressures.
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Affiliation(s)
- Biranchi Patra
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - Yoshiko Kon
- Department of Biochemistry, University of Rochester School of Medicine, Rochester, NY 14627, USA
| | - Gitanjali Yadav
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.,National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anthony W Sevold
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - Jesse P Frumkin
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | | | - Arend Hintze
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - Bjørn Østman
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - Jory Schossau
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - Ashish Bhan
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - Bruz Marzolf
- Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
| | | | - Amardeep Kaur
- Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
| | - Nitin S Baliga
- Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
| | - Elizabeth J Grayhack
- Department of Biochemistry, University of Rochester School of Medicine, Rochester, NY 14627, USA
| | - Christoph Adami
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
| | - David J Galas
- Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
| | - Alpan Raval
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.,Institute of Mathematical Sciences, Claremont Graduate University, Claremont, CA 91711, USA
| | - Eric M Phizicky
- Department of Biochemistry, University of Rochester School of Medicine, Rochester, NY 14627, USA
| | - Animesh Ray
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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171
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Chuong EB, Elde NC, Feschotte C. Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet 2016; 18:71-86. [PMID: 27867194 DOI: 10.1038/nrg.2016.139] [Citation(s) in RCA: 762] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs. Many recent studies reinvigorate the idea that these elements are pervasively co-opted for the regulation of host genes. We argue that the inherent genetic properties of TEs and the conflicting relationships with their hosts facilitate their recruitment for regulatory functions in diverse genomes. We review recent findings supporting the long-standing hypothesis that the waves of TE invasions endured by organisms for eons have catalysed the evolution of gene-regulatory networks. We also discuss the challenges of dissecting and interpreting the phenotypic effect of regulatory activities encoded by TEs in health and disease.
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Affiliation(s)
- Edward B Chuong
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84103, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84103, USA
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84103, USA
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172
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Zhou W, Brockmöller T, Ling Z, Omdahl A, Baldwin IT, Xu S. Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana. eLife 2016; 5:e19531. [PMID: 27813478 PMCID: PMC5115867 DOI: 10.7554/elife.19531] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023] Open
Abstract
Herbivore-induced defenses are widespread, rapidly evolving and relevant for plant fitness. Such induced defenses are often mediated by early defense signaling (EDS) rapidly activated by the perception of herbivore associated elicitors (HAE) that includes transient accumulations of jasmonic acid (JA). Analyzing 60 HAE-induced leaf transcriptomes from closely-related Nicotiana species revealed a key gene co-expression network (M4 module) which is co-activated with the HAE-induced JA accumulations but is elicited independently of JA, as revealed in plants silenced in JA signaling. Functional annotations of the M4 module were consistent with roles in EDS and a newly identified hub gene of the M4 module (NaLRRK1) mediates a negative feedback loop with JA signaling. Phylogenomic analysis revealed preferential gene retention after genome-wide duplications shaped the evolution of HAE-induced EDS in Nicotiana. These results highlight the importance of genome-wide duplications in the evolution of adaptive traits in plants.
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Affiliation(s)
- Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Thomas Brockmöller
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Zhihao Ling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ashton Omdahl
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Brigham Young University, Provo, United States
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
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173
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Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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174
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Negi P, Rai AN, Suprasanna P. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1448. [PMID: 27777577 PMCID: PMC5056178 DOI: 10.3389/fpls.2016.01448] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/12/2016] [Indexed: 05/02/2023]
Abstract
The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
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Affiliation(s)
| | | | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreTrombay, India
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175
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Zhou M, Tao G, Pi P, Zhu Y, Bai Y, Meng X. Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla). PLANTA 2016; 244:775-787. [PMID: 27160169 DOI: 10.1007/s00425-016-2544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/01/2016] [Indexed: 06/05/2023]
Abstract
Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.
