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Frese AN, Mariossi A, Levine MS, Wühr M. Quantitative proteome dynamics across embryogenesis in a model chordate. iScience 2024; 27:109355. [PMID: 38510129 PMCID: PMC10951915 DOI: 10.1016/j.isci.2024.109355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
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Affiliation(s)
- Alexander N. Frese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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2
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Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L. Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development 2022; 149:275867. [PMID: 35770682 PMCID: PMC9307994 DOI: 10.1242/dev.200594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences. Summary: Analyses of the relationships between chromatin architecture and regulatory activities at the HoxD locus show that ancestral transcription patterns can be maintained while new regulations evolve.
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Affiliation(s)
- Aurélie Hintermann
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Isabel Guerreiro
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Lucille Lopez-Delisle
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Christopher Chase Bolt
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Sandra Gitto
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Denis Duboule
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
- Collège de France 3 , 11 Place Marcelin Berthelot, 75005 Paris , France
| | - Leonardo Beccari
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
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3
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Functional conserved non-coding elements among tunicates and chordates. Dev Biol 2019; 448:101-110. [DOI: 10.1016/j.ydbio.2018.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 11/22/2022]
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4
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Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res 2018; 45:12611-12624. [PMID: 29121339 PMCID: PMC5728398 DOI: 10.1093/nar/gkx1074] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks–dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.
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Affiliation(s)
- Dimitris Polychronopoulos
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - James W D King
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Alexander J Nash
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Ge Tan
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
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5
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Basu S, Patil S, Mapleson D, Russo MT, Vitale L, Fevola C, Maumus F, Casotti R, Mock T, Caccamo M, Montresor M, Sanges R, Ferrante MI. Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. THE NEW PHYTOLOGIST 2017; 215:140-156. [PMID: 28429538 PMCID: PMC5485032 DOI: 10.1111/nph.14557] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 02/25/2017] [Indexed: 05/03/2023]
Abstract
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes. We also identified a small number of conserved noncoding elements. Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein-coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis-related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient-replete conditions. The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.
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Affiliation(s)
- Swaraj Basu
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Shrikant Patil
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Monia Teresa Russo
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Laura Vitale
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Cristina Fevola
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Raffaella Casotti
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Mario Caccamo
- Earlham InstituteNorwich Research ParkNorwichNR4 7UGUK
| | - Marina Montresor
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Remo Sanges
- Biology and Evolution of Marine OrganismsStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
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6
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Yue JX, Kozmikova I, Ono H, Nossa CW, Kozmik Z, Putnam NH, Yu JK, Holland LZ. Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle. Genome Biol Evol 2016; 8:2387-405. [PMID: 27412606 PMCID: PMC5010895 DOI: 10.1093/gbe/evw158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.
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Affiliation(s)
- Jia-Xing Yue
- Biosciences at Rice, Rice University, Houston, Texas Present address: Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, INSERM U1081, Nice 06107 France
| | - Iryna Kozmikova
- Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic
| | - Hiroki Ono
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California
| | - Carlos W Nossa
- Biosciences at Rice, Rice University, Houston, Texas Present address: Gene by Gene Ltd., Houston, TX 77008
| | - Zbynek Kozmik
- Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic
| | - Nicholas H Putnam
- Biosciences at Rice, Rice University, Houston, Texas Present address: Dovetail Genomics, Santa Cruz, CA 95060
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California
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7
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Lemaire P, Piette J. Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley. Open Biol 2016; 5:150053. [PMID: 26085517 PMCID: PMC4632506 DOI: 10.1098/rsob.150053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology. We also briefly comment on the more philosophical reflections of Huxley on individuality. In the second part, we stress the originality and relevance of past and future studies of tunicates in the resolution of major biological issues. In particular, we focus on the complex relationship between genotype and phenotype and the phenomenon of developmental system drift. We propose that more than 150 years after Huxley's papers, tunicate embryos are still worth studying in their own right, independently of their evolutionary proximity to vertebrates, as they provide original and crucial insights into the process of animal evolution. Tunicates are still at the forefront of biological research.
