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Kingsley EP, Hager ER, Lassance JM, Turner KM, Harringmeyer OS, Kirby C, Neugeboren BI, Hoekstra HE. Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development. Nat Ecol Evol 2024; 8:791-805. [PMID: 38378804 PMCID: PMC11009118 DOI: 10.1038/s41559-024-02346-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Variation in the size and number of axial segments underlies much of the diversity in animal body plans. Here we investigate the evolutionary, genetic and developmental mechanisms driving tail-length differences between forest and prairie ecotypes of deer mice (Peromyscus maniculatus). We first show that long-tailed forest mice perform better in an arboreal locomotion assay, consistent with tails being important for balance during climbing. We then identify six genomic regions that contribute to differences in tail length, three of which associate with caudal vertebra length and the other three with vertebra number. For all six loci, the forest allele increases tail length, indicative of the cumulative effect of natural selection. Two of the genomic regions associated with variation in vertebra number contain Hox gene clusters. Of those, we find an allele-specific decrease in Hoxd13 expression in the embryonic tail bud of long-tailed forest mice, consistent with its role in axial elongation. Additionally, we find that forest embryos have more presomitic mesoderm than prairie embryos and that this correlates with an increase in the number of neuromesodermal progenitors, which are modulated by Hox13 paralogues. Together, these results suggest a role for Hoxd13 in the development of natural variation in adaptive morphology on a microevolutionary timescale.
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Affiliation(s)
- Evan P Kingsley
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Emily R Hager
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jean-Marc Lassance
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- GIGA Institute, University of Liège, Liège, Belgium
| | - Kyle M Turner
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Centre for Teaching Support & Innovation, University of Toronto, Toronto, Ontario, Canada
| | - Olivia S Harringmeyer
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Christopher Kirby
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Beverly I Neugeboren
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Environmental Health and Safety, Harvard University, Cambridge, MA, USA
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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2
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Wu CS, Ma ZY, Zheng GD, Zou SM, Zhang XJ, Zhang YA. Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution. BMC Genomics 2022; 23:271. [PMID: 35392810 PMCID: PMC8988418 DOI: 10.1186/s12864-022-08503-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/23/2022] [Indexed: 12/18/2022] Open
Abstract
Background The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well as its unique body plan and environmental adaptation. Results We assembled the chromosome-level grass carp genome using the PacBio sequencing and chromosome structure capture technique. The final genome assembly has a total length of 893.2 Mb with a contig N50 of 19.3 Mb and a scaffold N50 of 35.7 Mb. About 99.85% of the assembled contigs were anchored into 24 chromosomes. Based on the prediction, this genome contained 30,342 protein-coding genes and 43.26% repetitive sequences. Furthermore, we determined that the large genome size can be attributed to the DNA-mediated transposable elements which accounted for 58.9% of the repetitive sequences in grass carp. We identified that the grass carp has only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes. Enrichment analyses of significantly expanded and positively selected genes reflected evolutionary adaptation of grass carp to the feeding habits. We also detected the loss of conserved non-coding regulatory elements associated with the development of the immune system, nervous system, and digestive system, which may be critical for grass carp herbivorous traits. Conclusions The high-quality reference genome reported here provides a valuable resource for the genetic improvement and molecular-guided breeding of the grass carp. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08503-x.
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Affiliation(s)
- Chang-Song Wu
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zi-You Ma
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Guo-Dong Zheng
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Shu-Ming Zou
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xu-Jie Zhang
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, China. .,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China.