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Affiliation(s)
- Mingbing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
| | - Guiyun Tao
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Peiyao Pi
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Yihang Zhu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Youhuang Bai
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Xianwen Meng
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
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176
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Helitron-like transposons contributed to the mating system transition from out-crossing to self-fertilizing in polyploid Brassica napus L. Sci Rep 2016; 6:33785. [PMID: 27650318 PMCID: PMC5030654 DOI: 10.1038/srep33785] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/01/2016] [Indexed: 12/19/2022] Open
Abstract
The mating system transition in polyploid Brassica napus (AACC) from out-crossing to selfing is a typical trait to differentiate it from their diploid progenitors. Elucidating the mechanism of mating system transition has profound consequences for understanding the speciation and evolution in B. napus. Functional complementation experiment has shown that the insertion of 3.6 kb into the promoter of self-incompatibility male determining gene, BnSP11-1 leads to its loss of function in B. napus. The inserted fragment was found to be a non-autonomous Helitron transposon. Further analysis showed that the inserted 3.6 kb non-autonomous Helitron transposon was widely distributed in B. napus accessions which contain the S haplotype BnS-1. Through promoter deletion analysis, an enhancer and a putative cis-regulatory element (TTCTA) that were required for spatio-temporal specific expression of BnSP11-1 were identified, and both might be disrupted by the insertion of Helitron transposon. We suggested that the insertion of Helitron transposons in the promoter of BnSP11-1 gene had altered the mating system and might facilitated the speciation of B. napus. Our findings have profound consequences for understanding the self-compatibility in B. napus as well as for the trait variations during evolutionary process of plant polyploidization.
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177
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Abstract
Structurally and functionally diverged sex chromosomes have evolved in many animals as well as in some plants. Sex chromosomes represent a specific genomic region(s) with locally suppressed recombination. As a consequence, repetitive sequences involving transposable elements, tandem repeats (satellites and microsatellites), and organellar DNA accumulate on the Y (W) chromosomes. In this paper, we review the main types of repetitive elements, their gathering on the Y chromosome, and discuss new findings showing that not only accumulation of various repeats in non-recombining regions but also opposite processes form Y chromosome. The aim of this review is also to discuss the mechanisms of repetitive DNA spread involving (retro) transposition, DNA polymerase slippage or unequal crossing-over, as well as modes of repeat removal by ectopic recombination. The intensity of these processes differs in non-recombining region(s) of sex chromosomes when compared to the recombining parts of genome. We also speculate about the relationship between heterochromatinization and the formation of heteromorphic sex chromosomes.
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178
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Bordiya Y, Zheng Y, Nam JC, Bonnard AC, Choi HW, Lee BK, Kim J, Klessig DF, Fei Z, Kang HG. Pathogen Infection and MORC Proteins Affect Chromatin Accessibility of Transposable Elements and Expression of Their Proximal Genes in Arabidopsis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:674-687. [PMID: 27482822 DOI: 10.1094/mpmi-01-16-0023-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To assess the role of MORC1 in epigenetics in relation to plant immunity, genome-wide chromatin accessibility was compared between mock- or Pseudomonas syringae pv. tomato-inoculated wild type (WT) Arabidopsis, the morc1/2 double mutant, or both. Most changes in chromatin accessibility, scored by DNase I hypersensitive sites (DHSs), were located in the promoters of genes and transposable elements (TEs). Comparisons between morc1/2 and WT receiving the same treatment revealed differential DHSs (dDHSs) predominantly associated with heterochromatic TEs. By contrast, comparisons between mock- and P. syringae pv. tomato-inoculated plants from the same genotype showed dDHSs associated with biotic and abiotic stress-related genes; a smaller but significant population was in TEs. Moreover, many defense genes, including PR-1, PR-2, and PR-5, were proximal to P. syringae pv. tomato-induced, TE-associated dDHSs. A random subset of these defense genes showed moderately delayed or reduced expression or both in P. syringae pv. tomato-infected morc1/2 as compared with WT. MORC1 was physically bound to chromatin in a P. syringae pv. tomato infection-responsive manner at sites dispersed throughout the genome. Notably, silencing of TE-associated dDHSs proximal to these infection-induced, MORC1-interacting sites led to significant suppression of P. syringae pv. tomato-induced transcription of adjacent defense genes, including PR-1. These results provide evidence that MORC1 is associated with TEs and suggest that a subset of these TEs may help regulate their proximal defense genes.