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Affiliation(s)
- Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
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8
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Jiang BC, Yang T, He LN, Tao YX, Gao YJ. Altered T-UCRs expression profile in the spinal cord of mice with neuropathic pain. TRANSLATIONAL PERIOPERATIVE AND PAIN MEDICINE 2016; 1:1-10. [PMID: 27500182 PMCID: PMC4971523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Spinal cord plays an important role in the transmission and modulation of nociceptive information. Global changes in gene expression in the spinal cord contribute to the induction and maintenance of neuropathic pain. Transcribed Ultraconserved Regions (T-UCRs), a novel class of long noncoding RNAs, can regulate gene expression at both transcriptional and post-transcriptional levels and are related to many human diseases such as cancer, Alzheimer's disease, and heart diseases. In this study, we screened abnormal T-UCRs expression in the spinal cord under spinal nerve ligation (SNL)-induced neuropathic pain condition. Microarray data showed the alternation of T-UCRs at the transcriptional level in the spinal cord 10 days after SNL. Among 78 altered T-UCRs, 23 T-UCRs were upregulated by more than 1.5-fold and 55 ones downregulated by less than 0.5-fold after SNL. Hierarchical cluster analysis of T-UCRs expression profiles showed the opposite expression pattern between SNL and sham-operated mice. The quantitative real-time reverse transcription polymerase chain reaction analysis further confirmed the expression patterns of uc.305, uc.189, uc.46, and uc.217 after SNL. The gene ontology annotation and signaling pathway analysis for the T-UCRs host genes indicated that differentially expressed T-UCRs were involved in several intracellular activities and signaling pathways, including Ephrin receptor activity, soluble NSF attachment protein receptor (SNARE) interactions in vesicular transport pathway, and WNT signaling pathway. Collectively, the current data suggest the possible role of T-UCR in the pathogenesis of neuropathic pain. T-UCRs may serve as a new kind of target for the treatment of neuropathic pain.
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Affiliation(s)
- Bao-Chun Jiang
- Pain Research Laboratory, Institute of Nautical Medicine, Jiangsu Key Laboratory of Inflammation and Molecular Drug Target, Nantong University, Nantong, Jiangsu 226019, China
| | - Tian Yang
- Pain Research Laboratory, Institute of Nautical Medicine, Jiangsu Key Laboratory of Inflammation and Molecular Drug Target, Nantong University, Nantong, Jiangsu 226019, China
| | - Li-Na He
- Pain Research Laboratory, Institute of Nautical Medicine, Jiangsu Key Laboratory of Inflammation and Molecular Drug Target, Nantong University, Nantong, Jiangsu 226019, China
| | - Yuan-Xiang Tao
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Yong-Jing Gao
- Pain Research Laboratory, Institute of Nautical Medicine, Jiangsu Key Laboratory of Inflammation and Molecular Drug Target, Nantong University, Nantong, Jiangsu 226019, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
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Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos. BIOMED RESEARCH INTERNATIONAL 2015; 2015:316735. [PMID: 26273607 PMCID: PMC4530217 DOI: 10.1155/2015/316735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022]
Abstract
Evolutionary developmental biology (EVO-DEVO) tries to decode evolutionary constraints on the stages of embryonic development. Two models--the "funnel-like" model and the "hourglass" model--have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED) were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA). Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.
