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Ren H, Huang L, Zhang H, Huang M, Meng J, Luo D. Unveiling the role of RARs in stomach adenocarcinoma: clinical implications and prognostic biomarkers. Transl Cancer Res 2024; 13:3974-3995. [PMID: 39262490 PMCID: PMC11384927 DOI: 10.21037/tcr-23-2154] [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: 11/22/2023] [Accepted: 07/10/2024] [Indexed: 09/13/2024]
Abstract
Background Retinoic acid receptors (RARs) family are known to play a significant role in the occurrence and development of tumors. However, the relationship between RARs and stomach adenocarcinoma (STAD) has not yet been clearly identified. The aim of this study is to evaluate the expression profile and clinical value of the RARs family in STAD. Methods The expression level, clinical characteristics, prognostic value, immunity-related evaluations, genetic alteration and methylation site of RARs in STAD were explored using a series of online databases including gene expression profiling interactive analysis (GEPIA), tumor immune estimation resource (TIMER), University of Alabama at Birmingham cancer data (UALCAN), Human Protein Atlas (HPA), Kaplan-Meier plotter, gene set cancer analysis (GSCA), cBioPortal, MethSurv, GeneMANIA, LinkedOmics, Metascape, Search tool for the retrieval of interacting genes (STRING), tumor immune single-cell hub (TISCH) and cancer cell line encyclopedia (CCLE). Results We discovered dramatically increased expression of RARA and decreased expression of RARB in STAD tissues, and many clinical variables were closely related to RARs. Notably, higher expressions of RARA and RARB as well as lower expression of RARG correlated with worse overall survival (OS) for STAD patients. The clinical value of prognostic model indicated that RARs were identified to be potential prognostic biomarkers for STAD patients. Moreover, RARB was closely related to immune cell infiltration, which had effect on the role of RARB in STAD prognosis. And the genetic alteration of RARB was significantly associated with the longer disease-free survival (DFS) of STAD patients. Additionally, some CpG sites of the RARs family were related with the prognosis of STAD patients. Functional enrichment analyses indicated that several pathways in STAD might be pivotal pathways regulated by RARs. At the single-cell level, there was some extent of infiltration of tumor microenvironment-related cells in the RARs expression in STAD. Conclusions Our results evaluated the expression profile and clinical values of RARs in patients with STAD, which provided a basis for future in-depth exploration of the specific mechanisms of each member of RARs in STAD.
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Affiliation(s)
- Hongyue Ren
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou, China
| | - Lifeng Huang
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou, China
| | - Haiyan Zhang
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou, China
| | - Meirong Huang
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou, China
| | - Jiarong Meng
- Department of Pathology, Dongnan Hospital of Xiamen University, School of Medicine, Xiamen University, Zhangzhou, China
| | - Deqing Luo
- Department of Orthopaedic Surgery, Dongnan Hospital of Xiamen University, School of Medicine, Xiamen University, Zhangzhou, China
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2
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Goncalves MB, Wu Y, Clarke E, Grist J, Moehlin J, Mendoza-Parra MA, Hobbs C, Kalindjian B, Fok H, Mander AP, Hassanin H, Bendel D, Täubel J, Mant T, Carlstedt T, Jack J, Corcoran JPT. C286, an orally available retinoic acid receptor β agonist drug, regulates multiple pathways to achieve spinal cord injury repair. Front Mol Neurosci 2024; 17:1411384. [PMID: 39228795 PMCID: PMC11368863 DOI: 10.3389/fnmol.2024.1411384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Retinoic acid receptor β2 (RARβ2) is an emerging therapeutic target for spinal cord injuries (SCIs) with a unique multimodal regenerative effect. We have developed a first-in-class RARβ agonist drug, C286, that modulates neuron-glial pathways to induce functional recovery in a rodent model of sensory root avulsion. Here, using genome-wide and pathway enrichment analysis of avulsed rats' spinal cords, we show that C286 also influences the extracellular milieu (ECM). Protein expression studies showed that C286 upregulates tenascin-C, integrin-α9, and osteopontin in the injured cord. Similarly, C286 remodulates these ECM molecules, hampers inflammation and prevents tissue loss in a rodent model of spinal cord contusion C286. We further demonstrate C286's efficacy in human iPSC-derived neurons, with treatment resulting in a significant increase in neurite outgrowth. Additionally, we identify a putative efficacy biomarker, S100B, which plasma levels correlated with axonal regeneration in nerve-injured rats. We also found that other clinically available retinoids, that are not RARβ specific agonists, did not lead to functional recovery in avulsed rats, demonstrating the requirement for RARβ specific pathways in regeneration. In a Phase 1 trial, the single ascending dose (SAD) cohorts showed increases in expression of RARβ2 in white blood cells correlative to increased doses and at the highest dose administered, the pharmacokinetics were similar to the rat proof of concept (POC) studies. Collectively, our data suggests that C286 signalling in neurite/axonal outgrowth is conserved between species and across nerve injuries. This warrants further clinical testing of C286 to ascertain POC in a broad spectrum of neurodegenerative conditions.
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Affiliation(s)
- Maria B. Goncalves
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Yue Wu
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Earl Clarke
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - John Grist
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Julien Moehlin
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Évry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - Marco Antonio Mendoza-Parra
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Évry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - Carl Hobbs
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Barret Kalindjian
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Henry Fok
- NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Adrian P. Mander
- Centre for Trials Research, Cardiff University, Cardiff, United Kingdom
| | - Hana Hassanin
- Surrey Clinical Research Centre, University of Surrey, Guildford, United Kingdom
| | - Daryl Bendel
- Surrey Clinical Research Centre, University of Surrey, Guildford, United Kingdom
| | - Jörg Täubel
- Richmond Pharmacology Limited, London, United Kingdom
| | - Tim Mant
- NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Thomas Carlstedt
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Julian Jack
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
| | - Jonathan P. T. Corcoran
- Neuroscience Drug Discovery Unit, Wolfson Sensory, Pain and Regeneration Centre, King's College London, Guy's Campus, London, United Kingdom
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3
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Wilson AE, Liberles DA. Expectations of duplicate gene retention under the gene duplicability hypothesis. BMC Ecol Evol 2023; 23:76. [PMID: 38097959 PMCID: PMC10720195 DOI: 10.1186/s12862-023-02174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Gene duplication is an important process in evolution. What causes some genes to be retained after duplication and others to be lost is a process not well understood. The most prevalent theory is the gene duplicability hypothesis, that something about the function and number of interacting partners (number of subunits of protein complex, etc.), determines whether copies have more opportunity to be retained for long evolutionary periods. Some genes are also more susceptible to dosage balance effects following WGD events, making them more likely to be retained for longer periods of time. One would expect these processes that affect the retention of duplicate copies to affect the conditional probability ratio after consecutive whole genome duplication events. The probability that a gene will be retained after a second whole genome duplication event (WGD2), given that it was retained after the first whole genome duplication event (WGD1) versus the probability a gene will be retained after WGD2, given it was lost after WGD1 defines the probability ratio that is calculated. RESULTS Since duplicate gene retention is a time heterogeneous process, the time between the events (t1) and the time since the most recent event (t2) are relevant factors in calculating the expectation for observation in any genome. Here, we use a survival analysis framework to predict the probability ratio for genomes with different values of t1 and t2 under the gene duplicability hypothesis, that some genes are more susceptible to selectable functional shifts, some more susceptible to dosage compensation, and others only drifting. We also predict the probability ratio with different values of t1 and t2 under the mutational opportunity hypothesis, that probability of retention for certain genes changes in subsequent events depending upon how they were previously retained. These models are nested such that the mutational opportunity model encompasses the gene duplicability model with shifting duplicability over time. Here we present a formalization of the gene duplicability and mutational opportunity hypotheses to characterize evolutionary dynamics and explanatory power in a recently developed statistical framework. CONCLUSIONS This work presents expectations of the gene duplicability and mutational opportunity hypotheses over time under different sets of assumptions. This expectation will enable formal testing of processes leading to duplicate gene retention.
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Affiliation(s)
- Amanda E Wilson
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA.