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Affiliation(s)
- Yogendra Bordiya
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
| | - Yi Zheng
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
| | - Ji-Chul Nam
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
| | - April C Bonnard
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
| | - Hyong Woo Choi
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
| | - Bum-Kyu Lee
- 3 Department of Molecular Biosciences, The University of Texas at Austin, U.S.A.; and
| | - Jonghwan Kim
- 3 Department of Molecular Biosciences, The University of Texas at Austin, U.S.A.; and
| | - Daniel F Klessig
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
| | - Zhangjun Fei
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
- 4 USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY, U.S.A
| | - Hong-Gu Kang
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
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179
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Wei B, Liu H, Liu X, Xiao Q, Wang Y, Zhang J, Hu Y, Liu Y, Yu G, Huang Y. Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. BMC Genomics 2016; 17:536. [PMID: 27485608 PMCID: PMC4971691 DOI: 10.1186/s12864-016-2847-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 06/20/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Transposons (transposable elements or TEs) are DNA sequences that can change their position within the genome. A large number of TEs have been identified in reference genome of each crop(named accumulated TEs), which are the important part of genome. However, whether there existed TEs with different insert positions in resequenced crop accession genomes from those of reference genome (named non-reference transposable elements, non-ref TEs), and what the characteristics (such as the number, type and distribution) are. To identify and characterize crop non-ref TEs, we analyzed non-ref TEs in more than 125 accessions from rice (Oryza sativa), maize (Zea mays) and sorghum (Sorghum bicolor) using resequenced data with paired-end mapping methods. RESULTS We identified 13,066, 23,866 and 35,679 non-ref TEs in rice, maize and sorghum, respectively. Genome-wide characterization analysis shows that most of non-ref TEs were unique and non-ref TE classes shows different among rice, maize and sorghum. We found that non-ref TEs have a strong positive correlation with gene number and have a bias toward insertion near genes, but with a preference for avoiding coding regions in maize and sorghum. The genes affected by non-ref TE insertion were functionally enriched for stress response mechanisms in all three crops. CONCLUSIONS These observations suggest that transposon insertion is not a random event and it makes genomic diversity, which may affect the intraspecific adaption and evolution of crops.
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Affiliation(s)
- Bin Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xin Liu
- Beijing Genome Institute and the Key Laboratory of Genomics of the Minister of Agriculture, Shenzhen, 518083, China
| | - Qianlin Xiao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongbin Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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180
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Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J, Weigel D, Gutierrez-Marcos J. Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. eLife 2016; 5:13546. [PMID: 27242129 PMCID: PMC4887212 DOI: 10.7554/elife.13546] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal 'short-term stress memory' with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.
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Affiliation(s)
- Anjar Wibowo
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Gianpiero Marconi
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.,Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
| | - Julius Durr
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jonathan Price
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jorg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ranjith Papareddy
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Hadi Putra
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jorge Kageyama
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jorg Becker
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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181
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Hirsch CD, Springer NM. Transposable element influences on gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:157-165. [PMID: 27235540 DOI: 10.1016/j.bbagrm.2016.05.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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182
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Wang L, Peng Q, Zhao J, Ren F, Zhou H, Wang W, Liao L, Owiti A, Jiang Q, Han Y. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation. PLANT MOLECULAR BIOLOGY 2016; 91:179-91. [PMID: 26941188 DOI: 10.1007/s11103-016-0454-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Jianbo Zhao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Fei Ren
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Albert Owiti
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Quan Jiang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China.
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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183
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Rey O, Danchin E, Mirouze M, Loot C, Blanchet S. Adaptation to Global Change: A Transposable Element-Epigenetics Perspective. Trends Ecol Evol 2016; 31:514-526. [PMID: 27080578 DOI: 10.1016/j.tree.2016.03.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/21/2022]
Abstract
Understanding how organisms cope with global change is a major scientific challenge. The molecular pathways underlying rapid adaptive phenotypic responses to global change remain poorly understood. Here, we highlight the relevance of two environment-sensitive molecular elements: transposable elements (TEs) and epigenetic components (ECs). We first outline the sensitivity of these elements to global change stressors and review how they interact with each other. We then propose an integrative molecular engine coupling TEs and ECs and allowing organisms to fine-tune phenotypes in a real-time fashion, adjust the production of phenotypic and genetic variation, and produce heritable phenotypes with different levels of transmission fidelity. We finally discuss the implications of this molecular engine in the context of global change.
