1
|
Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky AE, Schoch E, Gagliani EK, Herr AB, Gebelein B, Kovall RA. Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface. Nucleic Acids Res 2024:gkae522. [PMID: 38874471 DOI: 10.1093/nar/gkae522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the following question: How do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely 7 bp apart. However, the mechanistic basis for Gsx-DNA binding and cooperativity is poorly understood. Here, we used biochemical, biophysical, structural and modeling approaches to (i) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation, (ii) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions, (iii) solve a high-resolution monomer/DNA structure that reveals that Gsx2 induces a 20° bend in DNA, (iv) identify a Gsx2 protein-protein interface required for cooperative DNA binding and (v) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors.
Collapse
Affiliation(s)
- Jordan A Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| |
Collapse
|
2
|
Wanninger A. Hox, homology, and parsimony: An organismal perspective. Semin Cell Dev Biol 2024; 152-153:16-23. [PMID: 36670036 DOI: 10.1016/j.semcdb.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/21/2022] [Accepted: 01/08/2023] [Indexed: 01/20/2023]
Abstract
Hox genes are important regulators in animal development. They often show a mosaic of conserved (e.g., longitudinal axis patterning) and lineage-specific novel functions (e.g., development of skeletal, sensory, or locomotory systems). Despite extensive research over the past decades, it remains controversial at which node in the animal tree of life the Hox cluster evolved. Its presence already in the last common metazoan ancestor has been proposed, although the genomes of both putative earliest extant metazoan offshoots, the ctenophores and the poriferans, are devoid of Hox sequences. The lack of Hox genes in the supposedly "simple"-built poriferans and their low number in cnidarians and the basally branching bilaterians, the xenacoelomorphs, seems to support the classical notion that the number of Hox genes is correlated with the degree of animal complexity. However, the 4-fold increase of the Hox cluster in xiphosurans, a basally branching chelicerate clade, as well as the situation in some teleost fishes that show a multitude of Hox genes compared to, e.g., human, demonstrates, that there is no per se direct correlation between organismal complexity and Hox number. Traditional approaches have tried to base homology on the morphological level on shared expression profiles of individual genes, but recent data have shown that, in particular with respect to Hox and other regulatory genes, complex gene-gene interactions rather than expression signatures of individual genes alone are responsible for shaping morphological traits during ontogeny. Accordingly, for sound homology assessments and reconstructions of character evolution on organ system level, additional independent datasets (e.g., morphological, developmental) need to be included in any such analyses. If supported by solid data, proposed structural homology should be regarded as valid and not be rejected solely on the grounds of non-parsimonious distribution of the character over a given phylogenetic topology.
Collapse
Affiliation(s)
- Andreas Wanninger
- University of Vienna, Department of Evolutionary Biology, Unit for Integrative Zoology, Djerassiplatz 1, 1030 Vienna, Austria.
| |
Collapse
|
3
|
Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky AE, Schoch E, Gagliani EK, Herr AB, Gebelein B, Kovall RA. Cooperative Gsx2-DNA Binding Requires DNA Bending and a Novel Gsx2 Homeodomain Interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570805. [PMID: 38106145 PMCID: PMC10723402 DOI: 10.1101/2023.12.08.570805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the question - how do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely seven base pairs apart. However, the mechanistic basis for Gsx DNA binding and cooperativity are poorly understood. Here, we used biochemical, biophysical, structural, and modeling approaches to (1) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation; (2) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions; (3) solve a high-resolution monomer/DNA structure that reveals Gsx2 induces a 20° bend in DNA; (4) identify a Gsx2 protein-protein interface required for cooperative DNA binding; and (5) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors, thereby providing a deeper understanding of HD specificity.
Collapse
Affiliation(s)
- Jordan A. Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K. Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A. Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| |
Collapse
|
4
|
Khan S, Pradhan SJ, Giraud G, Bleicher F, Paul R, Merabet S, Shashidhara LS. A Micro-evolutionary Change in Target Binding Sites as a Key Determinant of Ultrabithorax Function in Drosophila. J Mol Evol 2023; 91:616-627. [PMID: 37341745 DOI: 10.1007/s00239-023-10123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023]
Abstract
Hox genes encode Homeodomain-containing transcription factors, which specify segmental identities along the anterior-posterior axis. Functional changes in Hox genes have been directly implicated in the evolution of body plans across the metazoan lineage. The Hox protein Ultrabithorax (Ubx) is expressed and required in developing third thoracic (T3) segments in holometabolous insects studied so far, particularly, of the order Coleoptera, Lepidoptera and Diptera. Ubx function is key to specify differential development of the second (T2) and T3 thoracic segments in these insects. While Ubx is expressed in the third thoracic segment in developing larvae of Hymenopteran Apis mellifera, the morphological differences between T2 and T3 are subtle. To identify evolutionary changes that are behind the differential function of Ubx in Drosophila and Apis, which are diverged for more than 350 million years, we performed comparative analyses of genome wide Ubx-binding sites between these two insects. Our studies reveal that a motif with a TAAAT core is a preferred binding site for Ubx in Drosophila, but not in Apis. Biochemical and transgenic assays suggest that in Drosophila, the TAAAT core sequence in the Ubx binding sites is required for Ubx-mediated regulation of two of its target genes studied here; CG13222, a gene that is normally upregulated by Ubx and vestigial (vg), whose expression is repressed by Ubx in T3. Interestingly, changing the TAAT site to a TAAAT site was sufficient to bring an otherwise unresponsive enhancer of the vg gene from Apis under the control of Ubx in a Drosophila transgenic assay. Taken together, our results suggest an evolutionary mechanism by which critical wing patterning genes might have come under the regulation of Ubx in the Dipteran lineage.