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4
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Serrano C, Lopes-Marques M, Amorim A, João Prata M, Azevedo L. A partial duplication of an X-linked gene exclusive of a primate lineage (Macaca). Gene 2023; 851:146997. [DOI: 10.1016/j.gene.2022.146997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022]
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5
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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6
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Peterson KJ, Beavan A, Chabot PJ, McPeek MA, Pisani D, Fromm B, Simakov O. MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events. Mol Biol Evol 2022; 39:msab344. [PMID: 34865078 PMCID: PMC8789304 DOI: 10.1093/molbev/msab344] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Whole-genome duplications (WGDs) have long been considered the causal mechanism underlying dramatic increases to morphological complexity due to the neo-functionalization of paralogs generated during these events. Nonetheless, an alternative hypothesis suggests that behind the retention of most paralogs is not neo-functionalization, but instead the degree of the inter-connectivity of the intended gene product, as well as the mode of the WGD itself. Here, we explore both the causes and consequences of WGD by examining the distribution, expression, and molecular evolution of microRNAs (miRNAs) in both gnathostome vertebrates as well as chelicerate arthropods. We find that although the number of miRNA paralogs tracks the number of WGDs experienced within the lineage, few of these paralogs experienced changes to the seed sequence, and thus are functionally equivalent relative to their mRNA targets. Nonetheless, in gnathostomes, although the retention of paralogs following the 1R autotetraploidization event is similar across the two subgenomes, the paralogs generated by the gnathostome 2R allotetraploidization event are retained in higher numbers on one subgenome relative to the second, with the miRNAs found on the preferred subgenome showing both higher expression of mature miRNA transcripts and slower molecular evolution of the precursor miRNA sequences. Importantly, WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
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Affiliation(s)
- Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Alan Beavan
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Mark A McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Bastian Fromm
- Arctic University Museum of Norway, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
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7
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Mottes F, Villa C, Osella M, Caselle M. The impact of whole genome duplications on the human gene regulatory networks. PLoS Comput Biol 2021; 17:e1009638. [PMID: 34871317 PMCID: PMC8675932 DOI: 10.1371/journal.pcbi.1009638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/16/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
This work studies the effects of the two rounds of Whole Genome Duplication (WGD) at the origin of the vertebrate lineage on the architecture of the human gene regulatory networks. We integrate information on transcriptional regulation, miRNA regulation, and protein-protein interactions to comparatively analyse the role of WGD and Small Scale Duplications (SSD) in the structural properties of the resulting multilayer network. We show that complex network motifs, such as combinations of feed-forward loops and bifan arrays, deriving from WGD events are specifically enriched in the network. Pairs of WGD-derived proteins display a strong tendency to interact both with each other and with common partners and WGD-derived transcription factors play a prominent role in the retention of a strong regulatory redundancy. Combinatorial regulation and synergy between different regulatory layers are in general enhanced by duplication events, but the two types of duplications contribute in different ways. Overall, our findings suggest that the two WGD events played a substantial role in increasing the multi-layer complexity of the vertebrate regulatory network by enhancing its combinatorial organization, with potential consequences on its overall robustness and ability to perform high-level functions like signal integration and noise control. Lastly, we discuss in detail the RAR/RXR pathway as an illustrative example of the evolutionary impact of WGD duplications in human. Gene duplication is one of the main mechanisms driving genome evolution. The duplication of a genomic segment can be the result of a local event, involving only a small portion of the genome, or of a dramatic duplication of the whole genome, which is however only rarely retained. All vertebrates descend from two rounds of Whole-Genome Duplication (WGD) that occurred approximately 500 Mya. We show that these events influenced in unique ways the evolution of different human gene regulatory networks, with sizeable effects on their current structure. We find that WGDs statistically increased the presence of specific classes of simple genetic circuits, considered to be fundamental building blocks of more sophisticated circuitry and commonly associated to complex functions. Our findings support the hypothesis that these rare, large-scale events have played a substantial role in the emergence of complex traits in vertebrates.
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Affiliation(s)
| | - Chiara Villa
- School of Mathematics and Statistics, University of St Andrews, Mathematical Institute, North Haugh, St Andrews, United Kingdom
| | - Matteo Osella
- Department of Physics, University of Turin & INFN, Turin, Italy
| | - Michele Caselle
- Department of Physics, University of Turin & INFN, Turin, Italy
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8
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Jin K, Jin Q, Cai Z, Huang B, Wei L, Zhang M, Guo W, Liu Y, Wang X. Molecular Characterization of Retinoic Acid Receptor CgRAR in Pacific Oyster ( Crassostrea gigas). Front Physiol 2021; 12:666842. [PMID: 33897474 PMCID: PMC8060629 DOI: 10.3389/fphys.2021.666842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Retinoic acid (RA) signaling pathways mediated by RA receptors (RARs) are essential for many physiological processes such as organ development, regeneration, and differentiation in animals. Recent studies reveal that RARs identified in several mollusks, including Pacific oyster Crassostrea gigas, have a different function mechanism compared with that in chordates. In this report, we identified the molecular characteristics of CgRAR to further explore the mechanism of RAR in mollusks. RT-qPCR analysis shows that CgRAR has a higher expression level in the hemocytes and gonads, indicating that CgRAR may play roles in the processes of development and metabolism. The mRNA expression level of both CgRAR and CgRXR was analyzed by RT-qPCR after injection with RA. The elevated expression of CgRAR and CgRXR was detected upon all-trans-RA (ATRA) exposure. Finally, according to the results of Yeast Two-Hybrid assay and co-immunoprecipitation analysis, CgRAR and CgRXR can interact with each other through the C-terminal region. Taken together, our results suggest that CgRAR shows a higher expression level in gonads and hemocytes. ATRA exposure up-regulates the expression of CgRAR and CgRXR. Besides, CgRAR can interact with CgRXR to form a heterodimer complex.
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Affiliation(s)
- Kaidi Jin
- School of Agriculture, Ludong University, Yantai, China
| | - Qianqian Jin
- School of Agriculture, Ludong University, Yantai, China
| | - Zhongqiang Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao, China
| | - Baoyu Huang
- School of Agriculture, Ludong University, Yantai, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Meiwei Zhang
- School of Agriculture, Ludong University, Yantai, China
| | - Wen Guo
- Center for Mollusc Study and Development, Marine Biology Institute of Shandong Province, Qingdao, China
| | - Yaqiong Liu
- School of Agriculture, Ludong University, Yantai, China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
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9
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Fujino H. Why PGD 2 has different functions from PGE 2. Bioessays 2020; 43:e2000213. [PMID: 33165991 DOI: 10.1002/bies.202000213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023]
Abstract
Prostaglandin (PG) D2 and PGE2 are positional isomers; however, they sometimes exhibit opposite physiological functions, such as in cancer development. Because DP receptors are considered to be a duplicated copy of EP2 receptors, PGD2 and PGE2 cross-react with both receptors. These prostanoids may act as biased agonists for each receptor. In reviewing this field, a hypothesis was proposed to explain the opposed effects of these prostanoids from the viewpoints of the evolution of, mutations in, and biased activities of their receptors. Previous findings showing more mutations/variations in DP receptors than EP2 receptors among individuals worldwide indicate that DP receptors are still in a rapid evolutionary stage. The opposing effects of these prostanoids on cancer development may be attributed to the biased activity of PGE2 for DP receptors, which may incidentally develop during the process of the old ligand, PGE2 gaining selectivity to newly diverged DP receptors.
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Affiliation(s)
- Hiromichi Fujino
- Department of Pharmacology for Life Sciences, Graduate School of Pharmaceutical Sciences & Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
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10
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Lallemand T, Leduc M, Landès C, Rizzon C, Lerat E. An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. Genes (Basel) 2020; 11:E1046. [PMID: 32899740 PMCID: PMC7565063 DOI: 10.3390/genes11091046] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question.
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Affiliation(s)
- Tanguy Lallemand
- IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; (T.L.); (M.L.); (C.L.)
| | - Martin Leduc
- IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; (T.L.); (M.L.); (C.L.)
| | - Claudine Landès
- IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; (T.L.); (M.L.); (C.L.)
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), Université d’Evry Val d’Essonne, Université Paris-Saclay, UMR CNRS 8071, ENSIIE, USC INRAE, 23 bvd de France, CEDEX, 91037 Evry Paris, France;
| | - Emmanuelle Lerat
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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11
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Draut H, Liebenstein T, Begemann G. New Insights into the Control of Cell Fate Choices and Differentiation by Retinoic Acid in Cranial, Axial and Caudal Structures. Biomolecules 2019; 9:E860. [PMID: 31835881 PMCID: PMC6995509 DOI: 10.3390/biom9120860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
Retinoic acid (RA) signaling is an important regulator of chordate development. RA binds to nuclear RA receptors that control the transcriptional activity of target genes. Controlled local degradation of RA by enzymes of the Cyp26a gene family contributes to the establishment of transient RA signaling gradients that control patterning, cell fate decisions and differentiation. Several steps in the lineage leading to the induction and differentiation of neuromesodermal progenitors and bone-producing osteogenic cells are controlled by RA. Changes to RA signaling activity have effects on the formation of the bones of the skull, the vertebrae and the development of teeth and regeneration of fin rays in fish. This review focuses on recent advances in these areas, with predominant emphasis on zebrafish, and highlights previously unknown roles for RA signaling in developmental processes.
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12
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Fonseca ESS, Hiromori Y, Kaite Y, Ruivo R, Franco JN, Nakanishi T, Santos MM, Castro LFC. An Orthologue of the Retinoic Acid Receptor (RAR) Is Present in the Ecdysozoa Phylum Priapulida. Genes (Basel) 2019; 10:genes10120985. [PMID: 31795452 PMCID: PMC6947571 DOI: 10.3390/genes10120985] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022] Open
Abstract
Signalling molecules and their cognate receptors are central components of the Metazoa endocrine system. Defining their presence or absence in extant animal lineages is critical to accurately devise evolutionary patterns, physiological shifts and the impact of endocrine disrupting chemicals. Here, we address the evolution of retinoic acid (RA) signalling in the Priapulida worm, Priapulus caudatus Lamarck, 1816, an Ecdysozoa. RA signalling has been shown to be central to chordate endocrine homeostasis, participating in multiple developmental and physiological processes. Priapulids, with their slow rate of molecular evolution and phylogenetic position, represent a key taxon to investigate the early phases of Ecdysozoa evolution. By exploring a draft genome assembly, we show, by means of phylogenetics and functional assays, that an orthologue of the nuclear receptor retinoic acid receptor (RAR) subfamily, a central mediator of RA signalling, is present in Ecdysozoa, contrary to previous perception. We further demonstrate that the Priapulida RAR displays low-affinity for retinoids (similar to annelids), and is not responsive to common endocrine disruptors acting via RAR. Our findings provide a timeline for RA signalling evolution in the Bilateria and give support to the hypothesis that the increase in RA affinity towards RAR is a late acquisition in the evolution of the Metazoa.
