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Abstract
The idea that much of our genome is irrelevant to fitness-is not the product of positive natural selection at the organismal level-remains viable. Claims to the contrary, and specifically that the notion of "junk DNA" should be abandoned, are based on conflating meanings of the word "function". Recent estimates suggest that perhaps 90% of our DNA, though biochemically active, does not contribute to fitness in any sequence-dependent way, and possibly in no way at all. Comparisons to vertebrates with much larger and smaller genomes (the lungfish and the pufferfish) strongly align with such a conclusion, as they have done for the last half-century.
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Affiliation(s)
- W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Tyler D P Brunet
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of History and Philosophy of Science, University of Cambridge, Cambridge, UK
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52
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Horváth V, Merenciano M, González J. Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response. Trends Genet 2017; 33:832-841. [DOI: 10.1016/j.tig.2017.08.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/02/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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53
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Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC. Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. Genome Biol 2017; 18:198. [PMID: 29065907 PMCID: PMC5655803 DOI: 10.1186/s13059-017-1335-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/03/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. RESULTS The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers comprise transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos. CONCLUSIONS The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and non-allelic homologous recombination and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole-genome duplication.
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Affiliation(s)
- Dei M Elurbe
- Radboud University Medical Center, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands
| | - Sarita S Paranjpe
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands
| | - Georgios Georgiou
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands
| | - Ila van Kruijsbergen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Ryan Lister
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Martijn A Huynen
- Radboud University Medical Center, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.
| | - Simon J van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.
| | - Gert Jan C Veenstra
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.
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54
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Jiang X, Tang H, Ye Z, Lynch M. Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. Genome Biol Evol 2017; 9:362-374. [PMID: 28057730 PMCID: PMC5381639 DOI: 10.1093/gbe/evw302] [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] [Accepted: 12/29/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.
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Affiliation(s)
- Xiaoqian Jiang
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, Indiana
| | - Zhiqiang Ye
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana
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55
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Abstract
What made us human? Gene expression changes clearly played a significant part in human evolution, but pinpointing the causal regulatory mutations is hard. Comparative genomics enabled the identification of human accelerated regions (HARs) and other human-specific genome sequences. The major challenge in the past decade has been to link diverged sequences to uniquely human biology. This review discusses approaches to this problem, progress made at the molecular level, and prospects for moving towards genetic causes for uniquely human biology.
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Affiliation(s)
- Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, 94158, USA. .,Department of Epidemiology & Biostatistics, Institute for Human Genetics, Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158, USA.
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56
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Gouveia JG, Wolf IR, Vilas-Boas LA, Heslop-Harrison JS, Schwarzacher T, Dias AL. Repetitive DNA in the Catfish Genome: rDNA, Microsatellites, and Tc1-Mariner Transposon Sequences in Imparfinis Species (Siluriformes, Heptapteridae). J Hered 2017; 108:650-657. [PMID: 28821184 DOI: 10.1093/jhered/esx065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/15/2017] [Indexed: 11/13/2022] Open
Abstract
Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I. schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis.
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Affiliation(s)
- Juceli Gonzalez Gouveia
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Ivan Rodrigo Wolf
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Laurival Antonio Vilas-Boas
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Trude Schwarzacher
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Ana Lúcia Dias
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
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57
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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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58
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Franke V, Ganesh S, Karlic R, Malik R, Pasulka J, Horvat F, Kuzman M, Fulka H, Cernohorska M, Urbanova J, Svobodova E, Ma J, Suzuki Y, Aoki F, Schultz RM, Vlahovicek K, Svoboda P. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res 2017; 27:1384-1394. [PMID: 28522611 PMCID: PMC5538554 DOI: 10.1101/gr.216150.116] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/15/2017] [Indexed: 12/11/2022]
Abstract
Retrotransposons are "copy-and-paste" insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified more than 800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons. The LTR-mediated gene remodeling also extends to hamster, human, and bovine oocytes. The LTRs function in a stage-specific manner during the oocyte-to-embryo transition by activating transcription, altering protein-coding sequences, producing noncoding RNAs, and even supporting evolution of new protein-coding genes. These functions result, for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles. The functional potential of the studied LTRs is even higher, because we show that dormant LTR promoter activity can rescue loss of an essential upstream promoter. We also report a novel protein-coding gene evolution-D6Ertd527e-in which an MT LTR provided a promoter and the 5' exon with a functional start codon while the bulk of the protein-coding sequence evolved through a CAG repeat expansion. Altogether, ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale. ERVL LTRs thus offer means for a comprehensive survey of the genome's expression potential, tightly intertwining with gene expression and evolution in the germline.
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Affiliation(s)
- Vedran Franke
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Sravya Ganesh
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Rosa Karlic
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Radek Malik
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Josef Pasulka
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Filip Horvat
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Maja Kuzman
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Helena Fulka
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Marketa Cernohorska
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Jana Urbanova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
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59
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Rebeiz M, Tsiantis M. Enhancer evolution and the origins of morphological novelty. Curr Opin Genet Dev 2017; 45:115-123. [PMID: 28527813 DOI: 10.1016/j.gde.2017.04.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/25/2017] [Accepted: 04/27/2017] [Indexed: 01/07/2023]
Abstract
A central goal of evolutionary biology is to understand the genetic origin of morphological novelties-i.e. anatomical structures unique to a taxonomic group. Elaboration of morphology during development depends on networks of regulatory genes that activate patterned gene expression through transcriptional enhancer regions. We summarize recent case studies and genome-wide investigations that have uncovered diverse mechanisms though which new enhancers arise. We also discuss how these enhancer-originating mechanisms have clarified the history of genetic networks underlying diversification of genital structures in flies, limbs and neural crest in chordates, and plant leaves. These studies have identified enhancers that were pivotal for morphological divergence and highlighted how novel genetic networks shaping form emerged from pre-existing ones.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15215, USA.
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany.
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60
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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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61
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Simakov O, Kawashima T. Independent evolution of genomic characters during major metazoan transitions. Dev Biol 2016; 427:179-192. [PMID: 27890449 DOI: 10.1016/j.ydbio.2016.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages. In this review we describe recent advances in our understanding of ancestral metazoan coding and non-coding features, as deduced from genomic comparisons. Some genomic changes such as innovations in gene and linkage content occur at different rates across metazoan clades, suggesting some level of independence among genomic characters. While their contribution to biological innovation remains largely unclear, we review recent literature about certain genomic changes that do correlate with changes to specific developmental pathways and metazoan innovations. In particular, we discuss the origins of the recently described pharyngeal cluster which is conserved across deuterostome genomes, and highlight different genomic features that have contributed to the evolution of this group. We also assess our current capacity to infer ancestral metazoan states from gene models and comparative genomics tools and elaborate on the future directions of metazoan comparative genomics relevant to evo-devo studies.