Collapse
Affiliation(s)
- Soumen Khan
- Indian Institute of Science Education and Research (IISER), Pune, 411008, India.
| | - Saurabh J Pradhan
- Indian Institute of Science Education and Research (IISER), Pune, 411008, India
| | - Guillaume Giraud
- IGFL, ENS Lyon, UMR5242, 32 Av. Tony Garnier, 69007, Lyon, France
| | | | - Rachel Paul
- IGFL, ENS Lyon, UMR5242, 32 Av. Tony Garnier, 69007, Lyon, France
| | - Samir Merabet
- IGFL, ENS Lyon, UMR5242, 32 Av. Tony Garnier, 69007, Lyon, France
| | - L S Shashidhara
- Indian Institute of Science Education and Research (IISER), Pune, 411008, India.
- Ashoka University, Sonipat, Haryana, 131029, India.
| |
Collapse
|
5
|
Nicolini F, Martelossi J, Forni G, Savojardo C, Mantovani B, Luchetti A. Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1046960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Hox and ParaHox genes (HPHGs) are key developmental genes that pattern regional identity along the anterior–posterior body axis of most animals. Here, we identified HPHGs in tadpole shrimps (Pancrustacea, Branchiopoda, Notostraca), an iconic example of the so-called “living fossils” and performed a comparative genomics analysis of HPHGs and the Hox cluster among major branchiopod lineages. Notostraca possess the entire Hox complement, and the Hox cluster seems to be split into two different subclusters, although we were not able to support this finding with chromosome-level assemblies. However, the genomic structure of Hox genes in Notostraca appears more derived than that of Daphnia spp., which instead retains the plesiomorphic condition of a single compact cluster. Spinicaudata and Artemia franciscana show instead a Hox cluster subdivided across two or more genomic scaffolds with some orthologs either duplicated or missing. Yet, branchiopod HPHGs are similar among the various clades in terms of both intron length and number, as well as in their pattern of molecular evolution. Sequence substitution rates are in fact generally similar for most of the branchiopod Hox genes and the few differences we found cannot be traced back to natural selection, as they are not associated with any signals of diversifying selection or substantial switches in selective modes. Altogether, these findings do not support a significant stasis in the Notostraca Hox cluster and further confirm how morphological evolution is not tightly associated with genome dynamics.
Collapse
|
6
|
Wang S, Liu Q, Huang X, Yang C, Chen L, Han M, Shu Y, Wang M, Li W, Hu F, Wen M, Luo K, Wang Y, Zhou R, Zhang C, Tao M, Zhao R, Tang C, Liu S. The rapid variation of Hox clusters reveals a clear evolutionary path in a crucian carp-like homodiploid fish lineage. REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
7
|
Giraud G, Paul R, Duffraisse M, Khan S, Shashidhara LS, Merabet S. Developmental Robustness: The Haltere Case in Drosophila. Front Cell Dev Biol 2021; 9:713282. [PMID: 34368162 PMCID: PMC8343187 DOI: 10.3389/fcell.2021.713282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a “self-sufficient” molecular model to explain the development of a particular flight organ that is under the control of the Hox gene Ultrabithorax (Ubx) in the fruit fly Drosophila melanogaster. Our model is based on a candidate RNAi screen and additional genetic analyses that all converge to an autonomous and cofactor-independent mode of action for Ubx. We postulate that this self-sufficient molecular mechanism is possible due to an unusually high expression level of the Hox protein. We propose that high dosage could constitute a so far poorly investigated molecular strategy for allowing Hox proteins to both innovate and stabilize new forms during evolution.
Collapse
Affiliation(s)
| | | | | | - Soumen Khan
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - L S Shashidhara
- Indian Institute of Science Education and Research (IISER), Pune, India.,Ashoka University, Sonipat, India
| | | |
Collapse
|
8
|
Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL. Nat Commun 2020; 11:2223. [PMID: 32376862 PMCID: PMC7203112 DOI: 10.1038/s41467-020-16024-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 04/08/2020] [Indexed: 11/09/2022] Open
Abstract
Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable to the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.
Collapse
|
9
|
Li K, Sun X, Chen M, Sun Y, Tian R, Wang Z, Xu S, Yang G. Evolutionary changes of Hox genes and relevant regulatory factors provide novel insights into mammalian morphological modifications. Integr Zool 2018; 13:21-35. [PMID: 28685945 PMCID: PMC5817400 DOI: 10.1111/1749-4877.12271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The diversity of body plans of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial and aquatic habitats. However, the genetic basis of those phenotypic modifications, which have occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head–tail axis of animal embryos and the main regulatory factors (Mll, Bmi1 and E2f6) that control the expression of Hox genes. A deflected density of repetitive elements and lineage‐specific radical mutations of Mll have been determined in marine mammals with morphological changes, suggesting that evolutionary changes may alter Hox gene expression in these lineages, leading to the morphological modification of these lineages. Although no positive selection was detected at certain ancestor nodes of lineages, the increased ω values of Hox genes implied the relaxation of functional constraints of these genes during the mammalian evolutionary process. More importantly, 49 positively‐selected sites were identified in mammalian lineages with phenotypic modifications, indicating adaptive evolution acting on Hox genes and regulatory factors. In addition, 3 parallel amino acid substitutions in some Hox genes were examined in marine mammals, which might be responsible for their streamlined body.
Collapse
Affiliation(s)
- Kui Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaohui Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Meixiu Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yingying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
10
|
Sex combs reduced (Scr) regulatory region of Drosophila revisited. Mol Genet Genomics 2017; 292:773-787. [DOI: 10.1007/s00438-017-1309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/08/2017] [Indexed: 10/19/2022]
|
11
|
Arcanjo FG, Silva EP. [Pangenesis, genes, epigenesis]. HISTORIA, CIENCIAS, SAUDE--MANGUINHOS 2017; 24:707-726. [PMID: 29019604 DOI: 10.1590/s0104-59702017000300009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 05/01/2016] [Indexed: 06/07/2023]
Abstract
In 1868, Darwin published his book The variation of animals and plants under domestication, which laid out his theory of heredity. This included the assumption that development was essential to understanding the evolutionary process. This present article reassesses the Darwinian theory of pangenesis in order to revisit its historical value. The conclusion is that the theory of pangenesis was well-suited to its time, and additionally, reflections of this assumption can be found in work in new areas known as evolutionary biology of development (evo-devo) and epigenetics.