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Grice J, Noyvert B, Doglio L, Elgar G. A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PLoS One 2015; 10:e0130413. [PMID: 26131856 PMCID: PMC4489388 DOI: 10.1371/journal.pone.0130413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/19/2015] [Indexed: 12/17/2022] Open
Abstract
Background Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive. Results Here, we identify a shared sequence signature (syntax) within a heterogeneous set of conserved vertebrate hindbrain enhancers composed of spatially co-occurring PBX-HOX and MEIS/PREP transcription factor binding motifs. We use this syntax to accurately predict hindbrain enhancers in 89% of cases (67/75 predicted elements) from a set of conserved non-coding elements (CNEs). Furthermore, mutagenesis of the sites abolishes activity or generates ectopic expression, demonstrating their requirement for segmentally restricted enhancer activity in the hindbrain. We refine and use our syntax to predict over 3,000 hindbrain enhancers across the human genome. These sequences tend to be located near developmental transcription factors and are enriched in known hindbrain activating elements, demonstrating the predictive power of this simple model. Conclusion Our findings support the theory that hundreds of CNEs, and perhaps thousands of regions across the human genome, function to coordinate gene expression in the developing hindbrain. We speculate that deeply conserved sequences of this kind contributed to the co-option of new genes into the hindbrain gene regulatory network during early vertebrate evolution by linking patterns of hox expression to downstream genes involved in segmentation and patterning, and evolutionarily newer instances may have continued to contribute to lineage-specific elaboration of the hindbrain.
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Affiliation(s)
- Joseph Grice
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Boris Noyvert
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Laura Doglio
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Greg Elgar
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
- * E-mail:
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11
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Vassalli QA, Anishchenko E, Caputi L, Sordino P, D'Aniello S, Locascio A. Regulatory elements retained during chordate evolution: Coming across tunicates. Genesis 2014; 53:66-81. [DOI: 10.1002/dvg.22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Quirino Attilio Vassalli
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Evgeniya Anishchenko
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Luigi Caputi
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Paolo Sordino
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
- CNR ISAFOM, Institute for Agricultural and Forest Systems in the Mediterranean, Unitá organizzativa di supporto; Catania Italy
| | - Salvatore D'Aniello
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Annamaria Locascio
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
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12
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Silla T, Kepp K, Tai ES, Goh L, Davila S, Ivkovic TC, Calin GA, Voorhoeve PM. Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding. PLoS One 2014; 9:e110692. [PMID: 25369454 PMCID: PMC4219694 DOI: 10.1371/journal.pone.0110692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/16/2014] [Indexed: 12/30/2022] Open
Abstract
Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF<0.5%) of which 75% is not present in dbSNP137. UCEs association studies for complex human traits can use this information to model expected background variation and thus necessary power for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.
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Affiliation(s)
- Toomas Silla
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Katrin Kepp
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - E. Shyong Tai
- Department of Medicine, National University of Singapore, Singapore, Singapore
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Liang Goh
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Tina Catela Ivkovic
- Experimental Therapeutics & Cancer Genetics, MD Anderson Cancer Center, Texas State University, Houston, Texas, United States of America
- Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - George A. Calin
- Experimental Therapeutics & Cancer Genetics, MD Anderson Cancer Center, Texas State University, Houston, Texas, United States of America
| | - P. Mathijs Voorhoeve
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore
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Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome. Nat Commun 2014; 5:4483. [PMID: 25047197 PMCID: PMC4109005 DOI: 10.1038/ncomms5483] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/23/2014] [Indexed: 01/22/2023] Open
Abstract
Elucidating the function of highly conserved regulatory sequences is a significant challenge in genomics today. Certain intragenic highly conserved elements have been associated with regulating levels of core components of the spliceosome and alternative splicing of downstream genes. Here we identify mutations in one such element, a regulatory alternative exon of SNRPB as the cause of cerebro-costo-mandibular syndrome. This exon contains a premature termination codon that triggers nonsense-mediated mRNA decay when included in the transcript. These mutations cause increased inclusion of the alternative exon and decreased overall expression of SNRPB. We provide evidence for the functional importance of this conserved intragenic element in the regulation of alternative splicing and development, and suggest that the evolution of such a regulatory mechanism has contributed to the complexity of mammalian development.