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Affiliation(s)
- Oleg Simakov
- Okinawa Institute of Science and Technology, Okinawa, Japan.
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62
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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: 777] [Impact Index Per Article: 97.1] [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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63
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Schemberger MO, Nogaroto V, Almeida MC, Artoni RF, Valente GT, Martins C, Moreira-Filho O, Cestari MM, Vicari MR. Sequence analyses and chromosomal distribution of the Tc1/Mariner element in Parodontidae fish (Teleostei: Characiformes). Gene 2016; 593:308-14. [DOI: 10.1016/j.gene.2016.08.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 07/31/2016] [Accepted: 08/20/2016] [Indexed: 10/21/2022]
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64
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Warren IA, Naville M, Chalopin D, Levin P, Berger CS, Galiana D, Volff JN. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates. Chromosome Res 2016; 23:505-31. [PMID: 26395902 DOI: 10.1007/s10577-015-9493-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.
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Affiliation(s)
- Ian A Warren
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.,Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Perrine Levin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chloé Suzanne Berger
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.
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65
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Göke J, Ng HH. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. EMBO Rep 2016; 17:1131-44. [PMID: 27402545 DOI: 10.15252/embr.201642743] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/20/2016] [Indexed: 12/25/2022] Open
Abstract
The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers.
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Affiliation(s)
- Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore Department of Biochemistry, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore School of Biological Sciences, Nanyang Technological University, Singapore
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66
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Evolutionary direction of processed pseudogenes. SCIENCE CHINA-LIFE SCIENCES 2016; 59:839-49. [PMID: 27333782 DOI: 10.1007/s11427-016-5074-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/08/2016] [Indexed: 10/21/2022]
Abstract
While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection.
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67
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Amarillo IE, Nievera I, Hagan A, Huchthagowder V, Heeley J, Hollander A, Koenig J, Austin P, Wang T. Integrated small copy number variations and epigenome maps of disorders of sex development. Hum Genome Var 2016; 3:16012. [PMID: 27340555 PMCID: PMC4899613 DOI: 10.1038/hgv.2016.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/24/2016] [Accepted: 03/26/2016] [Indexed: 02/03/2023] Open
Abstract
Small copy number variations (CNVs) have typically not been analyzed or reported in clinical settings and hence have remained underrepresented in databases and the literature. Here, we focused our investigations on these small CNVs using chromosome microarray analysis (CMA) data previously obtained from patients with atypical characteristics or disorders of sex development (DSD). Using our customized CMA track targeting 334 genes involved in the development of urogenital and reproductive structures and a less stringent analysis filter, we uncovered small genes with recurrent and overlapping CNVs as small as 1 kb, and small regions of homozygosity (ROHs), imprinting and position effects. Detailed analysis of these high-resolution data revealed CNVs and ROHs involving structural and functional domains, repeat elements, active transcription sites and regulatory regions. Integration of these genomic data with DNA methylation, histone modification and predicted RNA expression profiles in normal testes and ovaries suggested spatiotemporal and tissue-specific gene regulation. This study emphasized a DSD-specific and gene-targeted CMA approach that uncovered previously unanalyzed or unreported small genes and CNVs, contributing to the growing resources on small CNVs and facilitating the narrowing of the genomic gap for identifying candidate genes or regions. This high-resolution analysis tool could improve the diagnostic utility of CMA, not only in patients with DSD but also in other clinical populations. These integrated data provided a better genomic-epigenomic landscape of DSD and greater opportunities for downstream research.
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Affiliation(s)
- Ina E Amarillo
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA
| | - Isabelle Nievera
- Washington University in St Louis School of Medicine DSD Team , St Louis, MO, USA
| | - Andrew Hagan
- Division of Biology and Biomedical Sciences, Washington University in St Louis , St Louis, MO, USA
| | - Vishwa Huchthagowder
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine , St Louis, MO, USA
| | - Jennifer Heeley
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Abby Hollander
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Joel Koenig
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Paul Austin
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University in St Louis School of Medicine , St Louis, MO, USA
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68
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Thompson PJ, Macfarlan TS, Lorincz MC. Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire. Mol Cell 2016; 62:766-76. [PMID: 27259207 PMCID: PMC4910160 DOI: 10.1016/j.molcel.2016.03.029] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The life cycle of endogenous retroviruses (ERVs), also called long terminal repeat (LTR) retrotransposons, begins with transcription by RNA polymerase II followed by reverse transcription and re-integration into the host genome. While most ERVs are relics of ancient integration events, "young" proviruses competent for retrotransposition-found in many mammals, but not humans-represent an ongoing threat to host fitness. As a consequence, several restriction pathways have evolved to suppress their activity at both transcriptional and post-transcriptional stages of the viral life cycle. Nevertheless, accumulating evidence has revealed that LTR sequences derived from distantly related ERVs have been exapted as regulatory sequences for many host genes in a wide range of cell types throughout mammalian evolution. Here, we focus on emerging themes from recent studies cataloging the diversity of ERV LTRs acting as important transcriptional regulatory elements in mammals and explore the molecular features that likely account for LTR exaptation in developmental and tissue-specific gene regulation.
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Affiliation(s)
- Peter J Thompson
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Todd S Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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Huang K, Li CF, Wu J, Wei JH, Zou Y, Han MJ, Zhou ZY. Enhancer activity of Helitron in sericin-1 gene promoter from Bombyx mori. INSECT SCIENCE 2016; 23:396-405. [PMID: 27067405 DOI: 10.1111/1744-7917.12347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
Sericin is a kind of water-soluble protein expressed specifically in the middle silk gland of Bombyx mori. When the sericin-1 gene promoter was cloned and a transgenic vector was constructed to express a foreign protein, a specific Helitron, Bmhel-8, was identified in the sericin-1 gene promoter sequence in some genotypes of Bombyx mori and Bombyx mandarina. Given that the Bmhel-8 Helitron transposon was present only in some genotypes, it could be the source of allelic variation in the sericin-1 promoter. The length of the sericin-1 promoter sequence is approximately 1063 or 643 bp. The larger size of the sequence or allele is ascribed to the presence of Bmhel-8. Silkworm genotypes can be homozygous for either the shorter or larger promoter sequence or heterozygous, containing both alleles. Bmhel-8 in the sericin-1 promoter exhibits enhancer activity, as demonstrated by a dual-luciferase reporter system in BmE cell lines. Furthermore, Bmhel-8 displays enhancer activity in a sericin-1 promoter-driven gene expression system but does not regulate the tissue-specific expression of sericin-1.