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Affiliation(s)
- Elza S. S. Fonseca
- CIIMAR/CIMAR Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; (E.S.S.F.); (R.R.); (J.N.F.)
- FCUP—Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Youhei Hiromori
- Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu 501-1196, Japan; (Y.H.); (Y.K.)
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan
| | - Yoshifumi Kaite
- Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu 501-1196, Japan; (Y.H.); (Y.K.)
| | - Raquel Ruivo
- CIIMAR/CIMAR Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; (E.S.S.F.); (R.R.); (J.N.F.)
| | - João N. Franco
- CIIMAR/CIMAR Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; (E.S.S.F.); (R.R.); (J.N.F.)
| | - Tsuyoshi Nakanishi
- Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu 501-1196, Japan; (Y.H.); (Y.K.)
- Correspondence: (T.N.); (M.M.S.); (L.F.C.C.)
| | - Miguel M. Santos
- CIIMAR/CIMAR Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; (E.S.S.F.); (R.R.); (J.N.F.)
- FCUP—Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
- Correspondence: (T.N.); (M.M.S.); (L.F.C.C.)
| | - L. Filipe C. Castro
- CIIMAR/CIMAR Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; (E.S.S.F.); (R.R.); (J.N.F.)
- FCUP—Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
- Correspondence: (T.N.); (M.M.S.); (L.F.C.C.)
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13
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Abstract
A gene duplication can lead to all sorts of problems in a cell. However, it can also lead to all sorts of benefits. Beneficial or not, the gene duplicates might be kept in the genome because of several different reasons. For instance, if natural selection works towards optimizing one function of a gene at the expense of another, then gene duplication could resolve this conflict by separating the functions in two genes. Here, we outline evolutionary incentives to keep a duplicated gene in the genome, focusing on divergence in expression and trade-off resolution as featured in a new and exciting paper published in this edition of PLOS Biology.
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Affiliation(s)
- Johan Hallin
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- PROTEO, Le réseau québécois de recherche sur la fonction, la structure et l’ingénierie des protéines, Université Laval, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | - Christian R. Landry
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- PROTEO, Le réseau québécois de recherche sur la fonction, la structure et l’ingénierie des protéines, Université Laval, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
- * E-mail:
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14
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Grandchamp A, Piégu B, Monget P. Genes Encoding Teleost Fish Ligands and Associated Receptors Remained in Duplicate More Frequently than the Rest of the Genome. Genome Biol Evol 2019; 11:1451-1462. [PMID: 31087101 PMCID: PMC6540934 DOI: 10.1093/gbe/evz078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
Signaling through ligand/receptor interactions is a widespread mechanism across all living taxa. During evolution, however, there has been a diversification in multigene families and changes in their interaction patterns. Among the events that led to the creation of new genes is the whole-genome duplication, which made possible some major innovations. Teleost fishes descended from a common ancestor which underwent one such whole-genome duplication. In our study, we investigated the effect of complete genome duplication on the evolution of ligand–receptor pairs in teleosts. We selected ten teleost species and used bioinformatics programs and phylogenetic tools in order to study the evolution of the human ligands and receptors that have orthologous genes in fishes, as well as the rest of the fish genomes. We established that since the complete duplication of the fish genomes, the conservation in duplicate copy of ligand and receptor genes is higher than expected. However, the ligand/receptor pair partners did not necessarily evolve in the same way, and a lot of situations occurred in which one of the partners returned in singleton copy when the other one was maintained in duplicate. This suggests that changes in interaction partners may have taken place during the evolution of teleosts. Moreover, the fate of the ligands and receptor coding genes is partly congruent with the phylogeny of teleosts. However, some incongruences can be observed. We suggest that these incongruences are correlated to the environment.
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Affiliation(s)
- Anna Grandchamp
- PRC, UMR85, INRA, CNRS, IFCE, Université de Tours, Nouzilly, France
| | - Benoît Piégu
- PRC, UMR85, INRA, CNRS, IFCE, Université de Tours, Nouzilly, France
| | - Philippe Monget
- PRC, UMR85, INRA, CNRS, IFCE, Université de Tours, Nouzilly, France
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15
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A Behavioral Assay to Study Effects of Retinoid Pharmacology on Nervous System Development in a Marine Annelid. Methods Mol Biol 2019. [PMID: 31359398 DOI: 10.1007/978-1-4939-9585-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Autonomous animal locomotion, such as swimming, is modulated by neuronal networks acting on cilia or muscles. Understanding how these networks are formed and coordinated is a complex scientific problem, which requires various technical approaches. Among others, behavioral studies of developing animals treated with exogenous substances have proven to be a successful approach for studying the functions of neuronal networks. One such substance crucial for the proper development of the nervous system is the vitamin A-derived morphogen retinoic acid (RA). In the larva of the marine annelid Platynereis dumerilii , for example, RA is involved in the specification and differentiation of individual neurons and responsible for orchestrating the swimming behavior of the developing larva. Here, we report a workflow to analyze the effects of RA on the locomotion of the P. dumerilii larva. We provide a protocol for both the treatment with RA and the recording of larval swimming behavior. Additionally, we present a pipeline for the analysis of the obtained data in terms of swimming speed and movement trajectory. This chapter thus summarizes the methodology for analyzing the effects of a specific drug treatment on larval swimming behavior. We expect this approach to be readily adaptable to a wide variety of pharmacological compounds and aquatic species.
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16
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Pinet K, McLaughlin KA. Mechanisms of physiological tissue remodeling in animals: Manipulating tissue, organ, and organism morphology. Dev Biol 2019; 451:134-145. [DOI: 10.1016/j.ydbio.2019.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/21/2022]
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17
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Frank D, Sela-Donenfeld D. Hindbrain induction and patterning during early vertebrate development. Cell Mol Life Sci 2019; 76:941-960. [PMID: 30519881 PMCID: PMC11105337 DOI: 10.1007/s00018-018-2974-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/28/2022]
Abstract
The hindbrain is a key relay hub of the central nervous system (CNS), linking the bilaterally symmetric half-sides of lower and upper CNS centers via an extensive network of neural pathways. Dedicated neural assemblies within the hindbrain control many physiological processes, including respiration, blood pressure, motor coordination and different sensations. During early development, the hindbrain forms metameric segmented units known as rhombomeres along the antero-posterior (AP) axis of the nervous system. These compartmentalized units are highly conserved during vertebrate evolution and act as the template for adult brainstem structure and function. TALE and HOX homeodomain family transcription factors play a key role in the initial induction of the hindbrain and its specification into rhombomeric cell fate identities along the AP axis. Signaling pathways, such as canonical-Wnt, FGF and retinoic acid, play multiple roles to initially induce the hindbrain and regulate Hox gene-family expression to control rhombomeric identity. Additional transcription factors including Krox20, Kreisler and others act both upstream and downstream to Hox genes, modulating their expression and protein activity. In this review, we will examine the earliest embryonic signaling pathways that induce the hindbrain and subsequent rhombomeric segmentation via Hox and other gene expression. We will examine how these signaling pathways and transcription factors interact to activate downstream targets that organize the segmented AP pattern of the embryonic vertebrate hindbrain.
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Affiliation(s)
- Dale Frank
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
| | - Dalit Sela-Donenfeld
- Koret School of Veterinary Medicine, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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18
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André A, Ruivo R, Fonseca E, Froufe E, Castro LFC, Santos MM. The retinoic acid receptor (RAR) in molluscs: Function, evolution and endocrine disruption insights. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 208:80-89. [PMID: 30639747 DOI: 10.1016/j.aquatox.2019.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
Retinoid acid receptor (RAR)-dependent signalling pathways are essential for the regulation and maintenance of essential biological functions and are recognized targets of disruptive anthropogenic compounds. Recent studies put forward the inability of mollusc RARs to bind and respond to the canonical vertebrate ligand, retinoic acid: a feature that seems to have been lost during evolution. Yet, these studies were carried out in a limited number of molluscs. Therefore, using an in vitro transactivation assay, the present work aimed to characterize phylogenetically relevant mollusc RARs, as monomers or as functional units with RXR, not only in the presence of vertebrate bone fine ligands but also known endocrine disruptors, described to modulate retinoid-dependent pathways. In general, none of the tested mollusc RARs were able to activate reporter gene transcription when exposed to retinoic acid isomers, suggesting that the ability to respond to retinoic acid was lost across molluscs. Similarly, the analysed mollusc RAR were unresponsive towards organochloride pesticides. In contrast, transcriptional repressions were observed with the RAR/RXR unit upon exposure to retinoids or RXR-specific ligands. Loss-of-function and gain-of-function mutations further corroborate the obtained results and suggest that the repressive behaviour, observed with mollusc and human RAR/RXR heterodimers, is possibly mediated by ligand biding to RXR.