Collapse
Affiliation(s)
- Fernanda Gonçalves Arcanjo
- Mestranda, Programa de Pós-graduação em História das Ciências e das Técnicas e Epistemologia/Universidade Federal do Rio de Janeiro; pesquisadora, Laboratório de Genética Marinha e Evolução/Departamento de Biologia Marinha/ Universidade Federal Fluminense (UFF). Outeiro São João Batista, s.n. 24001-970 - Niterói - RJ - Brasil
| | - Edson Pereira Silva
- Professor, Laboratório de Genética Marinha e Evolução/Departamento de Biologia Marinha/UFF. Outeiro São João Batista, s.n. 24001-970 - Niterói - RJ - Brasil
| |
Collapse
|
12
|
Bobola N, Merabet S. Homeodomain proteins in action: similar DNA binding preferences, highly variable connectivity. Curr Opin Genet Dev 2016; 43:1-8. [PMID: 27768937 DOI: 10.1016/j.gde.2016.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022]
Abstract
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs. Clarifying how homeodomain transcription factors work is central to our understanding of development, disease and evolution.
Collapse
Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
| |
Collapse
|
13
|
Bergqvist C, Ramia P, Abbas O, Kurban M. Genetics of syndromic and non-syndromic hereditary nail disorders. Clin Genet 2016; 91:813-823. [PMID: 27613389 DOI: 10.1111/cge.12852] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/22/2016] [Accepted: 08/22/2016] [Indexed: 01/18/2023]
Abstract
The nail is a unique epithelial skin appendage made up of a fully keratinized nail plate. The nail can be affected in several systemic illnesses, dermatological diseases, and inherited nail disorders. Nail dystrophies can present as isolated disorders or as a part of syndromes. Substantial progress has been achieved in the management and diagnosis of nail diseases; however, not much is known about the underlying molecular controls of nail growth. The homeostasis and development of the nail appendage depend on the intricate interactions between the epidermis and underlying mesenchyme, and comprise different signaling pathways such as the WNT signaling pathway. Digit-tip regeneration in mice and humans has been a known fact for the past six decades; however, only recently the underlying biological mechanisms by which the nail organ achieves digit regeneration have been elucidated. Moreover, significant progress has been made in identifying nail stem cells and localizing stem cell niches in the nail unit. More fascinating, however, is the role they play in orchestrating the processes that lead to the regeneration of the digit. Further elucidating the role of nail stem cells and the signaling pathways driving epithelial-mesenchymal interactions in the nail unit might contribute to the development of novel therapeutic tools for amputees.
Collapse
Affiliation(s)
- C Bergqvist
- Department of Dermatology, American University of Beirut, Beirut, Lebanon
| | - P Ramia
- Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - O Abbas
- Department of Dermatology, American University of Beirut, Beirut, Lebanon
| | - M Kurban
- Department of Dermatology, American University of Beirut, Beirut, Lebanon.,Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon.,Department of Dermatology, Columbia University Medical Center, New York, NY, USA
| |
Collapse
|
14
|
Santos ME, Baldo L, Gu L, Boileau N, Musilova Z, Salzburger W. Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes. BMC Genomics 2016; 17:712. [PMID: 27600936 PMCID: PMC5012078 DOI: 10.1186/s12864-016-3046-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background Understanding the genetic basis of novel traits is a central topic in evolutionary biology. Two novel pigmentation phenotypes, egg-spots and blotches, emerged during the rapid diversification of East African cichlid fishes. Egg-spots are circular pigmentation markings on the anal fins of hundreds of derived haplochromine cichlids species, whereas blotches are patches of conspicuous anal fin pigmentation with ill-defined boundaries that occur in few species that belong to basal cichlid lineages. Both traits play an important role in the breeding behavior of this group of fishes. Knowledge about the origin, homology and underlying genetics of these pigmentation traits is sparse. Results Here, we present a comparative transcriptomic and differential gene expression analysis of egg-spots and blotches. We first conducted an RNA sequencing experiment where we compared egg-spot tissue with the remaining portion of egg-spot-free fin tissue using six individuals of Astatotilapia burtoni. We identified 1229 differentially expressed genes between the two tissue types. We then showed that rates of evolution of these genes are higher than average estimated on whole transcriptome data. Using quantitative real-time PCR, we found that 29 out of a subset of 46 differentially expressed genes showed an analogous expression pattern in another haplochromine species’ egg-spots, Cynotilapia pulpican, strongly suggesting that these genes are involved in the egg-spot phenotype. Among these are the previously identified egg-spot gene fhl2a, two known patterning genes (hoxC12a and bmp3) as well as other pigmentation related genes such as asip. Finally, we analyzed the expression patterns of the same gene subset in two species that feature blotches instead of egg-spots, one haplochromine species (Pseudocrenilabrus philander) and one ectodine species (Callochromis macrops), revealing that the expression patterns in blotches and egg-spots are rather distinct. Conclusions We identified several candidate genes that will serve as an important and useful resource for future research on the emergence and diversification of cichlid fishes’ egg-spots. Only a limited degree of conservation of gene expression patterns was detected between the egg-spots of the derived haplochromines and blotches from ancestral haplochromines, as well as between the two types of blotches, suggesting an independent origin of these traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3046-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- M Emília Santos
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure, CNRS UMR 5242, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.
| | - Laura Baldo
- Ecology Department, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Langyu Gu
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Nicolas Boileau
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Zuzana Musilova
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.,Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44, Prague, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| |
Collapse
|
15
|
Merabet S, Mann RS. To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins. Trends Genet 2016; 32:334-347. [PMID: 27066866 DOI: 10.1016/j.tig.2016.03.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding complexes with all Hox proteins. How this family of cofactors contributes to the highly diverse and specific functions of Hox proteins in vivo remains an important unsolved question. We review here the most recent advances in understanding the molecular mechanisms underlying Hox-TALE function. In particular, we discuss the role of DNA shape, DNA-binding affinity, and protein-protein interaction flexibility in dictating Hox-TALE specificity. We propose several models to explain how these mechanisms are integrated with each other in the context of the many distinct functions that Hox and TALE factors carry out in vivo.