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Affiliation(s)
- Ke Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- College of Forestry & Life Science, Chongqing University of Arts & Sciences, Yongchuan, China
| | - Chun-Feng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Jie Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Jun-Hong Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yong Zou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- College of Forestry & Life Science, Chongqing University of Arts & Sciences, Yongchuan, China
| | - Min-Jin Han
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ze-Yang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Laboratory of Animal Biology, Chongqing Normal University, Chongqing, China
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Rayan NA, Del Rosario RCH, Prabhakar S. Massive contribution of transposable elements to mammalian regulatory sequences. Semin Cell Dev Biol 2016; 57:51-56. [PMID: 27174439 DOI: 10.1016/j.semcdb.2016.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022]
Abstract
Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene regulatory program of higher organisms. This controversial idea gained acceptance only much later in the 1990s, when the first examples of TE-derived promoter sequences were uncovered. It is now known that half of the human genome is recognizably derived from TEs. It is thus important to understand the scope and nature of their contribution to gene regulation. Here, we provide a timeline of major discoveries in this area and discuss how transposons have revolutionized our understanding of mammalian genomes, with a special emphasis on the massive contribution of TEs to primate evolution. Our analysis of primate-specific functional elements supports a simple model for the rate at which new functional elements arise in unique and TE-derived DNA. Finally, we discuss some of the challenges and unresolved questions in the field, which need to be addressed in order to fully characterize the impact of TEs on gene regulation, evolution and disease processes.
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Affiliation(s)
- Nirmala Arul Rayan
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, 60 Biopolis Street, 138672, Singapore
| | - Ricardo C H Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, 60 Biopolis Street, 138672, Singapore.
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71
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Lowdon RF, Jang HS, Wang T. Evolution of Epigenetic Regulation in Vertebrate Genomes. Trends Genet 2016; 32:269-283. [PMID: 27080453 PMCID: PMC4842087 DOI: 10.1016/j.tig.2016.03.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/31/2022]
Abstract
Empirical models of sequence evolution have spurred progress in the field of evolutionary genetics for decades. We are now realizing the importance and complexity of the eukaryotic epigenome. While epigenome analysis has been applied to genomes from single-cell eukaryotes to human, comparative analyses are still relatively few and computational algorithms to quantify epigenome evolution remain scarce. Accordingly, a quantitative model of epigenome evolution remains to be established. We review here the comparative epigenomics literature and synthesize its overarching themes. We also suggest one mechanism, transcription factor binding site (TFBS) turnover, which relates sequence evolution to epigenetic conservation or divergence. Lastly, we propose a framework for how the field can move forward to build a coherent quantitative model of epigenome evolution.
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Affiliation(s)
- Rebecca F Lowdon
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Hyo Sik Jang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
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Annibalini G, Bielli P, De Santi M, Agostini D, Guescini M, Sisti D, Contarelli S, Brandi G, Villarini A, Stocchi V, Sette C, Barbieri E. MIR retroposon exonization promotes evolutionary variability and generates species-specific expression of IGF-1 splice variants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:757-68. [DOI: 10.1016/j.bbagrm.2016.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/07/2016] [Accepted: 03/23/2016] [Indexed: 12/18/2022]
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Affiliation(s)
- Vincent J Lynch
- Department of Human Genetics, The University of Chicago, 920 East 58th Street, CLSC 319C, Chicago, IL 60637, USA.
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74
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Bire S, Casteret S, Piégu B, Beauclair L, Moiré N, Arensbuger P, Bigot Y. Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2. PLoS Genet 2016; 12:e1005902. [PMID: 26939020 PMCID: PMC4777549 DOI: 10.1371/journal.pgen.1005902] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/05/2016] [Indexed: 12/31/2022] Open
Abstract
Transposable elements are driving forces for establishing genetic innovations such as transcriptional regulatory networks in eukaryotic genomes. Here, we describe a silencer situated in the last 300 bp of the Mos1 transposase open reading frame (ORF) which functions in vertebrate and arthropod cells. Functional silencers are also found at similar locations within three other animal mariner elements, i.e. IS630-Tc1-mariner (ITm) DD34D elements, Himar1, Hsmar1 and Mcmar1. These silencers are able to impact eukaryotic promoters monitoring strong, moderate or low expression as well as those of mariner elements located upstream of the transposase ORF. We report that the silencing involves at least two transcription factors (TFs) that are conserved within animal species, NFAT-5 and Alx1. These cooperatively act with YY1 to trigger the silencing activity. Four other housekeeping transcription factors (TFs), neuron restrictive silencer factor (NRSF), GAGA factor (GAF) and GTGT factor (GTF), were also found to have binding sites within mariner silencers but their impact in modulating the silencer activity remains to be further specified. Interestingly, an NRSF binding site was found to overlap a 30 bp motif coding a highly conserved PHxxYSPDLAPxD peptide in mariner transposases. We also present experimental evidence that silencing is mainly achieved by co-opting the host Polycomb Repressive Complex 2 pathway. However, we observe that when PRC2 is impaired another host silencing pathway potentially takes over to maintain weak silencer activity. Mariner silencers harbour features of Polycomb Response Elements, which are probably a way for mariner elements to self-repress their transcription and mobility in somatic and germinal cells when the required TFs are expressed. At the evolutionary scale, mariner elements, through their exaptation, might have been a source of silencers playing a role in the chromatin configuration in eukaryotic genomes. Transposons are mobile DNA sequences that have long co-evolved with the genome of their hosts. Consequently, they are involved in the generation of mutations, as well as the creation of genes and regulatory networks. Controlling the transposon activity, and consequently its negative effects on both the host soma and germ line, is a challenge for the survival of both the host and the transposon. To silence transposons, hosts often use defence mechanisms involving DNA methylation and RNA interference pathways. Here we show that mariner transposons can self-regulate their activity by using a silencer element located in their DNA sequence. The silencer element interferes with host housekeeping protein transcription factors involved in the polycomb silencing pathways. As the regulation of chromatin configuration by polycomb is an important regulator of animal development, our findings open the possibility that mariner silencers might have been exapted during animal evolution to participate in certain regulation pathways of their hosts. Since some of the TFs involved in mariner silencer activity play a role at different stages of nervous system development and neuron differentiation, it might be possible that mariner transposons can be active during some steps of cell differentiation. Interestingly, mariner transposons (i.e. IS630-Tc1-mariner (ITm) DD34D transposons) have so far only been found in genomes of animals having a nervous system.