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, China. .,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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3
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Fongang B, Kong F, Negi S, Braun W, Kudlicki A. A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes. Sci Rep 2016; 6:35415. [PMID: 27739488 PMCID: PMC5064350 DOI: 10.1038/srep35415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/29/2016] [Indexed: 02/06/2023] Open
Abstract
The homeobox encodes a DNA-binding domain found in transcription factors regulating key developmental processes. The most notable examples of homeobox containing genes are the Hox genes, arranged on chromosomes in the same order as their expression domains along the body axis. The mechanisms responsible for the synchronous regulation of Hox genes and the molecular function of their colinearity remain unknown. Here we report the discovery of a conserved structural signature of the 180-base pair DNA fragment comprising the homeobox. We demonstrate that the homeobox DNA has a characteristic 3-base-pair periodicity in the hydroxyl radical cleavage pattern. This periodic pattern is significant in most of the 39 mammalian Hox genes and in other homeobox-containing transcription factors. The signature is present in segmented bilaterian animals as evolutionarily distant as humans and flies. It remains conserved despite the fact that it would be disrupted by synonymous mutations, which raises the possibility of evolutionary selective pressure acting on the structure of the coding DNA. The homeobox coding DNA may therefore have a secondary function, possibly as a regulatory element. The existence of such element may have important consequences for understanding how these genes are regulated.
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Affiliation(s)
- Bernard Fongang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Fanping Kong
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Surendra Negi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrzej Kudlicki
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
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4
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Warnefors M, Hartmann B, Thomsen S, Alonso CR. Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. Mol Biol Evol 2016; 33:2294-306. [PMID: 27247329 PMCID: PMC4989106 DOI: 10.1093/molbev/msw101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa.
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Affiliation(s)
- Maria Warnefors
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Britta Hartmann
- Institute of Human Genetics, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University Medical Center Freiburg, Freiburg, Germany
| | - Stefan Thomsen
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Claudio R Alonso
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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5
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Martin KJ, Holland PWH. Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication. Mol Biol Evol 2014; 31:2592-611. [PMID: 24974377 PMCID: PMC4166920 DOI: 10.1093/molbev/msu202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/13/2022] Open
Abstract
Numerous ancient whole-genome duplications (WGD) have occurred during eukaryote evolution. In vertebrates, duplicated developmental genes and their functional divergence have had important consequences for morphological evolution. Although two vertebrate WGD events (1R/2R) occurred over 525 Ma, we have focused on the more recent 3R or TGD (teleost genome duplication) event which occurred approximately 350 Ma in a common ancestor of over 26,000 species of teleost fishes. Through a combination of whole genome and bacterial artificial chromosome clone sequencing we characterized all Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha. We find 45 Hox genes organized in only five clusters indicating that Pantodon has suffered more Hox cluster loss than other known species. Despite strong evidence for homology of the five Pantodon clusters to the four canonical pre-TGD vertebrate clusters (one HoxA, two HoxB, one HoxC, and one HoxD), we were unable to confidently resolve 1:1 orthology relationships between four of the Pantodon clusters and the eight post-TGD clusters of other teleosts. Phylogenetic analysis revealed that many Pantodon genes segregate outside the conventional "a" and "b" post-TGD orthology groups, that extensive topological incongruence exists between genes physically linked on a single cluster, and that signal divergence causes ambivalence in assigning 1:1 orthology in concatenated Hox cluster analyses. Out of several possible explanations for this phenomenon we favor a model which keeps with the prevailing view of a single TGD prior to teleost radiation, but which also considers the timing of diploidization after duplication, relative to speciation events. We suggest that although the duplicated hoxa clusters diploidized prior to divergence of osteoglossomorphs, the duplicated hoxb, hoxc, and hoxd clusters concluded diploidization independently in osteoglossomorphs and other teleosts. We use the term "tetralogy" to describe the homology relationship which exists between duplicated sequences which originate through a shared WGD, but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
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Affiliation(s)
- Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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6
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DeInnocentes P, Perry AL, Graff EC, Lutful Kabir FM, Curtis Bird R. Characterization of HOX gene expression in canine mammary tumour cell lines from spontaneous tumours. Vet Comp Oncol 2013; 13:322-36. [PMID: 24034269 DOI: 10.1111/vco.12062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 07/17/2013] [Accepted: 07/22/2013] [Indexed: 01/08/2023]
Abstract
Spatial/temporal controls of development are regulated by the homeotic (HOX) gene complex and require integration with oncogenes and tumour suppressors regulating cell cycle exit. Spontaneously derived neoplastic canine mammary carcinoma cell models were investigated to determine if HOX expression profiles were associated with neoplasia as HOX genes promote neoplastic potential in human cancers. Comparative assessment of human and canine breast cancer expression profiles revealed remarkable similarity for all four paralogous HOX gene clusters and several unlinked HOX genes. Five canine HOX genes were overexpressed with expression profiles consistent with oncogene-like character (HOXA1, HOXA13, HOXD4, HOXD9 and SIX1) and three HOX genes with underexpressed profiles (HOXA11, HOXC8 and HOXC9) were also identified as was an apparent nonsense mutation in HOXC6. This data, as well as a comparative analysis of similar data from human breast cancers suggested expression of selected HOX genes in canine mammary carcinoma could be contributing to the neoplastic phenotype.