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Affiliation(s)
- Ana André
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal; ICBAS - Institute of biomedical Sciences Abel Salazar, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal.
| | - Raquel Ruivo
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - Elza Fonseca
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Elsa Froufe
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Miguel M Santos
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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19
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Horton BM, Ryder TB, Moore IT, Balakrishnan CN. Gene expression in the social behavior network of the wire-tailed manakin (Pipra filicauda) brain. GENES BRAIN AND BEHAVIOR 2019; 19:e12560. [PMID: 30756473 DOI: 10.1111/gbb.12560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 01/22/2019] [Accepted: 02/10/2019] [Indexed: 12/16/2022]
Abstract
The vertebrate basal forebrain and midbrain contain a set of interconnected nuclei that control social behavior. Conserved anatomical structures and functions of these nuclei have now been documented among fish, amphibians, reptiles, birds and mammals, and these brain regions have come to be known as the vertebrate social behavior network (SBN). While it is known that nuclei (nodes) of the SBN are rich in steroid and neuropeptide activity linked to behavior, simultaneous variation in the expression of neuroendocrine genes among several SBN nuclei has not yet been described in detail. In this study, we use RNA-seq to profile gene expression across seven brain regions representing five nodes of the vertebrate SBN in a passerine bird, the wire-tailed manakin Pipra filicauda. Using weighted gene co-expression network analysis, we reconstructed sets of coregulated genes, showing striking patterns of variation in neuroendocrine gene expression across the SBN. We describe regional variation in gene networks comprising a broad set of hormone receptors, neuropeptides, steroidogenic enzymes, catecholamines and other neuroendocrine signaling molecules. Our findings show heterogeneous patterns of brain gene expression across nodes of the avian SBN and provide a foundation for future analyses of how the regulation of gene networks may mediate social behavior. These results highlight the importance of region-specific sampling in studies of the mechanisms of behavior.
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Affiliation(s)
- Brent M Horton
- Department of Biology, Millersville University, Millersville, Pennsylvania
| | - Thomas B Ryder
- Migratory Bird Center, Smithsonian Conservation Biology Institute, Front Royal, Virginia
| | - Ignacio T Moore
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia
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20
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Pinet K, Deolankar M, Leung B, McLaughlin KA. Adaptive correction of craniofacial defects in pre-metamorphic Xenopus laevis tadpoles involves thyroid hormone-independent tissue remodeling. Development 2019; 146:dev.175893. [DOI: 10.1242/dev.175893] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022]
Abstract
While it is well-established that some organisms can regenerate lost structures, the ability to remodel existing malformed structures has been less well studied. Thus, in this study we examined the ability of pre-metamorphic Xenopus laevis tadpoles to self-correct malformed craniofacial tissues and found that tadpoles can adaptively improve and normalize abnormal craniofacial morphology caused by numerous developmental perturbations. We then investigated the tissue-level and molecular mechanisms that mediate the self-correction of craniofacial defects in pre-metamorphic X. laevis tadpoles. Our studies revealed that this adaptive response involves morphological changes and the remodeling of cartilage tissue, prior to metamorphosis. RT-qPCR and RNA-Seq analysis of gene expression suggests a thyroid hormone-independent endocrine signaling pathway as the potential mechanism responsible for triggering the adaptive and corrective remodeling response in these larvae that involves mmp1 and mmp13 upregulation. Thus, investigating how malformed craniofacial tissues are naturally corrected in X. laevis tadpoles has led us to valuable insights regarding the maintenance and manipulation of craniofacial morphology in a vertebrate system. These insights may help in the development of novel therapies for developmental craniofacial anomalies in humans.
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Affiliation(s)
- Kaylinnette Pinet
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
| | - Manas Deolankar
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
| | - Brian Leung
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
| | - Kelly A. McLaughlin
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
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21
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Lorente-Martínez H, Agorreta A, Torres-Sánchez M, San Mauro D. Evidence of positive selection suggests possible role of aquaporins in the water-to-land transition of mudskippers. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0382-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Handberg-Thorsager M, Gutierrez-Mazariegos J, Arold ST, Kumar Nadendla E, Bertucci PY, Germain P, Tomançak P, Pierzchalski K, Jones JW, Albalat R, Kane MA, Bourguet W, Laudet V, Arendt D, Schubert M. The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation. SCIENCE ADVANCES 2018; 4:eaao1261. [PMID: 29492455 PMCID: PMC5821490 DOI: 10.1126/sciadv.aao1261] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/10/2018] [Indexed: 06/02/2023]
Abstract
Retinoic acid (RA) is an important intercellular signaling molecule in vertebrate development, with a well-established role in the regulation of hox genes during hindbrain patterning and in neurogenesis. However, the evolutionary origin of the RA signaling pathway remains elusive. To elucidate the evolution of the RA signaling system, we characterized RA metabolism and signaling in the marine annelid Platynereis dumerilii, a powerful model for evolution, development, and neurobiology. Binding assays and crystal structure analyses show that the annelid retinoic acid receptor (RAR) binds RA and activates transcription just as vertebrate RARs, yet with a different ligand-binding pocket and lower binding affinity, suggesting a permissive rather than instructive role of RA signaling. RAR knockdown and RA treatment of swimming annelid larvae further reveal that the RA signal is locally received in the medial neuroectoderm, where it controls neurogenesis and axon outgrowth, whereas the spatial colinear hox gene expression in the neuroectoderm remains unaffected. These findings suggest that one early role of the new RAR in bilaterian evolution was to control the spatially restricted onset of motor and interneuron differentiation in the developing ventral nerve cord and to indicate that the regulation of hox-controlled anterior-posterior patterning arose only at the base of the chordates, concomitant with a high-affinity RAR needed for the interpretation of a complex RA gradient.
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Affiliation(s)
- Mette Handberg-Thorsager
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Juliana Gutierrez-Mazariegos
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Center for Computational Bioscience Research, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Eswar Kumar Nadendla
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Paola Y. Bertucci
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Pierre Germain
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Pavel Tomançak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Keely Pierzchalski
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Jace W. Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Michael Schubert
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
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23
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Fonseca E, Ruivo R, Lopes-Marques M, Zhang H, Santos MM, Venkatesh B, Castro LFC. LXRα and LXRβ Nuclear Receptors Evolved in the Common Ancestor of Gnathostomes. Genome Biol Evol 2017; 9:222-230. [PMID: 28057729 PMCID: PMC5381633 DOI: 10.1093/gbe/evw305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2016] [Indexed: 12/25/2022] Open
Abstract
Nuclear receptors (NRs) regulate numerous aspects of the endocrine system. They mediate endogenous and exogenous cues, ensuring a homeostatic control of development and metabolism. Gene duplication, loss and mutation have shaped the repertoire and function of NRs in metazoans. Here, we examine the evolution of a pivotal orchestrator of cholesterol metabolism in vertebrates, the liver X receptors (LXRs). Previous studies suggested that LXRα and LXRβ genes emerged in the mammalian ancestor. However, we show through genome analysis and functional assay that bona fide LXRα and LXRβ orthologues are present in reptiles, coelacanth and chondrichthyans but not in cyclostomes. These findings show that LXR duplicated before gnathostome radiation, followed by asymmetric paralogue loss in some lineages. We suggest that a tighter control of cholesterol levels in vertebrates was achieved through the exploitation of a wider range of oxysterols, an ability contingent on ligand-binding pocket remodeling.
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Affiliation(s)
- Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,Department of Biology, FCUP - Faculty of Sciences, U. Porto, Portugal
| | - Raquel Ruivo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal
| | - Mónica Lopes-Marques
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,ICBAS - Institute of Biomedical Sciences Abel Salazar - U. Porto, Portugal
| | - Huixian Zhang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Miguel M Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,Department of Biology, FCUP - Faculty of Sciences, U. Porto, Portugal
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,Department of Biology, FCUP - Faculty of Sciences, U. Porto, Portugal
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24
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Abstract
Nuclear receptors (NRs) form a superfamily of transcription factors that can be activated by ligands and are involved in a wide range of physiological processes. NRs are well conserved between vertebrate species. The zebrafish, an increasingly popular animal model system, contains a total of 73 NR genes, and orthologues of almost all human NRs are present. In this review article, an overview is presented of NR research in which the zebrafish has been used as a model. Research is described on the three most studied zebrafish NRs: the estrogen receptors (ERs), retinoic acid receptors (RARs) and peroxisome proliferator-activated receptors (PPARs). The studies on these receptors illustrate the versatility of the zebrafish as a model for ecotoxicological, developmental and biomedical research. Although the use of the zebrafish in NR research is still relatively limited, it is expected that in the next decade the full potential of this animal model will be exploited.