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Affiliation(s)
- Solenne Bire
- PRC, UMR INRA-CNRS 7247, PRC, Nouzilly, France
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | | | | | | | | | - Peter Arensbuger
- Biological Sciences Department, California State Polytechnic University, Pomona, California, United States of America
| | - Yves Bigot
- PRC, UMR INRA-CNRS 7247, PRC, Nouzilly, France
- * E-mail:
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Kim EZ, Wespiser AR, Caffrey DR. The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs. RNA (NEW YORK, N.Y.) 2016; 22:254-264. [PMID: 26654912 PMCID: PMC4712675 DOI: 10.1261/rna.048280.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Approximately 75% of the human genome is transcribed and many of these spliced transcripts contain primate-specific Alu elements, the most abundant mobile element in the human genome. The majority of exonized Alu elements are located in long noncoding RNAs (lncRNAs) and the untranslated regions of mRNA, with some performing molecular functions. To further assess the potential for Alu elements to be repurposed as functional RNA domains, we investigated the distribution and evolution of Alu elements in spliced transcripts. Our analysis revealed that Alu elements are underrepresented in mRNAs and lncRNAs, suggesting that most exonized Alu elements arising in the population are rare or deleterious to RNA function. When mRNAs and lncRNAs retain exonized Alu elements, they have a clear preference for Alu dimers, left monomers, and right monomers. mRNAs often acquire Alu elements when their genes are duplicated within Alu-rich regions. In lncRNAs, reverse-oriented Alu elements are significantly enriched and are not restricted to the 3' and 5' ends. Both lncRNAs and mRNAs primarily contain the Alu J and S subfamilies that were amplified relatively early in primate evolution. Alu J subfamilies are typically overrepresented in lncRNAs, whereas the Alu S dimer is overrepresented in mRNAs. The sequences of Alu dimers tend to be constrained in both lncRNAs and mRNAs, whereas the left and right monomers are constrained within particular Alu subfamilies and classes of RNA. Collectively, these findings suggest that Alu-containing RNAs are capable of forming stable structures and that some of these Alu domains might have novel biological functions.
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Affiliation(s)
- Eugene Z Kim
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Adam R Wespiser
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Daniel R Caffrey
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Cournac A, Koszul R, Mozziconacci J. The 3D folding of metazoan genomes correlates with the association of similar repetitive elements. Nucleic Acids Res 2016; 44:245-55. [PMID: 26609133 PMCID: PMC4705657 DOI: 10.1093/nar/gkv1292] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 10/13/2015] [Accepted: 11/04/2015] [Indexed: 12/11/2022] Open
Abstract
The potential roles of the numerous repetitive elements found in the genomes of multi-cellular organisms remain speculative. Several studies have suggested a role in stabilizing specific 3D genomic contacts. To test this hypothesis, we exploited inter-chromosomal contacts frequencies obtained from Hi-C experiments and show that the folding of the human, mouse and Drosophila genomes is associated with a significant co-localization of several specific repetitive elements, notably many elements of the SINE family. These repeats tend to be the oldest ones and are enriched in transcription factor binding sites. We propose that the co-localization of these repetitive elements may explain the global conservation of genome folding observed between homologous regions of the human and mouse genome. Taken together, these results support a contribution of specific repetitive elements in maintaining and/or reshaping genome architecture over evolutionary times.
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Affiliation(s)
- Axel Cournac
- LPTMC, Université Pierre et Marie Curie, Sorbonne université, 4 Place Jussieu 75005 Paris, France Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, F-75015 Paris, France CNRS, UMR3525, F-75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, F-75015 Paris, France CNRS, UMR3525, F-75015 Paris, France
| | - Julien Mozziconacci
- LPTMC, Université Pierre et Marie Curie, Sorbonne université, 4 Place Jussieu 75005 Paris, France
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Amselem J, Vigouroux M, Oberhaensli S, Brown JKM, Bindschedler LV, Skamnioti P, Wicker T, Spanu PD, Quesneville H, Sacristán S. Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics 2015; 16:917. [PMID: 26556056 PMCID: PMC4641428 DOI: 10.1186/s12864-015-2185-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022] Open
Abstract
Background The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resistant barley, MLK1 and MLA10 resistance proteins recognize the presence of AVRK1 and AVRA10, eliciting the hypersensitive response typical of gene for gene interactions. Avrk1 and Avra10 have more than 1350 homologues in Bgh genome, forming the EKA (Effectors homologous to Avrk1 and Avra10) gene family. Results We tested the hypothesis that the EKA family originated from degenerate copies of Class I LINE retrotransposons by analysing the EKA family in the genome of Bgh isolate DH14 with bioinformatic tools specially developed for the analysis of Transposable Elements (TE) in genomes. The Class I LINE retrotransposon copies homologous to Avrk1 and Avra10 represent 6.5 % of the Bgh annotated genome and, among them, we identified 293 AVR/effector candidate genes. We also experimentally identified peptides that indicated the translation of several predicted proteins from EKA family members, which had higher relative abundance in haustoria than in hyphae. Conclusions Our analyses indicate that Avrk1 and Avra10 have evolved from part of the ORF1 gene of Class I LINE retrotransposons. The co-option of Avra10 and Avrk1 as effectors from truncated copies of retrotransposons explains the huge number of homologues in Bgh genome that could act as dynamic reservoirs from which new effector genes may evolve. These data provide further evidence for recruitment of retrotransposons in the evolution of new biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2185-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joelle Amselem
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France. .,INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, 78850, Thiverval-Grignon, France.
| | | | - Simone Oberhaensli
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - James K M Brown
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - Pari Skamnioti
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, TK 11855, Athens, Greece.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, UK.
| | - Hadi Quesneville
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France.
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
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Muiño JM, de Bruijn S, Pajoro A, Geuten K, Vingron M, Angenent GC, Kaufmann K. Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor. Mol Biol Evol 2015; 33:185-200. [PMID: 26429922 PMCID: PMC4693976 DOI: 10.1093/molbev/msv210] [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: 12/11/2022] Open
Abstract
Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
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Affiliation(s)
- Jose M Muiño
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands
| | - Suzanne de Bruijn
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Alice Pajoro
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Koen Geuten
- Laboratory of Molecular Plant Biology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Martin Vingron
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands Bioscience, Plant Research International, Wageningen, The Netherlands
| | - Kerstin Kaufmann
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
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79
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Patrushev LI, Kovalenko TF. Functions of noncoding sequences in mammalian genomes. BIOCHEMISTRY (MOSCOW) 2015; 79:1442-69. [PMID: 25749159 DOI: 10.1134/s0006297914130021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Most of the mammalian genome consists of nucleotide sequences not coding for proteins. Exons of genes make up only 3% of the human genome, while the significance of most other sequences remains unknown. Recent genome studies with high-throughput methods demonstrate that the so-called noncoding part of the genome may perform important functions. This hypothesis is supported by three groups of experimental data: 1) approximately 10% of the sequences, most of which are located in noncoding parts of the genome, is evolutionarily conserved and thus can be of functional importance; 2) up to 99% of the mammalian genome is being transcribed forming short and long noncoding RNAs in addition to common mRNA; and 3) mutations in noncoding parts of the genome can be accompanied by progression of pathological states of the organism. In the light of these data, in the review we consider the functional role of numerous known sequences of noncoding parts of the genome including introns, DNA methylation regions, enhancers and locus control regions, insulators, S/MAR sequences, pseudogenes, and genes of noncoding RNAs, as well as transposons and simple repeats of centromeric and telomeric regions of chromosomes. The assumption is made that the intergenic noncoding sequences without definite/clear functions can be involved in spatial organization of genetic loci in interphase nuclei.