Collapse
Affiliation(s)
- Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
| | | |
Collapse
|
16
|
Dediu D, Christiansen MH. Language Evolution: Constraints and Opportunities From Modern Genetics. Top Cogn Sci 2016; 8:361-70. [DOI: 10.1111/tops.12195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Dan Dediu
- Language and Genetics Department; Max Planck Institute for Psycholinguistics
| | | |
Collapse
|
17
|
|
18
|
Ichihashi Y, Tsukaya H. Behavior of Leaf Meristems and Their Modification. FRONTIERS IN PLANT SCIENCE 2015; 6:1060. [PMID: 26648955 PMCID: PMC4664833 DOI: 10.3389/fpls.2015.01060] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/13/2015] [Indexed: 05/06/2023]
Abstract
A major source of diversity in flowering plant form is the extensive variability of leaf shape and size. Leaf formation is initiated by recruitment of a handful of cells flanking the shoot apical meristem (SAM) to develop into a complex three-dimensional structure. Leaf organogenesis depends on activities of several distinct meristems that are established and spatiotemporally differentiated after the initiation of leaf primordia. Here, we review recent findings in the gene regulatory networks that orchestrate leaf meristem activities in a model plant Arabidopsis thaliana. We then discuss recent key studies investigating the natural variation in leaf morphology to understand how the gene regulatory networks modulate leaf meristems to yield a substantial diversity of leaf forms during the course of evolution.
Collapse
Affiliation(s)
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
- Bio-Next Project, Okazaki Institute for Integrative Bioscience, National Institutes of Natural SciencesOkazaki, Japan
| |
Collapse
|
19
|
Pick L. Hox genes, evo-devo, and the case of the ftz gene. Chromosoma 2015; 125:535-51. [PMID: 26596987 DOI: 10.1007/s00412-015-0553-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/11/2015] [Accepted: 10/15/2015] [Indexed: 12/29/2022]
Abstract
The discovery of the broad conservation of embryonic regulatory genes across animal phyla, launched by the cloning of homeotic genes in the 1980s, was a founding event in the field of evolutionary developmental biology (evo-devo). While it had long been known that fundamental cellular processes, commonly referred to as housekeeping functions, are shared by animals and plants across the planet-processes such as the storage of information in genomic DNA, transcription, translation and the machinery for these processes, universal codon usage, and metabolic enzymes-Hox genes were different: mutations in these genes caused "bizarre" homeotic transformations of insect body parts that were certainly interesting but were expected to be idiosyncratic. The isolation of the genes responsible for these bizarre phenotypes turned out to be highly conserved Hox genes that play roles in embryonic patterning throughout Metazoa. How Hox genes have changed to promote the development of diverse body plans remains a central issue of the field of evo-devo today. For this Memorial article series, I review events around the discovery of the broad evolutionary conservation of Hox genes and the impact of this discovery on the field of developmental biology. I highlight studies carried out in Walter Gehring's lab and by former lab members that have continued to push the field forward, raising new questions and forging new approaches to understand the evolution of developmental mechanisms.
Collapse
Affiliation(s)
- Leslie Pick
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD, 20742, USA.
| |
Collapse
|
20
|
Kuasne H, Cólus IMDS, Busso AF, Hernandez-Vargas H, Barros-Filho MC, Marchi FA, Scapulatempo-Neto C, Faria EF, Lopes A, Guimarães GC, Herceg Z, Rogatto SR. Genome-wide methylation and transcriptome analysis in penile carcinoma: uncovering new molecular markers. Clin Epigenetics 2015; 7:46. [PMID: 25908946 PMCID: PMC4407795 DOI: 10.1186/s13148-015-0082-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/06/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Despite penile carcinoma (PeCa) being a relatively rare neoplasm, it remains an important public health issue for poor and developing countries. Contrary to most tumors, limited data are available for markers that are capable of assisting in diagnosis, prognosis, and treatment of PeCa. We aimed to identify molecular markers for PeCa by evaluating their epigenomic and transcriptome profiles and comparing them with surrounding non-malignant tissue (SNT) and normal glans (NG). RESULTS Genome-wide methylation analysis revealed 171 hypermethylated probes in PeCa. Transcriptome profiling presented 2,883 underexpressed and 1,378 overexpressed genes. Integrative analysis revealed a panel of 54 genes with an inverse correlation between methylation and gene expression levels. Distinct methylome and transcriptome patterns were found for human papillomavirus (HPV)-positive (38.6%) and negative tumors. Interestingly, grade 3 tumors showed a distinct methylation profile when compared to grade 1. In addition, univariate analysis revealed that low BDNF methylation was associated with lymph node metastasis and shorter disease-free survival. CpG hypermethylation and gene underexpression were confirmed for a panel of genes, including TWIST1, RSOP2, SOX3, SOX17, PROM1, OTX2, HOXA3, and MEIS1. CONCLUSIONS A unique methylome signature was found for PeCa compared to SNT, with aberrant DNA methylation appearing to modulate the expression of specific genes. This study describes new pathways with the potential to regulate penile carcinogenesis, including stem cell regulatory pathways and markers associated to a worse prognosis. These findings may be instrumental in the discovery and application of new genetic and epigenetic biomarkers in PeCa.