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Affiliation(s)
- P DeInnocentes
- Department of Pathobiology, Auburn University, Auburn, AL, 36849, USA.,AURIC-Auburn University Research Initiative in Cancer, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - A L Perry
- Department of Pathobiology, Auburn University, Auburn, AL, 36849, USA
| | - E C Graff
- Department of Pathobiology, Auburn University, Auburn, AL, 36849, USA.,Department of Anatomy, Physiology and Pharmacology, Auburn University, Auburn, AL, 36849, USA
| | - F M Lutful Kabir
- Department of Pathobiology, Auburn University, Auburn, AL, 36849, USA.,AURIC-Auburn University Research Initiative in Cancer, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - R Curtis Bird
- Department of Pathobiology, Auburn University, Auburn, AL, 36849, USA.,AURIC-Auburn University Research Initiative in Cancer, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
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7
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Ryu T, Seridi L, Ravasi T. The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol 2012; 12:236. [PMID: 23217155 PMCID: PMC3556307 DOI: 10.1186/1471-2148-12-236] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 11/09/2012] [Indexed: 11/10/2022] Open
Abstract
Background Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors.
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Affiliation(s)
- Taewoo Ryu
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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8
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Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths. Gene 2012; 505:324-32. [DOI: 10.1016/j.gene.2012.05.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/20/2022]
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9
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Abstract
New studies show that novel long-range enhancers of developmental genes can emerge by exaptation of protein-coding sequences with no previous regulatory function.
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Affiliation(s)
- David Fredman
- Institute of Clinical Sciences, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London, UK
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10
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Eichenlaub MP, Ettwiller L. De novo genesis of enhancers in vertebrates. PLoS Biol 2011; 9:e1001188. [PMID: 22069375 PMCID: PMC3206014 DOI: 10.1371/journal.pbio.1001188] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/22/2011] [Indexed: 02/02/2023] Open
Abstract
Whole genome duplication in teleost fish reveals that a few changes in non-regulatory genomic sequences are a source for generating new enhancers. Evolutionary innovation relies partially on changes in gene regulation. While a growing body of evidence demonstrates that such innovation is generated by functional changes or translocation of regulatory elements via mobile genetic elements, the de novo generation of enhancers from non-regulatory/non-mobile sequences has, to our knowledge, not previously been demonstrated. Here we show evidence for the de novo genesis of enhancers in vertebrates. For this, we took advantage of the massive gene loss following the last whole genome duplication in teleosts to systematically identify regions that have lost their coding capacity but retain sequence conservation with mammals. We found that these regions show enhancer activity while the orthologous coding regions have no regulatory activity. These results demonstrate that these enhancers have been de novo generated in fish. By revealing that minor changes in non-regulatory sequences are sufficient to generate new enhancers, our study highlights an important playground for creating new regulatory variability and evolutionary innovation. The genome of each living organism contains thousands of genes, and the precise control of the timing and location of expression of these genes is key for normal development and homeostasis of each individual. Despite the oftentimes high genetic similarity between organisms, the source of phenotypic differences, for example between human and mouse, is thought to originate mainly from changes in how and when genes are expressed. This is partially determined by enhancers, that contribute to the control of gene expression. For decades, duplication of existing genomic enhancers, mobile elements, and changes in the sequence of existing enhancers were believed to be the major ways of increasing the number and modifying the activity of enhancers. In this study, we show that enhancers don't have to be derived from pre-existing ones but can also appear de novo in regions of the genome that were previously not regulating gene expression. We analyzed teleost fish genomes and found three regions for which a limited number of changes in the DNA sequence was sufficient to generate new enhancers. We predict that such a process is frequent in vertebrate genomes, making de novo generation of enhancers an important mechanism for creating variation in gene expression.