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Affiliation(s)
- Olivier Rey
- CNRS, UPS, Station d'Écologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France; Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Etienne Danchin
- CNRS, UPS, ENFA, Évolution & Diversité Biologique (EDB) UMR 5174, 118 Route de Narbonne, 31062 Toulouse, Cedex 9, France; Université Paul Sabatier, Évolution & Diversité Biologique (EDB), 31062 Toulouse, Cedex 9, France
| | - Marie Mirouze
- Institut de Recherche pour le Développement, UMR232 DIADE Diversité Adaptation et Développement des Plantes, Laboratoire Génome et Développement des Plantes, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Céline Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France; CNRS UMR3525, Paris, France
| | - Simon Blanchet
- CNRS, UPS, Station d'Écologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France; CNRS, UPS, ENFA, Évolution & Diversité Biologique (EDB) UMR 5174, 118 Route de Narbonne, 31062 Toulouse, Cedex 9, France.
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184
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A Stress-Activated Transposon in Arabidopsis Induces Transgenerational Abscisic Acid Insensitivity. Sci Rep 2016; 6:23181. [PMID: 26976262 PMCID: PMC4791638 DOI: 10.1038/srep23181] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/25/2016] [Indexed: 01/05/2023] Open
Abstract
Transposable elements (TEs), or transposons, play an important role in adaptation. TE insertion can affect host gene function and provides a mechanism for rapid increases in genetic diversity, particularly because many TEs respond to environmental stress. In the current study, we show that the transposition of a heat-activated retrotransposon, ONSEN, generated a mutation in an abscisic acid (ABA) responsive gene, resulting in an ABA-insensitive phenotype in Arabidopsis, suggesting stress tolerance. Our results provide direct evidence that a transposon activated by environmental stress could alter the genome in a potentially positive manner. Furthermore, the ABA-insensitive phenotype was inherited when the transcription was disrupted by an ONSEN insertion, whereas ABA sensitivity was recovered when the effects of ONSEN were masked by IBM2. These results suggest that epigenetic mechanisms in host plants typically buffered the effect of a new insertion, but could selectively “turn on” TEs when stressed.
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185
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Cao C, Xu J, Zheng G, Zhu XG. Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis. BMC Genomics 2016; 17:201. [PMID: 26955946 PMCID: PMC4782515 DOI: 10.1186/s12864-016-2519-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 02/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background C4 photosynthesis evolved from C3 photosynthesis and has higher light, water, and nitrogen use efficiencies. Several C4 photosynthesis genes show cell-specific expression patterns, which are required for these high resource-use efficiencies. However, the mechanisms underlying the evolution of cis-regulatory elements that control these cell-specific expression patterns remain elusive. Results In the present study, we tested the hypothesis that the cis-regulatory motifs related to C4 photosynthesis genes were recruited from non-photosynthetic genes and further examined potential mechanisms facilitating this recruitment. We examined 65 predicted bundle sheath cell-specific motifs, 17 experimentally validated cell-specific cis-regulatory elements, and 1,034 motifs derived from gene regulatory networks. Approximately 7, 5, and 1,000 of these three categories of motifs, respectively, were apparently recruited during the evolution of C4 photosynthesis. In addition, we checked 1) the distance between the acceptors and the donors of potentially recruited motifs in a chromosome, and 2) whether the potentially recruited motifs reside within the overlapping region of transposable elements and the promoter of donor genes. The results showed that 7, 4, and 658 of the potentially recruited motifs might have moved via the transposable elements. Furthermore, the potentially recruited motifs showed higher binding affinity to transcription factors compared to randomly generated sequences of the same length as the motifs. Conclusions This study provides molecular evidence supporting the hypothesis that transposon-driven recruitment of pre-existing cis-regulatory elements from non-photosynthetic genes into photosynthetic genes plays an important role during C4 evolution. The findings of the present study coincide with the observed repetitive emergence of C4 during evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2519-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chensi Cao
- CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Room 102, Physiology Building, 320 Yueyang Road, Shanghai, 200031, China.
| | - Jiajia Xu
- CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Room 102, Physiology Building, 320 Yueyang Road, Shanghai, 200031, China.
| | - Guangyong Zheng
- CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Room 102, Physiology Building, 320 Yueyang Road, Shanghai, 200031, China.
| | - Xin-Guang Zhu
- CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Room 102, Physiology Building, 320 Yueyang Road, Shanghai, 200031, China.