Collapse
Affiliation(s)
- Hellen Kuasne
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
- />Department of Biology, Londrina State University, Londrina, PR Brazil
| | | | - Ariane Fidelis Busso
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
| | | | - Mateus Camargo Barros-Filho
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
| | - Fabio Albuquerque Marchi
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
- />Inter-institutional Grad Program on Bioinformatics, Institute of Mathematics and Statistics, USP, São Paulo, SP Brazil
| | - Cristovam Scapulatempo-Neto
- />Department of Pathology, CPOM - Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP Brazil
| | | | - Ademar Lopes
- />Department of Pelvic Surgery, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Zdenko Herceg
- />Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Silvia Regina Rogatto
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
- />Department of Urology, Faculty of Medicine, UNESP, Botucatu, SP Brazil
| |
Collapse
|
21
|
Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:59-84. [PMID: 25704908 PMCID: PMC4339228 DOI: 10.1002/wdev.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/04/2014] [Accepted: 11/16/2014] [Indexed: 11/08/2022]
Abstract
UNLABELLED Gene expression is regulated through the activity of transcription factors (TFs) and chromatin-modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods have led to an explosion of both computational and empirical methods for CRM discovery in model and nonmodel organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against TFs or histone post-translational modifications, identification of nucleosome-depleted 'open' chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted TF-binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST The authors have declared no conflicts of interest for this article.
Collapse
Affiliation(s)
- Kushal Suryamohan
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| |
Collapse
|
22
|
Sivanantharajah L, Percival-Smith A. Differential pleiotropy and HOX functional organization. Dev Biol 2014; 398:1-10. [PMID: 25448696 DOI: 10.1016/j.ydbio.2014.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/31/2014] [Accepted: 11/01/2014] [Indexed: 12/14/2022]
Abstract
Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment.
Collapse
Affiliation(s)
- Lovesha Sivanantharajah
- Department of Biology, The University of Western Ontario, BGS231, London, Ontario, Canada N6A 5B7.
| | - Anthony Percival-Smith
- Department of Biology, The University of Western Ontario, BGS231, London, Ontario, Canada N6A 5B7
| |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
24
|
Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proc Natl Acad Sci U S A 2014; 111:E2616-21. [PMID: 24927584 DOI: 10.1073/pnas.1402835111] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Despite a long-standing interest in the genetic basis of morphological diversity, the molecular mechanisms that give rise to developmental variation are incompletely understood. Here, we use comparative transcriptomics coupled with the construction of gene coexpression networks to predict a gene regulatory network (GRN) for leaf development in tomato and two related wild species with strikingly different leaf morphologies. The core network in the leaf developmental GRN contains regulators of leaf morphology that function in global cell proliferation with peripheral gene network modules (GNMs). The BLADE-ON-PETIOLE (BOP) transcription factor in one GNM controls the core network by altering effective concentration of the KNOTTED-like HOMEOBOX gene product. Comparative network analysis and experimental perturbations of BOP levels suggest that variation in BOP expression could explain the diversity in leaf complexity among these species through dynamic rewiring of interactions in the GRN. The peripheral location of the BOP-containing GNM in the leaf developmental GRN and the phenotypic mimics of evolutionary diversity caused by alteration in BOP levels identify a key role for this GNM in canalizing the leaf morphospace by modifying the maturation schedule of leaves to create morphological diversity.
Collapse
|
25
|
Abstract
Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.
Collapse
|
26
|
Aufauvre J, Misme-Aucouturier B, Viguès B, Texier C, Delbac F, Blot N. Transcriptome analyses of the honeybee response to Nosema ceranae and insecticides. PLoS One 2014; 9:e91686. [PMID: 24646894 PMCID: PMC3960157 DOI: 10.1371/journal.pone.0091686] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/14/2014] [Indexed: 12/18/2022] Open
Abstract
Honeybees (Apis mellifera) are constantly exposed to a wide variety of environmental stressors such as parasites and pesticides. Among them, Nosema ceranae and neurotoxic insecticides might act in combination and lead to a higher honeybee mortality. We investigated the molecular response of honeybees exposed to N. ceranae, to insecticides (fipronil or imidacloprid), and to a combination of both stressors. Midgut transcriptional changes induced by these stressors were measured in two independent experiments combining a global RNA-Seq transcriptomic approach with the screening of the expression of selected genes by quantitative RT-PCR. Although N. ceranae-insecticide combinations induced a significant increase in honeybee mortality, we observed that they did not lead to a synergistic effect. According to gene expression profiles, chronic exposure to insecticides had no significant impact on detoxifying genes but repressed the expression of immunity-related genes. Honeybees treated with N. ceranae, alone or in combination with an insecticide, showed a strong alteration of midgut immunity together with modifications affecting cuticle coatings and trehalose metabolism. An increasing impact of treatments on gene expression profiles with time was identified suggesting an absence of stress recovery which could be linked to the higher mortality rates observed.
Collapse
Affiliation(s)
- Julie Aufauvre
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Barbara Misme-Aucouturier
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Bernard Viguès
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Catherine Texier
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Frédéric Delbac
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Nicolas Blot
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
- * E-mail:
| |
Collapse
|
27
|
Ramakrishnan S. Morphogenesis, morphology and men: pattern formation from embryo to mind. AI & SOCIETY 2013. [DOI: 10.1007/s00146-013-0504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
28
|
Mallo M, Alonso CR. The regulation of Hox gene expression during animal development. Development 2013; 140:3951-63. [PMID: 24046316 DOI: 10.1242/dev.068346] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hox genes encode a family of transcriptional regulators that elicit distinct developmental programmes along the head-to-tail axis of animals. The specific regional functions of individual Hox genes largely reflect their restricted expression patterns, the disruption of which can lead to developmental defects and disease. Here, we examine the spectrum of molecular mechanisms controlling Hox gene expression in model vertebrates and invertebrates and find that a diverse range of mechanisms, including nuclear dynamics, RNA processing, microRNA and translational regulation, all concur to control Hox gene outputs. We propose that this complex multi-tiered regulation might contribute to the robustness of Hox expression during development.