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Affiliation(s)
- L I Patrushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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80
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Franchini LF, Pollard KS. Genomic approaches to studying human-specific developmental traits. Development 2015; 142:3100-12. [DOI: 10.1242/dev.120048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Changes in developmental regulatory programs drive both disease and phenotypic differences among species. Linking human-specific traits to alterations in development is challenging, because we have lacked the tools to assay and manipulate regulatory networks in human and primate embryonic cells. This field was transformed by the sequencing of hundreds of genomes – human and non-human – that can be compared to discover the regulatory machinery of genes involved in human development. This approach has identified thousands of human-specific genome alterations in developmental genes and their regulatory regions. With recent advances in stem cell techniques, genome engineering, and genomics, we can now test these sequences for effects on developmental gene regulation and downstream phenotypes in human cells and tissues.
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Affiliation(s)
- Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- Institute for Human Genetics, Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158, USA
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81
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Abstract
There is a huge variety of RNA- and DNA-containing entities that multiply within and propagate between cells across all kingdoms of life, having no cells of their own. Apart from cellular organisms, these entities (viroids, plasmids, mobile elements and viruses among others) are the only ones with distinct genetic identities but which are not included in any traditional tree of life. We suggest to introduce or, rather, revive the distinct category of acellular organisms, Acytota, as an additional, undeservedly ignored full-fledged kingdom of life. Acytota are indispensable players in cellular life and its evolution. The six traditional kingdoms (Cytota) and Acytota together complete the classification of the biological world (Biota), leaving nothing beyond.
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Affiliation(s)
- Edward N Trifonov
- a Genome Diversity Center, Institute of Evolution , University of Haifa, Mount Carmel , Haifa 3498838 , Israel
| | - Eduard Kejnovsky
- b Department of Plant Developmental Genetics , Institute of Biophysics, Academy of Sciences of the Czech Republic , Brno , Czech Republic
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82
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Grandi FC, Rosser JM, Newkirk SJ, Yin J, Jiang X, Xing Z, Whitmore L, Bashir S, Ivics Z, Izsvák Z, Ye P, Yu YE, An W. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. Genome Res 2015; 25:1135-46. [PMID: 25995269 PMCID: PMC4509998 DOI: 10.1101/gr.185132.114] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/19/2015] [Indexed: 11/25/2022]
Abstract
Long interspersed elements (LINEs), through both self-mobilization and trans-mobilization of short interspersed elements and processed pseudogenes, have made an indelible impact on the structure and function of the human genome. One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the genome are associated with repetitive DNA, three-quarters of which are derived from retrotransposons. However, little is known about the epigenetic impact of newly inserted CGIs. We utilized a transgenic LINE-1 mouse model and tracked DNA methylation dynamics of individual germline insertions during mouse development. The retrotransposed GFP marker sequence, a strong CGI, is hypomethylated in male germ cells but hypermethylated in somatic tissues, regardless of genomic location. The GFP marker is similarly methylated when delivered into the genome via the Sleeping Beauty DNA transposon, suggesting that the observed methylation pattern may be independent of the mode of insertion. Comparative analyses between insertion- and non-insertion-containing alleles further reveal a graded influence of the retrotransposed CGI on flanking CpG sites, a phenomenon that we described as "sloping shores." Computational analyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are universal for hypomethylated CGIs in sperm and somatic tissues. Additionally, the slope of a hypomethylated CGI can be affected by closely positioned CGI neighbors. Finally, by tracing sloping shore dynamics through embryonic and germ cell reprogramming, we found evidence of bookmarking, a mechanism that likely determines which CGIs will be eventually hyper- or hypomethylated.
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Affiliation(s)
- Fiorella C Grandi
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - James M Rosser
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Simon J Newkirk
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA; Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota 57007, USA
| | - Jun Yin
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Leanne Whitmore
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Sanum Bashir
- Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Ping Ye
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota 57007, USA
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83
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Casane D, Fumey J, Laurenti P. [ENCODE apophenia or a panglossian analysis of the human genome]. Med Sci (Paris) 2015; 31:680-6. [PMID: 26152174 DOI: 10.1051/medsci/20153106023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world.
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Affiliation(s)
- Didier Casane
- Laboratoire Évolution, génomes, comportement, écologie, CNRS université Paris-Sud UMR 9191, IRD UMR 247, Avenue de la Terrasse, bâtiment 13, boîte postale 1, 91198 Gif-sur-Yvette, France - Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
| | - Julien Fumey
- Laboratoire Évolution, génomes, comportement, écologie, CNRS université Paris-Sud UMR 9191, IRD UMR 247, Avenue de la Terrasse, bâtiment 13, boîte postale 1, 91198 Gif-sur-Yvette, France
| | - Patrick Laurenti
- Laboratoire Évolution, génomes, comportement, écologie, CNRS université Paris-Sud UMR 9191, IRD UMR 247, Avenue de la Terrasse, bâtiment 13, boîte postale 1, 91198 Gif-sur-Yvette, France - Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
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84
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Putative regulation mechanism for the MSTN gene by a CpG island generated by the SINE marker Ins227bp. BMC Vet Res 2015; 11:138. [PMID: 26100061 PMCID: PMC4476204 DOI: 10.1186/s12917-015-0428-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 05/05/2015] [Indexed: 11/16/2022] Open
Abstract
Background A single nucleotide polymorphism (SNP) in the first intron of the myostatin gene (MSTN) is associated with aptness of elite Thoroughbreds to race over sprint, middle or long distances. This intronic marker (g.66493737 T ≻ C), a short interspersed nuclear element (SINE) of 227 bp (Ins227bp) insertion polymorphism in the MSTN promoter, and the adjacent SNP BIEC2-417495 have not been studied for their association with racing aptness of the average Thoroughbreds raced in countries with lower status of the racing industry. This study investigated these markers regarding their prevalence and association with performance in common race horses. Markers were genotyped by amplification refractory mutation system-quantitative PCR (ARMS-qPCR) or amplicon melting. Furthermore, we asked whether the Ins227bp marker might theoretically regulate the expression of myostatin by generating a novel target for DNA methylation or by changing binding sites for transcription factors. Putative sites for DNA methylation or binding of transcription factors were predicted by MethPrimer and by the softwares JASPAR, MatInspector and UniPROBE, respectively. Results Pairwise linkage disequilibrium between g.66493737 T ≻ C and Ins227bp was high (r2 = 0.93). A lower linkage was determined for g.66493737 T ≻ C and BIEC2-417495 (r2 = 0.69) as well as for BIEC2-417495 and Ins227bp (r2 = 0.76). The estimated frequencies for the presence of Ins227bp (I) indel and the C alleles at g.66493737 T ≻ C and BIEC2-417495 were 0.46, 0.47 and 0.43, respectively. Heterozygotes represented the most abundant genotype at each locus. The best racing distance (BRD) was significantly different between the homozygotes of each SNP (p = 0.01 to 0.03). C allele homozygotes at BIEC2-417495 or g.66493737 T ≻ C, as well as Ins227bp homozygotes earned most money on a mean distance ranging from 1211 to 1230 m. Heterozygotes earned most money on races over 1690 to 1709 m. The BRD for the T/T carriers at both SNP loci and for the SINE-free genotype was 1812 to 1854 m. Other performance parameters were not significantly different between the genotypes, except of the relative success score (RSS). The RSS was significantly slightly better on a distance of ≤1300 m for all carriers of the C allele and the Ins227bp compared to homozygous T genotypes and SINE-negative horses (p = 0.037 to 0.046). For distances of more than 1300 m the RSS was not significantly different between genotypes. In silico assessment indicated that the Ins227bp promoter insertion might have generated a CpG island and a few novel putative binding sites for transcription factors. Conclusions All three target polymorphisms (Ins227bp, g.66493737 T ≻ C, BIEC2-417495) are suitable markers to assess the ability of non-elite Thoroughbreds to race at short or longer distances. The CpG island generated by Ins227bp may cause training-induced silencing of MSTN expression. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0428-3) contains supplementary material, which is available to authorized users.