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Affiliation(s)
- Marcel J M Schaaf
- Institute of Biology (IBL)Leiden University, Leiden, The Netherlands
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25
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Janesick A, Tang W, Nguyen TTL, Blumberg B. RARβ2 is required for vertebrate somitogenesis. Development 2017; 144:1997-2008. [PMID: 28432217 DOI: 10.1242/dev.144345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/07/2017] [Indexed: 01/02/2023]
Abstract
During vertebrate somitogenesis, retinoic acid is known to establish the position of the determination wavefront, controlling where new somites are permitted to form along the anteroposterior body axis. Less is understood about how RAR regulates somite patterning, rostral-caudal boundary setting, specialization of myotome subdivisions or the specific RAR subtype that is required for somite patterning. Characterizing the function of RARβ has been challenging due to the absence of embryonic phenotypes in murine loss-of-function studies. Using the Xenopus system, we show that RARβ2 plays a specific role in somite number and size, restriction of the presomitic mesoderm anterior border, somite chevron morphology and hypaxial myoblast migration. Rarβ2 is the RAR subtype whose expression is most upregulated in response to ligand and its localization in the trunk somites positions it at the right time and place to respond to embryonic retinoid levels during somitogenesis. RARβ2 positively regulates Tbx3 a marker of hypaxial muscle, and negatively regulates Tbx6 via Ripply2 to restrict the anterior boundaries of the presomitic mesoderm and caudal progenitor pool. These results demonstrate for the first time an early and essential role for RARβ2 in vertebrate somitogenesis.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
| | - Weiyi Tang
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
| | - Tuyen T L Nguyen
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
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Carvalho JE, Theodosiou M, Chen J, Chevret P, Alvarez S, De Lera AR, Laudet V, Croce JC, Schubert M. Lineage-specific duplication of amphioxus retinoic acid degrading enzymes (CYP26) resulted in sub-functionalization of patterning and homeostatic roles. BMC Evol Biol 2017; 17:24. [PMID: 28103795 PMCID: PMC5247814 DOI: 10.1186/s12862-016-0863-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During embryogenesis, tight regulation of retinoic acid (RA) availability is fundamental for normal development. In parallel to RA synthesis, a negative feedback loop controlled by RA catabolizing enzymes of the cytochrome P450 subfamily 26 (CYP26) is crucial. In vertebrates, the functions of the three CYP26 enzymes (CYP26A1, CYP26B1, and CYP26C1) have been well characterized. By contrast, outside vertebrates, little is known about CYP26 complements and their biological roles. In an effort to characterize the evolutionary diversification of RA catabolism, we studied the CYP26 genes of the cephalochordate amphioxus (Branchiostoma lanceolatum), a basal chordate with a vertebrate-like genome that has not undergone the massive, large-scale duplications of vertebrates. RESULTS In the present study, we found that amphioxus also possess three CYP26 genes (CYP26-1, CYP26-2, and CYP26-3) that are clustered in the genome and originated by lineage-specific duplication. The amphioxus CYP26 cluster thus represents a useful model to assess adaptive evolutionary changes of the RA signaling system following gene duplication. The characterization of amphioxus CYP26 expression, function, and regulation by RA signaling demonstrated that, despite the independent origins of CYP26 duplicates in amphioxus and vertebrates, they convergently assume two main roles during development: RA-dependent patterning and protection against fluctuations of RA levels. Our analysis suggested that in amphioxus RA-dependent patterning is sustained by CYP26-2, while RA homeostasis is mediated by CYP26-1 and CYP26-3. Furthermore, comparisons of the regulatory regions of CYP26 genes of different bilaterian animals indicated that a CYP26-driven negative feedback system was present in the last common ancestor of deuterostomes, but not in that of bilaterians. CONCLUSIONS Altogether, this work reveals the evolutionary origins of the RA-dependent regulation of CYP26 genes and highlights convergent functions for CYP26 enzymes that originated by independent duplication events, hence establishing a novel selective mechanism for the genomic retention of gene duplicates.
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Affiliation(s)
- João E Carvalho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Maria Theodosiou
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France
| | - Jie Chen
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.,Present Address: Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, 43 Boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Susana Alvarez
- Departamento de Química Organica, Facultad de Química, Universidade de Vigo, 36310, Vigo, Spain
| | - Angel R De Lera
- Departamento de Química Organica, Facultad de Química, Universidade de Vigo, 36310, Vigo, Spain
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.,Present Address: Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232, Université Pierre et Marie Curie Paris, 1 avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
| | - Jenifer C Croce
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
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Holzer G, Markov GV, Laudet V. Evolution of Nuclear Receptors and Ligand Signaling. Curr Top Dev Biol 2017; 125:1-38. [DOI: 10.1016/bs.ctdb.2017.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Developmental Mechanism of Limb Field Specification along the Anterior-Posterior Axis during Vertebrate Evolution. J Dev Biol 2016; 4:jdb4020018. [PMID: 29615584 PMCID: PMC5831784 DOI: 10.3390/jdb4020018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
In gnathostomes, limb buds arise from the lateral plate mesoderm at discrete positions along the body axis. Specification of these limb-forming fields can be subdivided into several steps. The lateral plate mesoderm is regionalized into the anterior lateral plate mesoderm (ALPM; cardiac mesoderm) and the posterior lateral plate mesoderm (PLPM). Subsequently, Hox genes appear in a nested fashion in the PLPM and provide positional information along the body axis. The lateral plate mesoderm then splits into the somatic and splanchnic layers. In the somatic layer of the PLPM, the expression of limb initiation genes appears in the limb-forming region, leading to limb bud initiation. Furthermore, past and current work in limbless amphioxus and lampreys suggests that evolutionary changes in developmental programs occurred during the acquisition of paired fins during vertebrate evolution. This review presents these recent advances and discusses the mechanisms of limb field specification during development and evolution, with a focus on the role of Hox genes in this process.
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Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V. Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150484. [PMID: 27069642 PMCID: PMC4821253 DOI: 10.1098/rsos.150484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
Whole genome duplications (WGDs) have been classically associated with the origin of evolutionary novelties and the so-called duplication-degeneration-complementation model describes the possible fates of genes after duplication. However, how sequence divergence effectively allows functional changes between gene duplicates is still unclear. In the vertebrate lineage, two rounds of WGDs took place, giving rise to paralogous gene copies observed for many gene families. For the retinoic acid receptors (RARs), for example, which are members of the nuclear hormone receptor (NR) superfamily, a unique ancestral gene has been duplicated resulting in three vertebrate paralogues: RARα, RARβ and RARγ. It has previously been shown that this single ancestral RAR was neofunctionalized to give rise to a larger substrate specificity range in the RARs of extant jawed vertebrates (also called gnathostomes). To understand RAR diversification, the members of the cyclostomes (lamprey and hagfish), jawless vertebrates representing the extant sister group of gnathostomes, provide an intermediate situation and thus allow the characterization of the evolutionary steps that shaped RAR ligand-binding properties following the WGDs. In this study, we assessed the ligand-binding specificity of cyclostome RARs and found that their ligand-binding pockets resemble those of gnathostome RARα and RARβ. In contrast, none of the cyclostome receptors studied showed any RARγ-like specificity. Together, our results suggest that cyclostome RARs cover only a portion of the specificity repertoire of the ancestral gnathostome RARs and indicate that the establishment of ligand-binding specificity was a stepwise event. This iterative process thus provides a rare example for the diversification of receptor-ligand interactions of NRs following WGDs.
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Affiliation(s)
- Juliana Gutierrez-Mazariegos
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Eswar Kumar Nadendla
- Centre de Biochimie Structurale, Inserm U1054, CNRS UMR 5048, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Romain A. Studer
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI)—Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Susana Alvarez
- Departamento de Química Organica, Facultad de Química, Universidade de Vigo, 36310 Vigo, Spain
| | - Angel R. de Lera
- Departamento de Química Organica, Facultad de Química, Universidade de Vigo, 36310 Vigo, Spain
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm U1054, CNRS UMR 5048, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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Leckenby A, Hall N. Genomic changes during evolution of animal parasitism in eukaryotes. Curr Opin Genet Dev 2015; 35:86-92. [PMID: 26637954 DOI: 10.1016/j.gde.2015.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 12/21/2022]
Abstract
Understanding how pathogens have evolved to survive in close association with their hosts is an important step in unraveling the biology of host-pathogen interactions. Comparative genomics is a powerful tool to approach this problem as an increasing number of genomes of multiple pathogen species and strains become available. The ever-growing catalog of genome sequences makes comparison of organisms easier, but it also allows us to reconstitute the evolutionary processes occurring at the genomic level that may have led to the acquisition of pathogenic or parasitic mechanisms.
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Affiliation(s)
- Amber Leckenby
- Department of Functional and Comparative Genomics, The University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Neil Hall
- Department of Functional and Comparative Genomics, The University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.
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Zhu X, Wang W, Zhang X, Bai J, Chen G, Li L, Li M. All-Trans Retinoic Acid-Induced Deficiency of the Wnt/β-Catenin Pathway Enhances Hepatic Carcinoma Stem Cell Differentiation. PLoS One 2015; 10:e0143255. [PMID: 26571119 PMCID: PMC4646487 DOI: 10.1371/journal.pone.0143255] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/02/2015] [Indexed: 01/03/2023] Open
Abstract
Retinoic acid (RA) is an important biological signal that directly differentiates cells during embryonic development and tumorigenesis. However, the molecular mechanism of RA-mediated differentiation in hepatic cancer stem cells (hCSCs) is not well understood. In this study, we found that mRNA expressions of RA-biosynthesis-related dehydrogenases were highly expressed in hepatocellular carcinoma. All-trans retinoic acid (ATRA) differentiated hCSCs through inhibiting the function of β-catenin in vitro. ATRA also inhibited the function of PI3K-AKT and enhanced GSK-3β-dependent degradation of phosphorylated β-catenin. Furthermore, ATRA and β-catenin silencing both increased hCSC sensitivity to docetaxel treatment. Our results suggest that targeting β-catenin will provide extra benefits for ATRA-mediated treatment of hepatic cancer patients.
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Affiliation(s)
- Xinfeng Zhu
- Affiliated Calmette Hospital of Kunming Medical University, Kunming, Yunnan Province, 650011, P. R. China
| | - Wenxue Wang
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650091, P. R. China
| | - Xia Zhang
- Affiliated Calmette Hospital of Kunming Medical University, Kunming, Yunnan Province, 650011, P. R. China
| | - Jianhua Bai
- Affiliated Calmette Hospital of Kunming Medical University, Kunming, Yunnan Province, 650011, P. R. China
| | - Gang Chen
- Affiliated Calmette Hospital of Kunming Medical University, Kunming, Yunnan Province, 650011, P. R. China
| | - Li Li
- Affiliated Calmette Hospital of Kunming Medical University, Kunming, Yunnan Province, 650011, P. R. China
| | - Meizhang Li
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650091, P. R. China
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Abstract
Gene duplication is thought to play a key role in phenotypic innovation. While several processes have been hypothesized to drive the retention and functional evolution of duplicate genes, their genomic contributions have never been determined. We recently developed the first genome-wide method to classify these processes by comparing distances between expression profiles of duplicate genes and their ancestral single-copy orthologs. Application of our approach to spatial gene expression profiles in two Drosophila species revealed that a majority of young duplicate genes possess new functions, and that new functions are acquired rapidly-often within a few million years. Surprisingly, new functions tend to arise in younger copies of duplicate gene pairs. Moreover, we found that young duplicates are often specifically expressed in testes, whereas old duplicates are broadly expressed across several tissues, providing strong support for the hypothetical "out-of-testes" origin of new genes. In this Extra View, I discuss our findings in the context of theoretical predictions about gene duplication, with a particular emphasis on the importance of natural selection in the evolution of novel phenotypes.