Collapse
Affiliation(s)
- Moisés Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | | |
Collapse
|
29
|
Frank J, Poblete-Gutiérrez P, Giehl K. [Genetic hair diseases. An update]. Hautarzt 2013; 64:830-42. [PMID: 24177665 DOI: 10.1007/s00105-013-2578-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Patients suffering from hair loss or undesirable excessive hair growth are a challenge for dermatologists because the pathogenesis of most hair diseases is not well understood and therapeutic options are limited. This particularly holds true for genetic hair disorders, in which all current treatment attempts are unsuccessful. Furthermore, these diseases also pose a diagnostic challenge due to a broad range of clinical and genetic heterogeneity. However, the enormous progress in molecular biology over the past 20 years, in particular the availability of different new techniques such as whole exome and genome sequencing, has enabled us to elucidate the genetic basis of most monogenic hair disorders, given the availability of suitable index patients and families as well as adequate technical equipment and sufficient financial resources. In this review we provide an update on clinical and genetic aspects of selected monogenic and polygenic hair diseases manifesting with hypertrichosis and hypotrichosis.
Collapse
Affiliation(s)
- J Frank
- Hautklinik und Sektion für Genodermatosen, Medizinische Fakultät, Heinrich-Heine-Universität Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Deutschland,
| | | | | |
Collapse
|
30
|
Hueber SD, Rauch J, Djordjevic MA, Gunter H, Weiller GF, Frickey T. Analysis of central Hox protein types across bilaterian clades: On the diversification of central Hox proteins from an Antennapedia/Hox7-like protein. Dev Biol 2013; 383:175-85. [DOI: 10.1016/j.ydbio.2013.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/30/2013] [Accepted: 09/05/2013] [Indexed: 11/30/2022]
|
31
|
Marcinkiewicz KM, Gudas LJ. Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells. Exp Cell Res 2013; 320:128-43. [PMID: 24076275 DOI: 10.1016/j.yexcr.2013.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 12/18/2022]
Abstract
To gain insight into oral squamous cell carcinogenesis, we performed deep sequencing (RNAseq) of non-tumorigenic human OKF6-TERT1R and tumorigenic SCC-9 cells. Numerous homeobox genes are differentially expressed between OKF6-TERT1R and SCC-9 cells. Data from Oncomine, a cancer microarray database, also show that homeobox (HOX) genes are dysregulated in oral SCC patients. The activity of Polycomb repressive complexes (PRC), which causes epigenetic modifications, and retinoic acid (RA) signaling can control HOX gene transcription. HOXB7, HOXC10, HOXC13, and HOXD8 transcripts are higher in SCC-9 than in OKF6-TERT1R cells; using ChIP (chromatin immunoprecipitation) we detected PRC2 protein SUZ12 and the epigenetic H3K27me3 mark on histone H3 at these genes in OKF6-TERT1R, but not in SCC-9 cells. In contrast, IRX1, IRX4, SIX2 and TSHZ3 transcripts are lower in SCC-9 than in OKF6-TERT1R cells. We detected SUZ12 and the H3K27me3 mark at these genes in SCC-9, but not in OKF6-TERT1R cells. SUZ12 depletion increased HOXB7, HOXC10, HOXC13, and HOXD8 transcript levels and decreased the proliferation of OKF6-TERT1R cells. Transcriptional responses to RA are attenuated in SCC-9 versus OKF6-TERT1R cells. SUZ12 and H3K27me3 levels were not altered by RA at these HOX genes in SCC-9 and OKF6-TERT1R cells. We conclude that altered activity of PRC2 is associated with dysregulation of homeobox gene expression in human SCC cells, and that this dysregulation potentially plays a role in the neoplastic transformation of oral keratinocytes.
Collapse
Affiliation(s)
- Katarzyna M Marcinkiewicz
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | | |
Collapse
|
32
|
Posterior Hox gene reduction in an arthropod: Ultrabithorax and Abdominal-B are expressed in a single segment in the mite Archegozetes longisetosus. EvoDevo 2013; 4:23. [PMID: 23991696 PMCID: PMC3766265 DOI: 10.1186/2041-9139-4-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/15/2013] [Indexed: 01/18/2023] Open
Abstract
Background Hox genes encode transcription factors that have an ancestral role in all bilaterian animals in specifying regions along the antero-posterior axis. In arthropods (insects, crustaceans, myriapods and chelicerates), Hox genes function to specify segmental identity, and changes in Hox gene expression domains in different segments have been causal to the evolution of novel arthropod morphologies. Despite this, the roles of Hox genes in arthropods that have secondarily lost or reduced their segmental composition have been relatively unexplored. Recent data suggest that acariform mites have a reduced segmental component of their posterior body tagma, the opisthosoma, in that only two segments are patterned during embryogenesis. This is in contrast to the observation that in many extinct and extant chelicerates (that is, horseshoe crabs, scorpions, spiders and harvestmen) the opisthosoma is comprised of ten or more segments. To explore the role of Hox genes in this reduced body region, we followed the expression of the posterior-patterning Hox genes Ultrabithorax (Ubx) and Abdominal-B (Abd-B), as well as the segment polarity genes patched (ptc) and engrailed (en), in the oribatid mite Archegozetes longisetosus. Results We find that the expression patterns of ptc are in agreement with previous reports of a reduced mite opisthosoma. In comparison to the ptc and en expression patterns, we find that Ubx and Abd-B are expressed in a single segment in A. longisetosus, the second opisthosomal segment. Abd-B is initially expressed more posteriorly than Ubx, that is, into the unsegmented telson; however, this domain clears in subsequent stages where it remains in the second opisthosomal segment. Conclusions Our findings suggest that Ubx and Abd-B are expressed in a single segment in the opisthosoma. This is a novel observation, in that these genes are expressed in several segments in all studied arthropods. These data imply that a reduction in opisthosomal segmentation may be tied to a dramatically reduced Hox gene input in the opisthosoma.