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85
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A transposable element within the Non-canonical telomerase RNA of Arabidopsis thaliana modulates telomerase in response to DNA damage [corrected]. PLoS Genet 2015; 11:e1005281. [PMID: 26075395 PMCID: PMC4468102 DOI: 10.1371/journal.pgen.1005281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as critical factors in many biological processes, but little is known about how their regulatory functions evolved. One of the best-studied lncRNAs is TER, the essential RNA template for telomerase reverse transcriptase. We previously showed that Arabidopsis thaliana harbors three TER isoforms: TER1, TER2 and TER2S. TER1 serves as a canonical telomere template, while TER2 is a novel negative regulator of telomerase activity, induced in response to double-strand breaks (DSBs). TER2 contains a 529 nt intervening sequence that is removed along with 36 nt at the RNA 3’ terminus to generate TER2S, an RNA of unknown function. Here we investigate how A. thaliana TER2 acquired its regulatory function. Using data from the 1,001 Arabidopsis genomes project, we report that the intervening sequence within TER2 is derived from a transposable element termed DSB responsive element (DRE). DRE is found in the TER2 loci of most but not all A. thaliana accessions. By analyzing accessions with (TER2) and without DRE (TER2Δ) we demonstrate that this element is responsible for many of the unique properties of TER2, including its enhanced binding to TERT and telomerase inhibitory function. We show that DRE destabilizes TER2, and further that TER2 induction by DNA damage reflects increased RNA stability and not increased transcription. DRE-mediated changes in TER2 stability thus provide a rapid and sensitive switch to fine-tune telomerase enzyme activity. Altogether, our data shows that invasion of the TER2 locus by a small transposon converted this lncRNA into a DNA damage sensor that modulates telomerase enzyme activity in response to genome assault. Telomerase is a highly regulated enzyme whose activity is essential for long-term cellular proliferation. In the presence of DNA double-strand breaks (DSBs), telomerase activity must be curtailed to promote faithful DNA repair. We previously showed that the flowering plant Arabidopsis thaliana rapidly down-regulates telomerase in response to DSBs, and further that this mode of regulation is dependent on TER2, a non-canonical telomerase RNA subunit. Here we demonstrate that the unique regulatory properties of TER2 are conveyed by a transposable element (TE) embedded in the TER2 gene. A comparison of A. thaliana accessions with and without the TE revealed that the element increases the binding affinity of TER2 for the telomerase catalytic subunit TERT relative to the canonical telomerase RNA subunit. The TE also increases TER2 turnover. In response to DSBs, TER2 is induced and accumulates in TERT containing complexes in vivo. Thus, invasion of a TE endows TER2 with a DNA damage sensor to rapidly and reversibly modulate enzyme activity in response to genotoxic stress. These findings provide an example of how exaptation of a TE altered the function of a long noncoding RNA. In this case, a duplicated gene (TER2) was used as the platform, and the TE as the tool to engineer a novel mode of telomerase regulation.
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86
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Rebeiz M, Patel NH, Hinman VF. Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development. Annu Rev Genomics Hum Genet 2015; 16:103-31. [PMID: 26079281 DOI: 10.1146/annurev-genom-091212-153423] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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87
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Duque T, Sinha S. What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation. Genome Biol Evol 2015; 7:1415-31. [PMID: 25956793 PMCID: PMC4494070 DOI: 10.1093/gbe/evv080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is widespread interest today in understanding enhancers, which are regulatory elements typically harboring several transcription factor binding sites and mediating the combinatorial effect of transcription factors on gene expression. The evolution of enhancers poses interesting unanswered questions, for example, the evolutionary time taken for a typical enhancer to emerge or the factors shaping its evolution. Existing approaches to cis-regulatory evolution have often ignored the combinatorial nature and varied biochemical mechanisms of gene regulation encoded in enhancers. We report on our investigation of enhancer evolution through the use of PEBCRES, a framework for evolutionary simulation of enhancers that employs a mechanistic and well-supported sequence-to-expression model to assign fitness to the evolving enhancer genotype. We estimated the time necessary to evolve, from genomic background, enhancers capable of driving complex gene expression patterns similar to those involved in early development in Drosophila. We found the time-to-evolve to range between 0.5 and 10 Myr, and to vary greatly with the target expression pattern, complexity of the real enhancer known to encode that pattern, and the strength of input from specific transcription factors. To our knowledge, this is the first estimate of waiting times for realistic enhancers to evolve. The in silico evolved enhancers had, with a few interesting exceptions, site compositions similar to those seen in real enhancers for the same patterns. Our simulations also revealed that certain features of an enhancer might evolve not due to their biological function but as aids to the evolutionary process itself.