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186
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Crisp PA, Ganguly D, Eichten SR, Borevitz JO, Pogson BJ. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics. SCIENCE ADVANCES 2016; 2:e1501340. [PMID: 26989783 PMCID: PMC4788475 DOI: 10.1126/sciadv.1501340] [Citation(s) in RCA: 295] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/08/2015] [Indexed: 05/18/2023]
Abstract
Plants grow in dynamic environments where they can be exposed to a multitude of stressful factors, all of which affect their development, yield, and, ultimately, reproductive success. Plants are adept at rapidly acclimating to stressful conditions and are able to further fortify their defenses by retaining memories of stress to enable stronger or more rapid responses should an environmental perturbation recur. Indeed, one mechanism that is often evoked regarding environmental memories is epigenetics. Yet, there are relatively few examples of such memories; neither is there a clear understanding of their duration, considering the plethora of stresses in nature. We propose that this field would benefit from investigations into the processes and mechanisms enabling recovery from stress. An understanding of stress recovery could provide fresh insights into when, how, and why environmental memories are created and regulated. Stress memories may be maladaptive, hindering recovery and affecting development and potential yield. In some circumstances, it may be advantageous for plants to learn to forget. Accordingly, the recovery process entails a balancing act between resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting the epigenome and transcriptome and in altering memory. Exploration of this emerging area of research is becoming ever more tractable with advances in genomics, phenomics, and high-throughput sequencing methodology that will enable unprecedented profiling of high-resolution stress recovery time series experiments and sampling of large natural populations.
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187
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Gao D, Li Y, Kim KD, Abernathy B, Jackson SA. Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes. Genome Biol 2016; 17:7. [PMID: 26781660 PMCID: PMC4717578 DOI: 10.1186/s13059-015-0867-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/29/2015] [Indexed: 12/05/2022] Open
Abstract
Background Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood. Results Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in Oryza sativa. Conclusions We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Yupeng Li
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
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188
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Wei L, Cao X. The effect of transposable elements on phenotypic variation: insights from plants to humans. SCIENCE CHINA-LIFE SCIENCES 2016; 59:24-37. [PMID: 26753674 DOI: 10.1007/s11427-015-4993-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/16/2015] [Indexed: 11/25/2022]
Abstract
Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection.
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Affiliation(s)
- Liya Wei
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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189
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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190
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Pereira A. Plant Abiotic Stress Challenges from the Changing Environment. FRONTIERS IN PLANT SCIENCE 2016; 7:1123. [PMID: 27512403 PMCID: PMC4962010 DOI: 10.3389/fpls.2016.01123] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 05/04/2023]
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191
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Song Q, Guan X, Chen ZJ. Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton. PLoS Genet 2015; 11:e1005724. [PMID: 26710171 PMCID: PMC4692501 DOI: 10.1371/journal.pgen.1005724] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/14/2015] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites via distinct pathways. Cotton is an allotetraploid consisting of two progenitor genomes. Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis, but the molecular basis for this developmental transition is unknown. Here we analyzed methylome, transcriptome, and small RNAome and revealed distinct changes in CHH methylation during ovule and fiber development. In ovules, CHH hypermethylation in promoters correlated positively with siRNAs, inducing RNA-dependent DNA methylation (RdDM), and up-regulation of ovule-preferred genes. In fibers, the ovule-derived cells generated additional heterochromatic CHH hypermethylation independent of RdDM, which repressed transposable elements (TEs) and nearby genes including fiber-related genes. Furthermore, CHG and CHH methylation in genic regions contributed to homoeolog expression bias in ovules and fibers. Inhibiting DNA methylation using 5-aza-2'-deoxycytidine in cultured ovules has reduced fiber cell number and length, suggesting a potential role for DNA methylation in fiber development. Thus, RdDM-dependent methylation in promoters and RdDM-independent methylation in TEs and nearby genes could act as a double-lock feedback mechanism to mediate gene and TE expression, potentiating the transition from epidermal to fiber cells during ovule and seed development. Cotton is the world’s largest source of renewable textile fiber and is an allotetraploid crop consisting of two progenitor genomes. In plants, de novo CHH (H = A, T, or C) methylation depends on RNA-directed DNA methylation (RdDM) and CHROMOMETHYLASE2 (CMT2)-mediated pathways. The biological significance of the two pathways is largely unknown. Here we show dynamic roles of these two pathways in ovule and fiber development. RdDM-dependent CHH methylation is linked to gene activation in ovules, and additional CMT2-dependent methylation leads to silencing of transposons and nearby genes in fibers. Moreover, DNA methylation affects expression bias of homoeologous genes and fiber development. These findings provide novel insights into epigenetic regulation of organ development and polyploid evolution.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
| | - Xueying Guan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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192
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Zhao D, Ferguson AA, Jiang N. What makes up plant genomes: The vanishing line between transposable elements and genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:366-80. [PMID: 26709091 DOI: 10.1016/j.bbagrm.2015.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
Abstract
The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ann A Ferguson
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA.