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Affiliation(s)
- Raquel Assis
- a Department of Biology; Huck Institutes of the Life Sciences; Center for Medical Genomics; Pennsylvania State University; University Park, PA USA
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Gassié L, Lombard A, Moraldi T, Bibonne A, Leclerc C, Moreau M, Marlier A, Gilbert T. Hspa9 is required for pronephros specification and formation inXenopus laevis. Dev Dyn 2015; 244:1538-49. [DOI: 10.1002/dvdy.24344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 07/29/2015] [Accepted: 08/17/2015] [Indexed: 01/13/2023] Open
Affiliation(s)
- Lionel Gassié
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
| | | | - Tiphanie Moraldi
- Université Lyon 1 Institut Universitaire Technologique; Villeurbanne France
| | - Anne Bibonne
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
| | - Catherine Leclerc
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
| | - Marc Moreau
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
| | - Arnaud Marlier
- Yale' School of Medicine Department of Internal Medicine; New Haven Connecticut USA
| | - Thierry Gilbert
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
- Institut National de la Santé et de la Recherche Médicale; Toulouse France
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Radó-Trilla N, Arató K, Pegueroles C, Raya A, de la Luna S, Albà MM. Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors. Mol Biol Evol 2015; 32:2263-72. [PMID: 25931513 PMCID: PMC4540963 DOI: 10.1093/molbev/msv103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.
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Affiliation(s)
- Núria Radó-Trilla
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Krisztina Arató
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cinta Pegueroles
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Alicia Raya
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Susana de la Luna
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Campo-Paysaa F, Jandzik D, Takio-Ogawa Y, Cattell MV, Neef HC, Langeland JA, Kuratani S, Medeiros DM, Mazan S, Kuraku S, Laudet V, Schubert M. Evolution of retinoic acid receptors in chordates: insights from three lamprey species, Lampetra fluviatilis, Petromyzon marinus, and Lethenteron japonicum. EvoDevo 2015; 6:18. [PMID: 25984292 PMCID: PMC4432984 DOI: 10.1186/s13227-015-0016-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/20/2015] [Indexed: 01/13/2023] Open
Abstract
Background Retinoic acid (RA) signaling controls many developmental processes in chordates, from early axis specification to late organogenesis. The functions of RA are chiefly mediated by a subfamily of nuclear hormone receptors, the retinoic acid receptors (RARs), that act as ligand-activated transcription factors. While RARs have been extensively studied in jawed vertebrates (that is, gnathostomes) and invertebrate chordates, very little is known about the repertoire and developmental roles of RARs in cyclostomes, which are extant jawless vertebrates. Here, we present the first extensive study of cyclostome RARs focusing on three different lamprey species: the European freshwater lamprey, Lampetra fluviatilis, the sea lamprey, Petromyzon marinus, and the Japanese lamprey, Lethenteron japonicum. Results We identified four rar paralogs (rar1, rar2, rar3, and rar4) in each of the three lamprey species, and phylogenetic analyses indicate a complex evolutionary history of lamprey rar genes including the origin of rar1 and rar4 by lineage-specific duplication after the lamprey-hagfish split. We further assessed their expression patterns during embryonic development by in situ hybridization. The results show that lamprey rar genes are generally characterized by dynamic and highly specific expression domains in different embryonic tissues. In particular, lamprey rar genes exhibit combinatorial expression domains in the anterior central nervous system (CNS) and the pharyngeal region. Conclusions Our results indicate that the genome of lampreys encodes at least four rar genes and suggest that the lamprey rar complement arose from vertebrate-specific whole genome duplications followed by a lamprey-specific duplication event. Moreover, we describe a combinatorial code of lamprey rar expression in both anterior CNS and pharynx resulting from dynamic and highly specific expression patterns during embryonic development. This ‘RAR code’ might function in regionalization and patterning of these two tissues by differentially modulating the expression of downstream effector genes during development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0016-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florent Campo-Paysaa
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France ; MRC Centre for Developmental Neurobiology, New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL UK
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Ramaley Biology, 1800 Colorado Avenue, Boulder, CO 80309 USA ; Department of Zoology, Comenius University in Bratislava, Mlynska Dolina B-1, 84215 Bratislava, Slovakia
| | - Yoko Takio-Ogawa
- Laboratory for Evolutionary Morphology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Maria V Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Ramaley Biology, 1800 Colorado Avenue, Boulder, CO 80309 USA ; Department of Pediatrics, University of Colorado, Children's Hospital, 13065 East 17th Avenue, Aurora, CO 80045 USA
| | - Haley C Neef
- Department of Biology, Kalamazoo College, 1200 Academy Street, Kalamazoo, Michigan 49008 USA ; Division of Pediatric Gastroenterology, Department of Pediatrics and Communicable Diseases, University of Michigan, C.S. Mott Children's Hospital, 1540 East Hospital Drive SPC 4259, Ann Arbor, Michigan 48109 USA
| | - James A Langeland
- Department of Biology, Kalamazoo College, 1200 Academy Street, Kalamazoo, Michigan 49008 USA
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Ramaley Biology, 1800 Colorado Avenue, Boulder, CO 80309 USA
| | - Sylvie Mazan
- Sorbonne Universités, UPMC Université Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France ; CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Shigehiro Kuraku
- Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan ; Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France ; CNRS, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
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Samarut E, Fraher D, Laudet V, Gibert Y. ZebRA: An overview of retinoic acid signaling during zebrafish development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:73-83. [DOI: 10.1016/j.bbagrm.2014.05.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/26/2014] [Accepted: 05/27/2014] [Indexed: 11/15/2022]
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di Masi A, Leboffe L, De Marinis E, Pagano F, Cicconi L, Rochette-Egly C, Lo-Coco F, Ascenzi P, Nervi C. Retinoic acid receptors: from molecular mechanisms to cancer therapy. Mol Aspects Med 2015; 41:1-115. [PMID: 25543955 DOI: 10.1016/j.mam.2014.12.003] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 02/07/2023]
Abstract
Retinoic acid (RA), the major bioactive metabolite of retinol or vitamin A, induces a spectrum of pleiotropic effects in cell growth and differentiation that are relevant for embryonic development and adult physiology. The RA activity is mediated primarily by members of the retinoic acid receptor (RAR) subfamily, namely RARα, RARβ and RARγ, which belong to the nuclear receptor (NR) superfamily of transcription factors. RARs form heterodimers with members of the retinoid X receptor (RXR) subfamily and act as ligand-regulated transcription factors through binding specific RA response elements (RAREs) located in target genes promoters. RARs also have non-genomic effects and activate kinase signaling pathways, which fine-tune the transcription of the RA target genes. The disruption of RA signaling pathways is thought to underlie the etiology of a number of hematological and non-hematological malignancies, including leukemias, skin cancer, head/neck cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer, renal cell carcinoma, pancreatic cancer, liver cancer, glioblastoma and neuroblastoma. Of note, RA and its derivatives (retinoids) are employed as potential chemotherapeutic or chemopreventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. In humans, retinoids reverse premalignant epithelial lesions, induce the differentiation of myeloid normal and leukemic cells, and prevent lung, liver, and breast cancer. Here, we provide an overview of the biochemical and molecular mechanisms that regulate the RA and retinoid signaling pathways. Moreover, mechanisms through which deregulation of RA signaling pathways ultimately impact on cancer are examined. Finally, the therapeutic effects of retinoids are reported.
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Affiliation(s)
- Alessandra di Masi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Loris Leboffe
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Elisabetta De Marinis
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Francesca Pagano
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Laura Cicconi
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS UMR 7104 - Inserm U 964, University of Strasbourg, 1 rue Laurent Fries, BP10142, Illkirch Cedex F-67404, France.
| | - Francesco Lo-Coco
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy.
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, Roma I-00146, Italy.
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100.