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Affiliation(s)
- Thyago Duque
- Department of Computer Science, University of Illinois at Urbana-Champaign
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign Institute for Genomic Biology, University of Illinois at Urbana-Champaign
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88
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Ji Y, Marra NJ, DeWoody JA. Comparative analysis of active retrotransposons in the transcriptomes of three species of heteromyid rodents. Gene 2015; 562:95-106. [DOI: 10.1016/j.gene.2015.02.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 10/24/2022]
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89
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Aguirre LA, Alonso ME, Badía-Careaga C, Rollán I, Arias C, Fernández-Miñán A, López-Jiménez E, Aránega A, Gómez-Skarmeta JL, Franco D, Manzanares M. Long-range regulatory interactions at the 4q25 atrial fibrillation risk locus involve PITX2c and ENPEP. BMC Biol 2015; 13:26. [PMID: 25888893 PMCID: PMC4416339 DOI: 10.1186/s12915-015-0138-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/10/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Recent genome-wide association studies have uncovered genomic loci that underlie an increased risk for atrial fibrillation, the major cardiac arrhythmia in humans. The most significant locus is located in a gene desert at 4q25, approximately 170 kilobases upstream of PITX2, which codes for a transcription factor involved in embryonic left-right asymmetry and cardiac development. However, how this genomic region functionally and structurally relates to PITX2 and atrial fibrillation is unknown. RESULTS To characterise its function, we tested genomic fragments from 4q25 for transcriptional activity in a mouse atrial cardiomyocyte cell line and in transgenic mouse embryos, identifying a non-tissue-specific potentiator regulatory element. Chromosome conformation capture revealed that this region physically interacts with the promoter of the cardiac specific isoform of Pitx2. Surprisingly, this regulatory region also interacts with the promoter of the next neighbouring gene, Enpep, which we show to be expressed in regions of the developing mouse heart essential for cardiac electrical activity. CONCLUSIONS Our data suggest that de-regulation of both PITX2 and ENPEP could contribute to an increased risk of atrial fibrillation in carriers of disease-associated variants, and show the challenges that we face in the functional analysis of genome-wide disease associations.
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Affiliation(s)
- Luis A Aguirre
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - M Eva Alonso
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Claudio Badía-Careaga
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Isabel Rollán
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Cristina Arias
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, ctra. de Utrera km1, 41013, Seville, Spain.
| | - Elena López-Jiménez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Amelia Aránega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje de las Lagunillas s/n, 23071, Jaén, Spain.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, ctra. de Utrera km1, 41013, Seville, Spain.
| | - Diego Franco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje de las Lagunillas s/n, 23071, Jaén, Spain.
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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90
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Dhadi SR, Xu Z, Shaik R, Driscoll K, Ramakrishna W. Differential regulation of genes by retrotransposons in rice promoters. PLANT MOLECULAR BIOLOGY 2015; 87:603-13. [PMID: 25697955 DOI: 10.1007/s11103-015-0300-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 02/16/2015] [Indexed: 05/06/2023]
Abstract
Rice genome harbors genes and promoters with retrotransposon insertions. There is very little information about their function. The effect of retrotransposon insertions in four rice promoter regions on gene regulation, was investigated using promoter-reporter gene constructs with and without retrotransposons. Differences in expression levels of gus and egfp reporter genes in forward orientation and rfp in reverse orientation were evaluated in rice plants with transient expression employing quantitative RT-PCR analysis, histochemical GUS staining, and eGFP and RFP fluorescent microscopy. The presence of SINE in the promoter 1 (P1) resulted in higher expression levels of the reporter genes, whereas the presence of LINE in P2 or gypsy LTR retrotransposon in P3 reduced expression of the reporter genes. Furthermore, the SINE in P1 acts as an enhancer in contrast with the LINE in P2 and the gypsy LTR retrotransposon in P3 which act as silencers. CTAA and CGG motifs in these retrotransposons are the likely candidates for the downregulation compared to TCTT motif (SINE) which is a candidate for the upregulation of gene expression. The effect of retrotransposons on gene regulation correlated with the earlier investigation of conservation patterns of these four retrotransposon insertions in several rice accessions implying their evolutionary significance.
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Affiliation(s)
- Surendar Reddy Dhadi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
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91
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Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:403-16. [DOI: 10.1016/j.bbagrm.2014.07.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
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92
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Palazzo AF, Lee ES. Non-coding RNA: what is functional and what is junk? Front Genet 2015; 6:2. [PMID: 25674102 PMCID: PMC4306305 DOI: 10.3389/fgene.2015.00002] [Citation(s) in RCA: 501] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/06/2015] [Indexed: 12/12/2022] Open
Abstract
The genomes of large multicellular eukaryotes are mostly comprised of non-protein coding DNA. Although there has been much agreement that a small fraction of these genomes has important biological functions, there has been much debate as to whether the rest contributes to development and/or homeostasis. Much of the speculation has centered on the genomic regions that are transcribed into RNA at some low level. Unfortunately these RNAs have been arbitrarily assigned various names, such as “intergenic RNA,” “long non-coding RNAs” etc., which have led to some confusion in the field. Many researchers believe that these transcripts represent a vast, unchartered world of functional non-coding RNAs (ncRNAs), simply because they exist. However, there are reasons to question this Panglossian view because it ignores our current understanding of how evolution shapes eukaryotic genomes and how the gene expression machinery works in eukaryotic cells. Although there are undoubtedly many more functional ncRNAs yet to be discovered and characterized, it is also likely that many of these transcripts are simply junk. Here, we discuss how to determine whether any given ncRNA has a function. Importantly, we advocate that in the absence of any such data, the appropriate null hypothesis is that the RNA in question is junk.
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Affiliation(s)
| | - Eliza S Lee
- Department of Biochemistry, University of Toronto Toronto, ON, Canada
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Ayarpadikannan S, Lee HE, Han K, Kim HS. Transposable element-driven transcript diversification and its relevance to genetic disorders. Gene 2015; 558:187-94. [PMID: 25617522 DOI: 10.1016/j.gene.2015.01.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 01/13/2015] [Accepted: 01/20/2015] [Indexed: 12/14/2022]
Abstract
The human genome project and subsequent gene annotation projects have shown that the human genome contains 22,000-25,000 functional genes. Therefore, it is believed that the diversity of protein repertoire is achieved by the alternative splicing (AS) mechanism. Transposable elements (TEs) are mobile in nature and can therefore alter their position in the genome. The insertion of TEs into a new gene region can result in AS of a particular transcript through various mechanisms, including intron retention, and alternative donor or acceptor splice sites. TE-derived AS is thought to have played a part in primate evolution and in hominid radiation. However, TE-derived AS or genetic instability may sometimes result in genetic disorders. For the past two decades, numerous studies have been performed on TEs and their role in genomes. Accumulating evidence shows that the term 'junk DNA', previously used for TEs is a misnomer. Recent research has indicated that TEs may have clinical potential. However, to explore the feasibility of using TEs in clinical practice, additional studies are required. This review summarizes the available literature on TE-derived AS, alternative promoter, and alternative polyadenylation. The review covers the effects of TEs on coding genes and their clinical implications, and provides our perspectives and directions for future research.