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193
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Mascagni F, Barghini E, Giordani T, Rieseberg LH, Cavallini A, Natali L. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. Genome Biol Evol 2015; 7:3368-82. [PMID: 26608057 PMCID: PMC4700961 DOI: 10.1093/gbe/evv230] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower.
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Affiliation(s)
- Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Elena Barghini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Loren H Rieseberg
- The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
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194
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Klein BA, Chen T, Scott JC, Koenigsberg AL, Duncan MJ, Hu LT. Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis. Mob DNA 2015; 6:18. [PMID: 26448788 PMCID: PMC4596501 DOI: 10.1186/s13100-015-0049-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/23/2015] [Indexed: 12/26/2022] Open
Abstract
Background Repetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes. Such elements are known to be involved in transcriptional regulation, host-pathogen interactions and genome evolution. Results We identified a minisatellite contained within a miniature inverted-repeat transposable element (MITE) in Porphyromonas gingivalis. The P. gingivalis minisatellite and associated MITE, named ‘BrickBuilt’, comprises a tandemly repeating twenty-three nucleotide DNA sequence lacking spacer regions between repeats, and with flanking ‘leader’ and ‘tail’ subunits that include small inverted-repeat ends. Forms of the BrickBuilt MITE are found 19 times in the genome of P. gingivalis strain ATCC 33277, and also multiple times within the strains W83, TDC60, HG66 and JCVI SC001. BrickBuilt is always located intergenically ranging between 49 and 591 nucleotides from the nearest upstream and downstream coding sequences. Segments of BrickBuilt contain promoter elements with bidirectional transcription capabilities. Conclusions We performed a bioinformatic analysis of BrickBuilt utilizing existing whole genome sequencing, microarray and RNAseq data, as well as performing in vitro promoter probe assays to determine potential roles, mechanisms and regulation of the expression of these elements and their affect on surrounding loci. The multiplicity, localization and limited host range nature of MITEs and MITE-like elements in P. gingivalis suggest that these elements may play an important role in facilitating genome evolution as well as modulating the transcriptional regulatory system. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0049-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brian A Klein
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111 USA ; Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Jodie C Scott
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Andrea L Koenigsberg
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111 USA
| | - Margaret J Duncan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Linden T Hu
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111 USA
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195
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Dai S, Hou J, Long Y, Wang J, Li C, Xiao Q, Jiang X, Zou X, Zou J, Meng J. Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae. BMC PLANT BIOLOGY 2015; 15:149. [PMID: 26084405 PMCID: PMC4471910 DOI: 10.1186/s12870-015-0490-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/07/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae. RESULTS The characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened. CONCLUSION Monkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.
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Affiliation(s)
- Shutao Dai
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinna Hou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhenzhou, Henan, 450002, China.
| | - Yan Long
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jing Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Cong Li
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Qinqin Xiao
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxue Jiang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxiao Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jun Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinling Meng
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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196
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Sun C, Feschotte C, Wu Z, Mueller RL. DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biol 2015; 13:38. [PMID: 26067596 PMCID: PMC4495683 DOI: 10.1186/s12915-015-0145-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/03/2015] [Indexed: 01/06/2023] Open
Abstract
Background Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. Results Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. Conclusions Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0145-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng Sun
- Department of Biology, Colorado State University, Campus Delivery 1878, Fort Collins, CO, 80523-1878, USA.
| | - Cédric Feschotte
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, 84112, USA.
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Campus Delivery 1878, Fort Collins, CO, 80523-1878, USA.
| | - Rachel Lockridge Mueller
- Department of Biology, Colorado State University, Campus Delivery 1878, Fort Collins, CO, 80523-1878, USA.