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Carter CJ, Rand C, Mohammad I, Lepp A, Vesprini N, Wiebe O, Carlone R, Spencer GE. Expression of a retinoic acid receptor (RAR)-like protein in the embryonic and adult nervous system of a protostome species. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:51-67. [DOI: 10.1002/jez.b.22604] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
| | - Christopher Rand
- Department of Biological Sciences; Brock University; Ontario Canada
| | - Imtiaz Mohammad
- Department of Biological Sciences; Brock University; Ontario Canada
| | - Amanda Lepp
- Department of Biological Sciences; Brock University; Ontario Canada
| | | | - Olivia Wiebe
- Department of Biological Sciences; Brock University; Ontario Canada
| | - Robert Carlone
- Department of Biological Sciences; Brock University; Ontario Canada
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Gutierrez-Mazariegos J, Schubert M, Laudet V. Evolution of retinoic acid receptors and retinoic acid signaling. Subcell Biochem 2014; 70:55-73. [PMID: 24962881 DOI: 10.1007/978-94-017-9050-5_4] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Retinoic acid (RA) is a vitamin A-derived morphogen controlling important developmental processes in vertebrates, and more generally in chordates, including axial patterning and tissue formation and differentiation. In the embryo, endogenous RA levels are controlled by RA synthesizing and degrading enzymes and the RA signal is transduced by two retinoid receptors: the retinoic acid receptor (RAR) and the retinoid X receptor (RXR). Both RAR and RXR are members of the nuclear receptor superfamily of ligand-activated transcription factors and mainly act as heterodimers to activate the transcription of target genes in the presence of their ligand, all-trans RA. This signaling pathway was long thought to be a chordate innovation, however, recent findings of gene homologs involved in RA signaling in the genomes of a wide variety of non-chordate animals, including ambulacrarians (sea urchins and acorn worms) and lophotrochozoans (annelids and mollusks), challenged this traditional view and suggested that the RA signaling pathway might have a more ancient evolutionary origin than previously thought. In this chapter, we discuss the evolutionary history of the RA signaling pathway, and more particularly of the RARs, which might have experienced independent gene losses and duplications in different animal lineages. In sum, the available data reveal novel insights into the origin of the RA signaling pathway as well as into the evolutionary history of the RARs.
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Affiliation(s)
- Juliana Gutierrez-Mazariegos
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 07, France,
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Gutierrez-Mazariegos J, Nadendla EK, Lima D, Pierzchalski K, Jones JW, Kane M, Nishikawa JI, Hiromori Y, Nakanishi T, Santos MM, Castro LFC, Bourguet W, Schubert M, Laudet V. A mollusk retinoic acid receptor (RAR) ortholog sheds light on the evolution of ligand binding. Endocrinology 2014; 155:4275-86. [PMID: 25116705 PMCID: PMC4197984 DOI: 10.1210/en.2014-1181] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/06/2014] [Indexed: 11/19/2022]
Abstract
Nuclear receptors are transcription factors that regulate networks of target genes in response to small molecules. There is a strong bias in our knowledge of these receptors because they were mainly characterized in classical model organisms, mostly vertebrates. Therefore, the evolutionary origins of specific ligand-receptor couples still remain elusive. Here we present the identification and characterization of a retinoic acid receptor (RAR) from the mollusk Nucella lapillus (NlRAR). We show that this receptor specifically binds to DNA response elements organized in direct repeats as a heterodimer with retinoid X receptor. Surprisingly, we also find that NlRAR does not bind all-trans retinoic acid or any other retinoid we tested. Furthermore, NlRAR is unable to activate the transcription of reporter genes in response to stimulation by retinoids and to recruit coactivators in the presence of these compounds. Three-dimensional modeling of the ligand-binding domain of NlRAR reveals an overall structure that is similar to vertebrate RARs. However, in the ligand-binding pocket (LBP) of the mollusk receptor, the alteration of several residues interacting with the ligand has apparently led to an overall decrease in the strength of the interaction with the ligand. Accordingly, mutations of NlRAR at key positions within the LBP generate receptors that are responsive to retinoids. Altogether our data suggest that, in mollusks, RAR has lost its affinity for all-trans retinoic acid, highlighting the evolutionary plasticity of its LBP. When put in an evolutionary context, our results reveal new structural and functional features of nuclear receptors validated by millions of years of evolution that were impossible to reveal in model organisms.
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Affiliation(s)
- Juliana Gutierrez-Mazariegos
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Eswar Kumar Nadendla
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Daniela Lima
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Keely Pierzchalski
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Jace W. Jones
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Maureen Kane
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Jun-Ichi Nishikawa
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Youhei Hiromori
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Tsuyoshi Nakanishi
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Miguel M. Santos
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - L. Filipe C. Castro
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - William Bourguet
- Molecular Zoology Team (J.G.-M., V.L.), Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Université Lyon 1, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; Institut National de la Santé et de la Recherche Médicale Unité 1054 (E.K.N., W.B.), Centre de Biochimie Structurale, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5048, Universités Montpellier 1 and 2, 34967 Montpellier, France; CAS in Crystallography and Biophysics (E.K.N.), University of Madras, 600-005 Chennai, India; Centre of Marine and Environmental Research/Interdisciplinary Centre of Marine and Environmental Research (D.L., M.M.S., L.F.C.C.), FCUP–Department of Biology, Faculty of Sciences, University of Porto, 4050-123 Porto, Portugal; Department of Pharmaceutical Sciences (K.P., J.W.J., M.K.), School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Laboratory of Health Sciences (J.-I.N.), School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya, Hyogo 663-8179, Japan; Laboratory of Hygienic Chemistry and Molecular Toxicology (Y.H., T.N.), Gifu Pharmaceutical University, Gifu 501-1196, Japan; and Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Unité Mixte de Recherche 7009, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
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Signaling through retinoic acid receptors in cardiac development: Doing the right things at the right times. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:94-111. [PMID: 25134739 DOI: 10.1016/j.bbagrm.2014.08.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/19/2014] [Accepted: 08/04/2014] [Indexed: 11/23/2022]
Abstract
Retinoic acid (RA) is a terpenoid that is synthesized from vitamin A/retinol (ROL) and binds to the nuclear receptors retinoic acid receptor (RAR)/retinoid X receptor (RXR) to control multiple developmental processes in vertebrates. The available clinical and experimental data provide uncontested evidence for the pleiotropic roles of RA signaling in development of multiple embryonic structures and organs such eyes, central nervous system, gonads, lungs and heart. The development of any of these above-mentioned embryonic organ systems can be effectively utilized to showcase the many strategies utilized by RA signaling. However, it is very likely that the strategies employed to transfer RA signals during cardiac development comprise the majority of the relevant and sophisticated ways through which retinoid signals can be conveyed in a complex biological system. Here, we provide the reader with arguments indicating that RA signaling is exquisitely regulated according to specific phases of cardiac development and that RA signaling itself is one of the major regulators of the timing of cardiac morphogenesis and differentiation. We will focus on the role of signaling by RA receptors (RARs) in early phases of heart development. This article is part of a Special Issue entitled: Nuclear receptors in animal development.
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Hargreaves AD, Swain MT, Hegarty MJ, Logan DW, Mulley JF. Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins. Genome Biol Evol 2014; 6:2088-95. [PMID: 25079342 PMCID: PMC4231632 DOI: 10.1093/gbe/evu166] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2014] [Indexed: 11/23/2022] Open
Abstract
Snake venom has been hypothesized to have originated and diversified through a process that involves duplication of genes encoding body proteins with subsequent recruitment of the copy to the venom gland, where natural selection acts to develop or increase toxicity. However, gene duplication is known to be a rare event in vertebrate genomes, and the recruitment of duplicated genes to a novel expression domain (neofunctionalization) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions. Therefore, although this hypothesis concerning the evolution of snake venom is very unlikely and should be regarded with caution, it is nonetheless often assumed to be established fact, hindering research into the true origins of snake venom toxins. To critically evaluate this hypothesis, we have generated transcriptomic data for body tissues and salivary and venom glands from five species of venomous and nonvenomous reptiles. Our comparative transcriptomic analysis of these data reveals that snake venom does not evolve through the hypothesized process of duplication and recruitment of genes encoding body proteins. Indeed, our results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of nonvenomous reptiles and that these genes have therefore been restricted to the venom gland following duplication, not recruited. Thus, snake venom evolves through the duplication and subfunctionalization of genes encoding existing salivary proteins. These results highlight the danger of the elegant and intuitive "just-so story" in evolutionary biology.