Collapse
|
33
|
Ali R, Habib R, ud-Din N, Khan M, Ansar M, Ahmad W. Novel mutations in the geneHOXC13underlying pure hair and nail ectodermal dysplasia in consanguineous families. Br J Dermatol 2013; 169:478-80. [DOI: 10.1111/bjd.12302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- R.H. Ali
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University Islamabad; Islamabad Pakistan
| | - R. Habib
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University Islamabad; Islamabad Pakistan
| | - N. ud-Din
- Department of Zoology; University of Azad Jammu and Kashmir; Muzafarabad Pakistan
| | - M.N. Khan
- Department of Zoology; University of Azad Jammu and Kashmir; Muzafarabad Pakistan
| | - M. Ansar
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University Islamabad; Islamabad Pakistan
| | - W. Ahmad
- Department of Biochemistry; Faculty of Biological Sciences; Quaid-i-Azam University Islamabad; Islamabad Pakistan
| |
Collapse
|
34
|
Diepeveen ET, Kim FD, Salzburger W. Sequence analyses of the distal-less homeobox gene family in East African cichlid fishes reveal signatures of positive selection. BMC Evol Biol 2013; 13:153. [PMID: 23865956 PMCID: PMC3728225 DOI: 10.1186/1471-2148-13-153] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gen(om)e duplication events are hypothesized as key mechanisms underlying the origin of phenotypic diversity and evolutionary innovation. The diverse and species-rich lineage of teleost fishes is a renowned example of this scenario, because of the fish-specific genome duplication. Gene families, generated by this and other gene duplication events, have been previously found to play a role in the evolution and development of innovations in cichlid fishes - a prime model system to study the genetic basis of rapid speciation, adaptation and evolutionary innovation. The distal-less homeobox genes are particularly interesting candidate genes for evolutionary novelties, such as the pharyngeal jaw apparatus and the anal fin egg-spots. Here we study the dlx repertoire in 23 East African cichlid fishes to determine the rate of evolution and the signatures of selection pressure. RESULTS Four intact dlx clusters were retrieved from cichlid draft genomes. Phylogenetic analyses of these eight dlx loci in ten teleost species, followed by an in-depth analysis of 23 East African cichlid species, show that there is disparity in the rates of evolution of the dlx paralogs. Dlx3a and dlx4b are the fastest evolving dlx genes, while dlx1a and dlx6a evolved more slowly. Subsequent analyses of the nonsynonymous-synonymous substitution rate ratios indicate that dlx3b, dlx4a and dlx5a evolved under purifying selection, while signs of positive selection were found for dlx1a, dlx2a, dlx3a and dlx4b. CONCLUSIONS Our results indicate that the dlx repertoire of teleost fishes and cichlid fishes in particular, is shaped by differential selection pressures and rates of evolution after gene duplication. Although the divergence of the dlx paralogs are putative signs of new or altered functions, comparisons with available expression patterns indicate that the three dlx loci under strong purifying selection, dlx3b, dlx4a and dlx5a, are transcribed at high levels in the cichlids' pharyngeal jaw and anal fin. The dlx paralogs emerge as excellent candidate genes for the development of evolutionary innovations in cichlids, although further functional analyses are necessary to elucidate their respective contribution.
Collapse
Affiliation(s)
- Eveline T Diepeveen
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.
| | | | | |
Collapse
|
35
|
cis-regulatory change associated with snake body plan evolution. Proc Natl Acad Sci U S A 2013; 110:10473-4. [PMID: 23749870 DOI: 10.1073/pnas.1307778110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
36
|
Kippler M, Engström K, Mlakar SJ, Bottai M, Ahmed S, Hossain MB, Raqib R, Vahter M, Broberg K. Sex-specific effects of early life cadmium exposure on DNA methylation and implications for birth weight. Epigenetics 2013; 8:494-503. [PMID: 23644563 PMCID: PMC3741219 DOI: 10.4161/epi.24401] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary cadmium exposure was recently found to alter DNA methylation in adults, but data on effects early in life are lacking. Our objective was to evaluate associations between prenatal cadmium exposure, DNA methylation and birth weight. In total 127 mother-child pairs from rural Bangladesh were studied. For comparison, we included 56 children at 4.5 y. Cadmium concentrations in mothers’ blood (gestational week 14) and children’s urine were measured by ICPMS. Global DNA methylation was analyzed by Infinium HumanMethylation450K BeadChip in cord blood and children’s blood. Maternal cadmium exposure was associated with cord blood DNA methylation (p-value < 10–16). The association was markedly sex-specific. In boys, 96% of the top 500 CpG sites showed positive correlations (rS-values > 0.50), whereas most associations in girls were inverse; only 29% were positive (rS > 0.45). In girls we found overrepresentation of methylation changes in genes associated with organ development, morphology and mineralization of bone, whereas changes in boys were found in cell death-related genes. Several individual CpG sites that were positively associated with cadmium were inversely correlated with birth weight, although none statistically significant after correction for multiple comparisons. The associations were, however, fairly robust in multivariable-adjusted linear regression models. We identified CpG sites that were significantly associated with cadmium exposure in both newborns and 4.5-y-old children. In conclusion, cadmium exposure in early life appears to alter DNA methylation differently in girls and boys. This is consistent with previous findings of sex-specific cadmium toxicity. Cadmium-related changes in methylation were also related to lower birth weight.