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Polychronopoulos D, Sellis D, Almirantis Y. Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics. PLoS One 2014; 9:e95437. [PMID: 24787386 PMCID: PMC4008492 DOI: 10.1371/journal.pone.0095437] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/26/2014] [Indexed: 12/31/2022] Open
Abstract
Conserved, ultraconserved and other classes of constrained elements (collectively referred as CNEs here), identified by comparative genomics in a wide variety of genomes, are non-randomly distributed across chromosomes. These elements are defined using various degrees of conservation between organisms and several thresholds of minimal length. We here investigate the chromosomal distribution of CNEs by studying the statistical properties of distances between consecutive CNEs. We find widespread power-law-like distributions, i.e. linearity in double logarithmic scale, in the inter-CNE distances, a feature which is connected with fractality and self-similarity. Given that CNEs are often found to be spatially associated with genes, especially with those that regulate developmental processes, we verify by appropriate gene masking that a power-law-like pattern emerges irrespectively of whether elements found close or inside genes are excluded or not. An evolutionary model is put forward for the understanding of these findings that includes segmental or whole genome duplication events and eliminations (loss) of most of the duplicated CNEs. Simulations reproduce the main features of the observed size distributions. Power-law-like patterns in the genomic distributions of CNEs are in accordance with current knowledge about their evolutionary history in several genomes.
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Affiliation(s)
- Dimitris Polychronopoulos
- Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Athens, Greece
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Diamantis Sellis
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Yannis Almirantis
- Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Athens, Greece
- * E-mail:
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15
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Chen WC, Pauls S, Bacha J, Elgar G, Loose M, Shimeld SM. Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. Dev Biol 2014; 390:261-72. [PMID: 24680932 PMCID: PMC4010673 DOI: 10.1016/j.ydbio.2014.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 03/03/2014] [Accepted: 03/19/2014] [Indexed: 01/31/2023]
Abstract
Vertebrate genomes share numerous conserved non-coding elements, many of which function as enhancer elements and are hypothesised to be under evolutionary constraint due to a need to be bound by combinations of sequence-specific transcription factors. In contrast, few such conserved elements can be detected between vertebrates and their closest invertebrate relatives. Despite this lack of sequence identity, cross-species transgenesis has identified some cases where non-coding DNA from invertebrates drives reporter gene expression in transgenic vertebrates in patterns reminiscent of the expression of vertebrate orthologues. Such instances are presumed to reflect the presence of conserved suites of binding sites in the regulatory regions of invertebrate and vertebrate orthologues, such that both regulatory elements can correctly interpret the trans-activating environment. Shuffling of binding sites has been suggested to lie behind loss of sequence conservation; however this has not been experimentally tested. Here we examine the underlying basis of enhancer activity for the Ciona intestinalis βγ-crystallin gene, which drives expression in the lens of transgenic vertebrates despite the Ciona lineage predating the evolution of the lens. We construct an interactive gene regulatory network (GRN) for vertebrate lens development, allowing network interactions to be robustly catalogued and conserved network components and features to be identified. We show that a small number of binding motifs are necessary for Ciona βγ-crystallin expression, and narrow down the likely factors that bind to these motifs. Several of these overlap with the conserved core of the vertebrate lens GRN, implicating these sites in cross species function. However when we test these motifs in a transgenic vertebrate they prove to be dispensable for reporter expression in the lens. These results show that current models depicting cross species enhancer function as dependent on conserved binding sites can be overly simplistic, with sound evolutionary inference requiring detailed dissection of underlying mechanisms. Analysis of binding motifs in a Ciona enhancer that also works in vertebrate lens. Establishment of candidate transcription factors that may regulate this enhancer. Construction of a curated, interactive gene regulatory network of lens development. Public accessibility of this via a dedicated web site. Experimental test of binding motif function in cross species transgenesis.