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Affiliation(s)
| | - Laurence Ettwiller
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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11
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Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res 2011; 21:1916-28. [PMID: 21994248 DOI: 10.1101/gr.108753.110] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes--especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their synonymous sites. We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.
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Affiliation(s)
- Michael F Lin
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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12
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Suzuki R, Saitou N. Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes. DNA Res 2011; 18:177-87. [PMID: 21586532 PMCID: PMC3111233 DOI: 10.1093/dnares/dsr010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The primary role of a protein coding gene is to encode amino acids. Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally. However, if a certain region of a protein coding gene contains a functional nucleotide element (e.g. splicing signals), synonymous sites in the region may have selective pressure. The existence of such elements would be detected by searching regions of low nucleotide substitution. We explored invariant nucleotide sequences in 10 790 orthologous genes of six mammalian species (Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris), and extracted 4150 sequences whose conservation is significantly stronger than other regions of the gene and named them significantly conserved coding sequences (SCCSs). SCCSs are observed in 2273 genes. The genes are mainly involved with development, transcriptional regulation, and the neurons, and are expressed in the nervous system and the head and neck organs. No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs. These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.
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Affiliation(s)
- Rumiko Suzuki
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411-8540, Japan
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13
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A preliminary study of differentially expressed genes in expanded skin and normal skin: implications for adult skin regeneration. Arch Dermatol Res 2011; 303:125-33. [PMID: 21286735 DOI: 10.1007/s00403-011-1123-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 01/09/2011] [Accepted: 01/13/2011] [Indexed: 01/31/2023]
Abstract
In adults, severely damaged skin heals by scar formation and cannot regenerate to the original skin structure. However, tissue expansion is an exception, as normal skin regenerates under the mechanical stretch resulting from tissue expansion. This technique has been used clinically for defect repair and organ reconstruction for decades. However, the phenomenon of adult skin regeneration during tissue expansion has caused little attention, and the mechanism of skin regeneration during tissue expansion has not been fully understood. In this study, microarray analysis was performed on expanded human skin and normal human skin. Significant difference was observed in 77 genes, which suggest a network of several integrated cascades, including cytokines, extracellular, cytoskeletal, transmembrane molecular systems, ion or ion channels, protein kinases and transcriptional systems, is involved in the skin regeneration during expansion. Among these, the significant expression of some regeneration related genes, such as HOXA5, HOXB2 and AP1, was the first report in tissue expansion. Data in this study suggest a list of candidate genes, which may help to elucidate the fundamental mechanism of skin regeneration during tissue expansion and which may have implications for postnatal skin regeneration and therapeutic interventions in wound healing.
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14
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Abstract
A recent study in BMC Evolutionary Biology shows that many of the open reading frames in mammalian Hox genes are more conserved than expected on the basis of their protein sequence. The presence of highly conserved DNA elements is thus not confined to the noncoding DNA in neighboring regions but clearly overlaps with coding sequences. These findings support an emerging view that gene regulatory and coding sequences are likely to be more intermingled than once believed.
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Affiliation(s)
- Joost M Woltering
- National Research Centre 'Frontiers in Genetics', Department of Zoology and Animal Biology, University of Geneva, Switzerland
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