Collapse
Affiliation(s)
- Maria Kippler
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
Despite enormous body plan variation, genes regulating embryonic development are highly conserved. Here, we probe the mechanisms that predispose ancient regulatory genes to reutilization and diversification rather than evolutionary loss. The Hox gene fushi tarazu (ftz) arose as a homeotic gene but functions as a pair-rule segmentation gene in Drosophila. ftz shows extensive variation in expression and protein coding regions but has managed to elude loss from arthropod genomes. We asked what properties prevent this loss by testing the importance of different protein motifs and partners in the developing CNS, where ftz expression is conserved. Drosophila Ftz proteins with mutated protein motifs were expressed under the control of a neurogenic-specific ftz cis-regulatory element (CRE) in a ftz mutant background rescued for segmentation defects. Ftz CNS function did not require the variable motifs that mediate differential cofactor interactions involved in homeosis or segmentation, which vary in arthropods. Rather, CNS function did require the shared DNA-binding homeodomain, which plays less of a role in Ftz segmentation activity. The Antennapedia homeodomain substituted for Ftz homeodomain function in the Drosophila CNS, but full-length Antennapedia did not rescue CNS defects. These results suggest that a core CNS function retains ftz in arthropod genomes. Acquisition of a neurogenic CRE led to ftz expression in unique CNS cells, differentiating its role from neighboring Hox genes, rendering it nonredundant. The inherent flexibility of modular CREs and protein domains allows for stepwise acquisition of new functions, explaining broad retention of regulatory genes during animal evolution.
Collapse
Affiliation(s)
- Alison Heffer
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD 20742
| | - Jie Xiang
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD 20742
| | - Leslie Pick
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD 20742
| |
Collapse
|
38
|
Lin Z, Chen Q, Shi L, Lee M, Giehl KA, Tang Z, Wang H, Zhang J, Yin J, Wu L, Xiao R, Liu X, Dai L, Zhu X, Li R, Betz RC, Zhang X, Yang Y. Loss-of-function mutations in HOXC13 cause pure hair and nail ectodermal dysplasia. Am J Hum Genet 2012; 91:906-11. [PMID: 23063621 DOI: 10.1016/j.ajhg.2012.08.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/20/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022] Open
Abstract
Pure hair and nail ectodermal dysplasia (PHNED) is a congenital condition characterized by hypotrichosis and nail dystrophy. Autosomal-recessive PHNED has previously been mapped to chromosomal region 12q12-q14.1, which contains the type II hair keratin and HOXC clusters. Hoxc13-null mice are known to develop hair and nail defects very similar to those seen in human PHNED. We performed whole-exome sequencing in a consanguineous Chinese family affected by PHNED and identified a homozygous nonsense mutation (c.390C>A [p.Tyr130(∗)]) in HOXC13 in all affected individuals. In an additional affected female from a consanguineous Afghan family, we found a 27.6 kb homozygous microdeletion involving the first exon of HOXC13. We examined HOXC13 expression in scalp specimen obtained from the index individual of the Chinese family and detected dramatically reduced mRNA levels in skin tissue and nearly absent protein staining in hair follicles, suggesting a mechanism of nonsense-mediated mRNA decay. We also observed markedly decreased expression of four HOXC13 target genes in the specimen. Taken together, our results demonstrate that loss-of-function mutations in HOXC13 cause autosomal-recessive PHNED and further highlight the importance of HOXC13 in hair and nail development.
Collapse
Affiliation(s)
- Zhimiao Lin
- Department of Dermatology, Peking University First Hospital, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
The resiliency and adaptive ability of microbial life in real time on Earth relies heavily upon horizontal gene transfer. Based on that knowledge, how likely is earth based microbial life to colonize extraterrestrial targets such as Mars? To address this question, we consider manned and unmanned space exploration, the resident microbiota that is likely to inhabit those vehicles, the adaptive potential of that microbiota in an extraterrestrial setting especially with regards to mobile genetic elements, and the likelihood that Mars like environments could initiate and sustain colonization.
Collapse
|
40
|
Gaunt SJ, Paul YL. Changes in Cis-regulatory Elements during Morphological Evolution. BIOLOGY 2012; 1:557-74. [PMID: 24832508 PMCID: PMC4009813 DOI: 10.3390/biology1030557] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/30/2012] [Accepted: 10/09/2012] [Indexed: 11/23/2022]
Abstract
How have animals evolved new body designs (morphological evolution)? This requires explanations both for simple morphological changes, such as differences in pigmentation and hair patterns between different Drosophila populations and species, and also for more complex changes, such as differences in the forelimbs of mice and bats, and the necks of amphibians and reptiles. The genetic changes and pathways involved in these evolutionary steps require identification. Many, though not all, of these events occur by changes in cis-regulatory (enhancer) elements within developmental genes. Enhancers are modular, each affecting expression in only one or a few tissues. Therefore it is possible to add, remove or alter an enhancer without producing changes in multiple tissues, and thereby avoid widespread (pleiotropic) deleterious effects. Ideally, for a given step in morphological evolution it is necessary to identify (i) the change in phenotype, (ii) the changes in gene expression, (iii) the DNA region, enhancer or otherwise, affected, (iv) the mutation involved, (v) the nature of the transcription or other factors that bind to this site. In practice these data are incomplete for most of the published studies upon morphological evolution. Here, the investigations are categorized according to how far these analyses have proceeded.
Collapse
Affiliation(s)
| | - Yu-Lee Paul
- The Babraham Institute, Babraham, Cambridge, CB22 3AT, UK.
| |
Collapse
|
41
|
Siefert JL, Souza V, Eguiarte L, Olmedo-Alvarez G. Microbial stowaways: inimitable survivors or hopeless pioneers? ASTROBIOLOGY 2012; 12:710-715. [PMID: 22920519 DOI: 10.1089/ast.2012.0833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The resiliency of prokaryotic life has provided colonization across the globe and in the recesses of Earth's most extreme environments. Horizontal gene transfer provides access to a global bank of genetic resources that creates diversity and allows real-time adaptive potential to the clonal prokaryotic world. We assess the likelihood that this Earth-based strategy could provide survival and adaptive potential, in the case of microbial stowaways off Earth.
Collapse
Affiliation(s)
- Janet L Siefert
- Department of Statistics, Rice University, Houston, Texas, USA.
| | | | | | | |
Collapse
|