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Affiliation(s)
- Wei-Chung Chen
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Stefan Pauls
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Jamil Bacha
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Greg Elgar
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Matthew Loose
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK.
| | - Sebastian M Shimeld
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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16
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Holland LZ. Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:342-52. [DOI: 10.1002/jez.b.22569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Linda Z. Holland
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California San Diego; La Jolla California 92093-0202 USA
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17
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Makunin IV, Shloma VV, Stephen SJ, Pheasant M, Belyakin SN. Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One 2013; 8:e82362. [PMID: 24349264 PMCID: PMC3862641 DOI: 10.1371/journal.pone.0082362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022] Open
Abstract
Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.
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Affiliation(s)
- Igor V. Makunin
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
- * E-mail:
| | - Viktor V. Shloma
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
| | - Stuart J. Stephen
- Computational Biology Group, CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Michael Pheasant
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
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18
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Parallel evolution of chordate cis-regulatory code for development. PLoS Genet 2013; 9:e1003904. [PMID: 24282393 PMCID: PMC3836708 DOI: 10.1371/journal.pgen.1003904] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations. Vertebrates share many aspects of early development with our closest chordate ancestors, the tunicates. However, whilst the repertoire of genes that orchestrate development is essentially the same in the two lineages, the genomic code that regulates these genes appears to be very different, even though it is highly conserved within vertebrates themselves. Using comparative genomics, we have identified a parallel developmental code in tunicates and confirmed that this code, despite a lack of sequence conservation, associates with a similar repertoire of genes. However, the organisation of the code spatially is very different in the two lineages, strongly suggesting that most of it arose independently in vertebrates and tunicates, and in most cases lacking any direct sequence ancestry. We have assayed elements of the tunicate code, and found that at least some of them can regulate gene expression in zebrafish embryos. Our results suggest that regulatory code has arisen independently in different animal lineages but possesses some common functionality because its evolution has been driven by a similar cohort of developmental transcription factors. Our work helps illuminate how complex, stable gene regulatory networks evolve and become fixed within lineages.
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19
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Maeso I, Irimia M, Tena JJ, Casares F, Gómez-Skarmeta JL. Deep conservation of cis-regulatory elements in metazoans. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130020. [PMID: 24218633 DOI: 10.1098/rstb.2013.0020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite the vast morphological variation observed across phyla, animals share multiple basic developmental processes orchestrated by a common ancestral gene toolkit. These genes interact with each other building complex gene regulatory networks (GRNs), which are encoded in the genome by cis-regulatory elements (CREs) that serve as computational units of the network. Although GRN subcircuits involved in ancient developmental processes are expected to be at least partially conserved, identification of CREs that are conserved across phyla has remained elusive. Here, we review recent studies that revealed such deeply conserved CREs do exist, discuss the difficulties associated with their identification and describe new approaches that will facilitate this search.
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Affiliation(s)
- Ignacio Maeso
- Department of Zoology, University of Oxford, , Oxford, UK
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20
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Harmston N, Baresic A, Lenhard B. The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130021. [PMID: 24218634 PMCID: PMC3826495 DOI: 10.1098/rstb.2013.0021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Regions of several dozen to several hundred base pairs of extreme conservation have been found in non-coding regions in all metazoan genomes. The distribution of these elements within and across genomes has suggested that many have roles as transcriptional regulatory elements in multi-cellular organization, differentiation and development. Currently, there is no known mechanism or function that would account for this level of conservation at the observed evolutionary distances. Previous studies have found that, while these regions are under strong purifying selection, and not mutational coldspots, deletion of entire regions in mice does not necessarily lead to identifiable changes in phenotype during development. These opposing findings lead to several questions regarding their functional importance and why they are under strong selection in the first place. In this perspective, we discuss the methods and techniques used in identifying and dissecting these regions, their observed patterns of conservation, and review the current hypotheses on their functional significance.
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Affiliation(s)
- Nathan Harmston
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, , Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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21
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Ferg M, Armant O, Yang L, Dickmeis T, Rastegar S, Strähle U. Gene transcription in the zebrafish embryo: regulators and networks. Brief Funct Genomics 2013; 13:131-43. [PMID: 24152666 DOI: 10.1093/bfgp/elt044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
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Affiliation(s)
- Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany.
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