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Abstract
Environmental conditions can change the activity of plant genes via epigenetic effects that alter the competence of genetic information to be expressed. This may provide a powerful strategy for plants to adapt to environmental change. However, as epigenetic changes do not modify DNA sequences and are therefore reversible, only those epi-mutations that are transmitted through the germline can be expected to contribute to a long-term adaptive response. The major challenge for the investigation of epigenetic adaptation theories is therefore to identify genomic loci that undergo epigenetic changes in response to environmental conditions, which alter their expression in a heritable way and which improve the plant's ability to adapt to the inducing conditions. This review focuses on the role of DNA methylation as a prominent epigenetic mark that controls chromatin conformation, and on its potential in mediating expression changes in response to environmental signals.
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Affiliation(s)
- Peter Meyer
- Centre for Plant Sciences, University of Leeds, Leeds, UK
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198
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The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm. G3-GENES GENOMES GENETICS 2015; 5:1585-92. [PMID: 26019188 PMCID: PMC4528315 DOI: 10.1534/g3.115.018317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
TRIMs (terminal-repeat retrotransposons in miniature), which are characterized by their small size, have been discovered in all investigated vascular plants and even in animals. Here, we identified a highly conservative TRIM family referred to as Wukong elements in the maize genome. The Wukong family shows a distinct pattern of tandem arrangement in the maize genome suggesting a high rate of unequal crossing over. Estimation of insertion times implies a burst of retrotransposition activity of the Wukong family after the allotetraploidization of maize. Using next-generation sequencing data, we detected 87 new Wukong insertions in parents of the maize NAM population relative to the B73 reference genome and found abundant insertion polymorphism of Wukong elements in 75 re-sequenced maize lines, including teosinte, landraces, and improved lines. These results suggest that Wukong elements possessed a persistent retrotransposition activity throughout maize evolution. Moreover, the phylogenetic relationships among 76 maize inbreds and their relatives based on insertion polymorphisms of Wukong elements should provide us with reliable molecular markers for biodiversity and genetics studies.
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199
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Fablet M, Vieira C. Evolvability, epigenetics and transposable elements. Biomol Concepts 2015; 2:333-41. [PMID: 25962041 DOI: 10.1515/bmc.2011.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 07/11/2011] [Indexed: 12/31/2022] Open
Abstract
Evolvability can be defined as the capacity of an individual to evolve and thus to capture adaptive mutations. Transposable elements (TE) are an important source of mutations in organisms. Their capacity to transpose within a genome, sometimes at a high rate, and their copy number regulation are environment-sensitive, as are the epigenetic pathways that mediate TE regulation in a genome. In this review we revisit the way we see evolvability with regard to transposable elements and epigenetics.
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200
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Identification, Diversity and Evolution of MITEs in the Genomes of Microsporidian Nosema Parasites. PLoS One 2015; 10:e0123170. [PMID: 25898273 PMCID: PMC4405373 DOI: 10.1371/journal.pone.0123170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/27/2015] [Indexed: 11/29/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous DNA transposons, which are widespread in most eukaryotic genomes. However, genome-wide identification, origin and evolution of MITEs remain largely obscure in microsporidia. In this study, we investigated structural features for de novo identification of MITEs in genomes of silkworm microsporidia Nosema bombycis and Nosema antheraeae, as well as a honeybee microsporidia Nosema ceranae. A total of 1490, 149 and 83 MITE-related sequences from 89, 17 and five families, respectively, were found in the genomes of the above-mentioned species. Species-specific MITEs are predominant in each genome of microsporidian Nosema, with the exception of three MITE families that were shared by N. bombycis and N. antheraeae. One or multiple rounds of amplification occurred for MITEs in N. bombycis after divergence between N. bombycis and the other two species, suggesting that the more abundant families in N. bombycis could be attributed to the recent amplification of new MITEs. Significantly, some MITEs that inserted into the homologous protein-coding region of N. bombycis were recruited as introns, indicating that gene expansion occurred during the evolution of microsporidia. NbS31 and NbS24 had polymorphisms in different geographical strains of N. bombycis, indicating that they could still be active. In addition, several small RNAs in the MITEs in N. bombycis are mainly produced from both ends of the MITEs sequence.
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