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Affiliation(s)
- Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
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94
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Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet 2015; 11:e1004915. [PMID: 25569788 PMCID: PMC4287451 DOI: 10.1371/journal.pgen.1004915] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/24/2014] [Indexed: 11/25/2022] Open
Abstract
Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as “junk” DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize. Transposable elements are mobile DNA elements that are a prevalent component of many eukaryotic genomes. While transposable elements can often have deleterious effects through insertions into protein-coding genes they may also contribute to regulatory variation of gene expression. There are a handful of examples in which specific transposon insertions contribute to regulatory variation of nearby genes, particularly in response to environmental stress. We sought to understand the genome-wide influence of transposable elements on gene expression responses to abiotic stress in maize, a plant with many families of transposable elements located in between genes. Our analysis suggests that a small number of maize transposable element families may contribute to the response of nearby genes to abiotic stress by providing stress-responsive enhancer-like functions. The specific insertions of transposable elements are often polymorphic within a species. Our data demonstrate that allelic variation for insertions of the transposable elements associated with stress-responsive expression can contribute to variation in the regulation of nearby genes. Thus novel insertions of transposable elements provide a potential mechanism for genes to acquire cis-regulatory influences that could contribute to heritable variation for stress response.
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95
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Lee HE, Ayarpadikannan S, Kim HS. Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates. Genes Genet Syst 2015; 90:245-57. [DOI: 10.1266/ggs.15-00016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
- Genetic Engineering Institute, Pusan National University
| | - Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
- Genetic Engineering Institute, Pusan National University
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96
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Comeau AM, Dufour J, Bouvet GF, Jacobi V, Nigg M, Henrissat B, Laroche J, Levesque RC, Bernier L. Functional annotation of the Ophiostoma novo-ulmi genome: insights into the phytopathogenicity of the fungal agent of Dutch elm disease. Genome Biol Evol 2014; 7:410-30. [PMID: 25539722 PMCID: PMC4350166 DOI: 10.1093/gbe/evu281] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 12/18/2022] Open
Abstract
The ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years. We proceeded to annotate the genome of the O. novo-ulmi strain H327 that was sequenced in 2012. The 31.784-Mb nuclear genome (50.1% GC) is organized into 8 chromosomes containing a total of 8,640 protein-coding genes that we validated with RNA sequencing analysis. Approximately 53% of these genes have their closest match to Grosmannia clavigera kw1407, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (5%) orphans. A relatively small portion (∼3.4%) of the genome is occupied by repeat sequences; however, the mechanism of repeat-induced point mutation appears active in this genome. Approximately 76% of the proteins could be assigned functions using Gene Ontology analysis; we identified 311 carbohydrate-active enzymes, 48 cytochrome P450s, and 1,731 proteins potentially involved in pathogen-host interaction, along with 7 clusters of fungal secondary metabolites. Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted. Our analysis identified a specific genetic arsenal impacting the sexual and vegetative growth, phytopathogenicity, and signaling/plant-defense-degradation relationship between O. novo-ulmi and its elm host and insect vectors.
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Affiliation(s)
- André M Comeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada Present address: Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Josée Dufour
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Guillaume F Bouvet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Volker Jacobi
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Martha Nigg
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
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97
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Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res 2014; 24:1963-76. [PMID: 25319995 PMCID: PMC4248313 DOI: 10.1101/gr.168872.113] [Citation(s) in RCA: 300] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transposable elements (TEs) have been shown to contain functional binding sites for certain transcription factors (TFs). However, the extent to which TEs contribute to the evolution of TF binding sites is not well known. We comprehensively mapped binding sites for 26 pairs of orthologous TFs in two pairs of human and mouse cell lines (representing two cell lineages), along with epigenomic profiles, including DNA methylation and six histone modifications. Overall, we found that 20% of binding sites were embedded within TEs. This number varied across different TFs, ranging from 2% to 40%. We further identified 710 TF–TE relationships in which genomic copies of a TE subfamily contributed a significant number of binding peaks for a TF, and we found that LTR elements dominated these relationships in human. Importantly, TE-derived binding peaks were strongly associated with open and active chromatin signatures, including reduced DNA methylation and increased enhancer-associated histone marks. On average, 66% of TE-derived binding events were cell type-specific with a cell type-specific epigenetic landscape. Most of the binding sites contributed by TEs were species-specific, but we also identified binding sites conserved between human and mouse, the functional relevance of which was supported by a signature of purifying selection on DNA sequences of these TEs. Interestingly, several TFs had significantly expanded binding site landscapes only in one species, which were linked to species-specific gene functions, suggesting that TEs are an important driving force for regulatory innovation. Taken together, our data suggest that TEs have significantly and continuously shaped gene regulatory networks during mammalian evolution.
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Affiliation(s)
- Vasavi Sundaram
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Yong Cheng
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Peter Edge
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California 94305, USA;
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
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98
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Kapusta A, Feschotte C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet 2014; 30:439-52. [PMID: 25218058 PMCID: PMC4464757 DOI: 10.1016/j.tig.2014.08.004] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 02/08/2023]
Abstract
Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.
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Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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99
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Barrón MG, Fiston-Lavier AS, Petrov DA, González J. Population genomics of transposable elements in Drosophila. Annu Rev Genet 2014; 48:561-81. [PMID: 25292358 DOI: 10.1146/annurev-genet-120213-092359] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of the population dynamics of transposable elements (TEs) in Drosophila melanogaster indicate that consistent forces are affecting TEs independently of their modes of transposition and regulation. New sequencing technologies enable biologists to sample genomes at an unprecedented scale in order to quantify genome-wide polymorphism for annotated and novel TE insertions. In this review, we first present new insights gleaned from high-throughput data for population genomics studies of D. melanogaster. We then consider the latest population genomics models for TE evolution and present examples of functional evidence revealed by genome-wide studies of TE population dynamics in D. melanogaster. Although most of the TE insertions are deleterious or neutral, some TE insertions increase the fitness of the individual that carries them and play a role in genome adaptation.
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Affiliation(s)
- Maite G Barrón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain 08003; ,
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100
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Brosius J. The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function. Cold Spring Harb Perspect Biol 2014; 6:a016089. [PMID: 25081515 DOI: 10.1101/cshperspect.a016089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary principles valid today become apparent in such models already. Furthermore, many features of eukaryotic genome architecture might have their origins in an RNA or RNA/protein (RNP) world, including the onset of a further transition, when DNA replaced RNA as the genetic bookkeeper of the cell. Chromosome maintenance, splicing, and regulatory function via RNA may be deeply rooted in the RNA/RNP worlds. Mostly in eukaryotes, conversion from RNA to DNA is still ongoing, which greatly impacts the plasticity of extant genomes. Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery.
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Affiliation(s)
- Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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