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Affiliation(s)
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Matthew J Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - John F Mulley
- School of Biological Sciences, Bangor University, United Kingdom
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Janesick A, Nguyen TTL, Aisaki KI, Igarashi K, Kitajima S, Chandraratna RAS, Kanno J, Blumberg B. Active repression by RARγ signaling is required for vertebrate axial elongation. Development 2014; 141:2260-70. [PMID: 24821986 DOI: 10.1242/dev.103705] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retinoic acid receptor gamma 2 (RARγ2) is the major RAR isoform expressed throughout the caudal axial progenitor domain in vertebrates. During a microarray screen to identify RAR targets, we identified a subset of genes that pattern caudal structures or promote axial elongation and are upregulated by increased RAR-mediated repression. Previous studies have suggested that RAR is present in the caudal domain, but is quiescent until its activation in late stage embryos terminates axial elongation. By contrast, we show here that RARγ2 is engaged in all stages of axial elongation, not solely as a terminator of axial growth. In the absence of RA, RARγ2 represses transcriptional activity in vivo and maintains the pool of caudal progenitor cells and presomitic mesoderm. In the presence of RA, RARγ2 serves as an activator, facilitating somite differentiation. Treatment with an RARγ-selective inverse agonist (NRX205099) or overexpression of dominant-negative RARγ increases the expression of posterior Hox genes and that of marker genes for presomitic mesoderm and the chordoneural hinge. Conversely, when RAR-mediated repression is reduced by overexpressing a dominant-negative co-repressor (c-SMRT), a constitutively active RAR (VP16-RARγ2), or by treatment with an RARγ-selective agonist (NRX204647), expression of caudal genes is diminished and extension of the body axis is prematurely terminated. Hence, gene repression mediated by the unliganded RARγ2-co-repressor complex constitutes a novel mechanism to regulate and facilitate the correct expression levels and spatial restriction of key genes that maintain the caudal progenitor pool during axial elongation in Xenopus embryos.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
| | - Tuyen T L Nguyen
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
| | - Ken-ichi Aisaki
- Division of Cellular and Molecular Toxicology, Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Katsuhide Igarashi
- Division of Cellular and Molecular Toxicology, Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Satoshi Kitajima
- Division of Cellular and Molecular Toxicology, Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | | | - Jun Kanno
- Division of Cellular and Molecular Toxicology, Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-2300, USA
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Urushitani H, Katsu Y, Ohta Y, Shiraishi H, Iguchi T, Horiguchi T. Cloning and characterization of the retinoic acid receptor-like protein in the rock shell, Thais clavigera. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 142-143:403-413. [PMID: 24096236 DOI: 10.1016/j.aquatox.2013.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 06/02/2023]
Abstract
The organotin compounds have a high affinity for the retinoid X receptor (RXR), which is a transcriptional factor activated by retinoids that induce imposex in gastropods. However, the molecular mechanisms underlying the regulation of RXR and its related genes in gastropods remain unclear. We isolated a retinoic acid receptor (RAR)-like cDNA (TcRAR) in the rock shell, Thais clavigera, and examined the transcriptional activity of the TcRAR protein by using all-trans retinoic acid (ATRA). However, we did not observe any ligand-dependent transactivation by this protein. We also examined the transcriptional activity of the TcRAR-ligand binding domain fused with the GAL4-DNA binding domain by using retinoic acids, retinol, and organotins and again saw no noteworthy transcriptional induction by these chemicals. Use of a mammalian two-hybrid assay to assess the interaction of the TcRAR protein with the TcRXR isoforms suggested that TcRAR might form a heterodimer with the RXR isoforms. The transcriptional activity of domain-swapped TcRAR chimeric proteins (the A/B domain of TcRAR combined with the D-F domain of human RARα) was also examined and found to be ATRA-dependent. These results suggest that TcRAR is not activated by retinoic acids, but can form a heterodimer with TcRXR isoforms. These data contribute to our understanding of the mechanism by which RXR functions in gastropods.
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Affiliation(s)
- Hiroshi Urushitani
- Center for Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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Kawamura K, Shiohara M, Kanda M, Fujiwara S. Retinoid X receptor-mediated transdifferentiation cascade in budding tunicates. Dev Biol 2013; 384:343-55. [PMID: 24120377 DOI: 10.1016/j.ydbio.2013.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/26/2013] [Accepted: 10/03/2013] [Indexed: 10/26/2022]
Abstract
In the budding tunicate, Polyandrocarpa misakiensis, retinoic acid (RA) applied to buds promotes transdifferentiation of somatic cells to form the secondary body axis. This study investigated the gene cascade regulating such RA-triggered transdifferentiation in tunicates. Genes encoding retinoic acid receptor (RAR) and retinoid X receptor (RXR) were induced during transdifferentiation, and they responded to all-trans RA or 13-cis RA in vivo, whereas 9-cis RA had the least effects, demonstrating differences in the ligand preference between budding tunicates and vertebrates. In contrast to RAR mRNA, RXR mRNA could induce transdifferentiation-related genes such as RXR itself, ERK, and MYC in an RA-dependent manner and also induced β-catenin (β-CTN) RA-independently when it was introduced in vitro into tunicate cell lines that do not express endogenous RAR or RXR. Small interfering RNA (siRNA) of RXR dramatically attenuated not only RXR but also ERK and β-CTN gene activities. An ERK inhibitor severely blocked wound healing and dedifferentiation. β-CTN siRNA suppressed morphogenesis and redifferentiation, similar to RXR siRNA. These results indicate that in P. misakiensis, the main function of RA is to trigger positive feedback regulation of RXR rather than to activate RAR for unlocking downstream pathways for transdifferentiation. Our results may reflect an ancient mode of RA signaling in chordates.
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Affiliation(s)
- Kaz Kawamura
- Laboratory of Cellular and Molecular Biotechnology, Faculty of Science, Kochi University, 2-5-1 Akebono-Cho, Kochi 780-8520, Japan.
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Abstract
Gene duplication is a key source of genetic innovation that plays a role in the evolution of phenotypic complexity. Although several evolutionary processes can result in the long-term retention of duplicate genes, their relative contributions in nature are unknown. Here we develop a phylogenetic approach for comparing genome-wide expression profiles of closely related species to quantify the roles of conservation, neofunctionalization, subfunctionalization, and specialization in the preservation of duplicate genes. Application of our method to pairs of young duplicates in Drosophila shows that neofunctionalization, the gain of a novel function in one copy, accounts for the retention of almost two-thirds of duplicate genes. Surprisingly, novel functions nearly always originate in younger (child) copies, whereas older (parent) copies possess functions similar to those of ancestral genes. Further examination of such pairs reveals a strong bias toward RNA-mediated duplication events, implicating asymmetric duplication and positive selection in the evolution of new functions. Moreover, we show that young duplicate genes are expressed primarily in testes and that their expression breadth increases over evolutionary time. This finding supports the "out-of-testes" hypothesis, which posits that testes are a catalyst for the emergence of new genes that ultimately evolve functions in other tissues. Thus, our study highlights the importance of neofunctionalization and positive selection in the retention of young duplicates in Drosophila and illustrates how duplicates become incorporated into novel functional networks over evolutionary time.
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Clouse RM, Sharma PP, Giribet G, Wheeler WC. Elongation factor-1α, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid. Mol Phylogenet Evol 2013; 68:471-81. [PMID: 23669012 DOI: 10.1016/j.ympev.2013.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 03/21/2013] [Accepted: 04/22/2013] [Indexed: 11/17/2022]
Abstract
Identification of paralogy in candidate nuclear loci is an important prerequisite in phylogenetics and statistical phylogeography, but one that is often overlooked. One marker commonly assumed to be a single-copy gene and claimed to harbor great utility for inferring recent divergences is elongation factor-1α (EF-1α). To test this hypothesis, we systematically cloned EF-1α in three disjunct populations of the harvestman Metasiro americanus. Here we show that EF-1α has a large number of paralogs in this species. The paralogs do not evolve in a concerted manner, and the paralogs diverged prior to the population divergence. Moreover, the paralogs of M. americanus are not comparable to the highly divergent EF-1α paralogs found in bees and spiders, which are easily recognized and separated through the use of specific primers. We demonstrate statistically that our detection of paralogs cannot be attributed to amplification error. The presence of EF-1α paralogs in M. americanus prevents its use in statistical phylogeography, and the presence of out-paralogs argues against its use in phylogenetic inference among recently diverged clades. These data contradict the common assumption that EF-1α is for most or all taxa a single-copy gene, or that it has a small number of paralogs that are homogenized through gene conversion, unequal crossing over, or other processes.
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Affiliation(s)
- Ronald M Clouse
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York City, NY 10024, USA.
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Cañestro C, Albalat R, Irimia M, Garcia-Fernàndez J. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 2013; 24:83-94. [DOI: 10.1016/j.semcdb.2012.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
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Evolutionary, structural and functional interplay of the IκB family members. PLoS One 2013; 8:e54178. [PMID: 23372681 PMCID: PMC3553144 DOI: 10.1371/journal.pone.0054178] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 12/11/2012] [Indexed: 12/17/2022] Open
Abstract
A primary level of control for nuclear factor kappa B (NF-κB) is effected through its interactions with the inhibitor protein, inhibitor of kappa B (IκB). Several lines of evidence confirm the existence of multiple forms of IκB that appear to regulate NF-κB by distinct mechanisms. Therefore, we performed a comprehensive bioinformatics analysis to understand the evolutionary history and intrinsic functional diversity of IκB family members. Phylogenetic relationships were constructed to trace the evolution of the IκB family genes. Our phylogenetic analysis revealed 10 IκB subfamily members that clustered into 5 major clades. Since the ankyrin (ANK) domain appears to be more ancient than the Rel homology domain (RHD), our phylogenetic analysis suggests that some undefined ancestral set of ANK repeats acquired an RHD before any duplication and was later duplicated and then diverged into the different IκB subfamilies. Functional analysis identified several functionally divergent sites in the ANK repeat domains (ARDs) and revealed that this region has undergone strong purifying selection, suggesting its functional importance in IκB genes. Structural analysis showed that the major variations in the number of ANK repeats and high conformational changes in the finger loop ARD region contribute to the differing binding partner specificities, thereby leading to distinct IκB functions. In summary, our study has provided useful information about the phylogeny and structural and functional divergence of the IκB family. Additionally, we identified a number of amino acid sites that contribute to the predicted functional divergence of these proteins.
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50
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Tanaka M. Molecular and evolutionary basis of limb field specification and limb initiation. Dev Growth Differ 2012; 55:149-63. [PMID: 23216351 DOI: 10.1111/dgd.12017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 10/09/2012] [Indexed: 11/30/2022]
Abstract
Specification of limb field and initiation of limb development involve multiple steps, each of which is tightly regulated both spatially and temporally. Recent developmental analyses on various vertebrates have provided insights into the molecular mechanisms that specify limb field and have revealed several genetic interactions of signals involved in limb initiation processes. Furthermore, new approaches to the study of the developmental mechanisms of the lateral plate mesoderm of amphioxus and lamprey embryos have given us clues to understand the evolutionary scenarios that led to the acquisition of paired appendages during evolution. This review highlights such recent findings and discusses the mechanisms of limb field specification and limb bud initiation during development and evolution.
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Affiliation(s)
- Mikiko Tanaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
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