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Maekawa M, Saito S, Isobe D, Takemoto K, Miura Y, Dobashi Y, Yamasu K. The Oct4-related PouV gene, pou5f3, mediates isthmus development in zebrafish by directly and dynamically regulating pax2a. Cells Dev 2024:203933. [PMID: 38908828 DOI: 10.1016/j.cdev.2024.203933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Using a transgenic zebrafish line harboring a heat-inducible dominant-interference pou5f3 gene (en-pou5f3), we reported that this PouV gene is involved in isthmus development at the midbrain-hindbrain boundary (MHB), which patterns the midbrain and cerebellum. Importantly, the functions of pou5f3 reportedly differ before and after the end of gastrulation. In the present study, we examined in detail the effects of en-pou5f3 induction on isthmus development during embryogenesis. When en-pou5f3 was induced around the end of gastrulation (bud stage), the isthmus was abrogated or deformed by the end of somitogenesis (24 hours post-fertilization). At this stage, the expression of MHB markers -- such as pax2a, fgf8a, wnt1, and gbx2 -- was absent in embryos lacking the isthmus structure, whereas it was present, although severely distorted, in embryos with a deformed isthmus. We further found that, after en-pou5f3 induction at late gastrulation, pax2a, fgf8a, and wnt1 were immediately and irreversibly downregulated, whereas the expression of en2a and gbx2 was reduced only weakly and slowly. Induction of en-pou5f3 at early somite stages also immediately downregulated MHB genes, particularly pax2a, but their expression was restored later. Overall, the data suggested that pou5f3 directly upregulates at least pax2a and possibly fgf8a and wnt1, which function in parallel in establishing the MHB, and that the role of pou5f3 dynamically changes around the end of gastrulation. We next examined the transcriptional regulation of pax2a using both in vitro and in vivo reporter analyses; the results showed that two upstream 1.0-kb regions with sequences conserved among vertebrates specifically drove transcription at the MHB. These reporter analyses confirmed that development of the isthmic organizer is regulated by PouV through direct regulation of pax2/pax2a in vertebrate embryos.
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Affiliation(s)
- Masato Maekawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Shinji Saito
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Institute for Vaccine Research and Development, Hokkaido University, N21, W11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Daiki Isobe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kazumasa Takemoto
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U3156, Storrs, CT 06269, USA
| | - Yuhei Miura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yurie Dobashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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2
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Ferguson CA, Firulli BA, Zoia M, Osterwalder M, Firulli AB. Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs. Dev Dyn 2024; 253:215-232. [PMID: 37551791 DOI: 10.1002/dvdy.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The bHLH transcription factor HAND2 plays important roles in the development of the embryonic heart, face, limbs, and sympathetic and enteric nervous systems. To define how and when HAND2 regulates these developmental systems, requires understanding the transcriptional regulation of Hand2. RESULTS Remarkably, Hand2 is flanked by an extensive upstream gene desert containing a potentially diverse enhancer landscape. Here, we screened the regulatory interval 200 kb proximal to Hand2 for putative enhancers using evolutionary conservation and histone marks in Hand2-expressing tissues. H3K27ac signatures across embryonic tissues pointed to only two putative enhancer regions showing deep sequence conservation. Assessment of the transcriptional enhancer potential of these elements using transgenic reporter lines uncovered distinct in vivo enhancer activities in embryonic stomach and limb mesenchyme, respectively. Activity of the identified stomach enhancer was restricted to the developing antrum and showed expression within the smooth muscle and enteric neurons. Surprisingly, the activity pattern of the limb enhancer did not overlap Hand2 mRNA but consistently yielded a defined subectodermal anterior expression pattern within multiple transgenic lines. CONCLUSIONS Together, these results start to uncover the diverse regulatory potential inherent to the Hand2 upstream regulatory interval.
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Affiliation(s)
- Chloe A Ferguson
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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3
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Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Dev Biol 2021; 479:61-76. [PMID: 34310923 DOI: 10.1016/j.ydbio.2021.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022]
Abstract
Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.
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4
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Mookerjee-Basu J, Hua X, Ge L, Nicolas E, Li Q, Czyzewicz P, Zhongping D, Peri S, FuxmanBass JI, Walhout AJM, Kappes DJ. Functional Conservation of a Developmental Switch in Mammals since the Jurassic Age. Mol Biol Evol 2019; 36:39-53. [PMID: 30295892 DOI: 10.1093/molbev/msy191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
ThPOK is a "master regulator" of T lymphocyte lineage choice, whose presence or absence is sufficient to dictate development to the CD4 or CD8 lineages, respectively. Induction of ThPOK is transcriptionally regulated, via a lineage-specific silencer element, SilThPOK. Here, we take advantage of the available genome sequence data as well as site-specific gene targeting technology, to evaluate the functional conservation of ThPOK regulation across mammalian evolution, and assess the importance of motif grammar (order and orientation of TF binding sites) on SilThPOK function in vivo. We make three important points: First, the SilThPOK is present in marsupial and placental mammals, but is not found in available genome assemblies of nonmammalian vertebrates, indicating that it arose after divergence of mammals from other vertebrates. Secondly, by replacing the murine SilThPOK in situ with its marsupial equivalent using a knockin approach, we demonstrate that the marsupial SilThPOK supports correct CD4 T lymphocyte lineage-specification in mice. To our knowledge, this is the first in vivo demonstration of functional equivalency for a silencer element between marsupial and placental mammals using a definitive knockin approach. Finally, we show that alteration of the position/orientation of a highly conserved region within the murine SilThPOK is sufficient to destroy silencer activity in vivo, demonstrating that motif grammar of this "solid" synteny block is critical for silencer function. Dependence of SilThPOK function on motif grammar conserved since the mid-Jurassic age, 165 Ma, suggests that the SilThPOK operates as a silenceosome, by analogy with the previously proposed enhanceosome model.
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Affiliation(s)
- Jayati Mookerjee-Basu
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Xiang Hua
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Lu Ge
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Emmanuelle Nicolas
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Qin Li
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Philip Czyzewicz
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Dai Zhongping
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Suraj Peri
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Juan I FuxmanBass
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Dietmar J Kappes
- Blood Cell Development and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA
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5
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Minhas R, Paterek A, Łapiński M, Bazała M, Korzh V, Winata CL. A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Dev Dyn 2019; 248:837-849. [PMID: 31194899 PMCID: PMC6771876 DOI: 10.1002/dvdy.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 01/15/2023] Open
Abstract
Background Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis. Results We identified two novel tetrapod‐teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue‐specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression. Conclusion This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression. Identified a novel enhancer near zebrafish zic3/zic6 locus. The novel enhancer drives tissue‐specific expression in the habenula. Zebrafish transgenic line generated in this study can be a useful resource for studying development of habenula.
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Affiliation(s)
- Rashid Minhas
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aleksandra Paterek
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Clinical Physiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Bazała
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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6
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Hajheidari M, Koncz C, Bucher M. Chromatin Evolution-Key Innovations Underpinning Morphological Complexity. FRONTIERS IN PLANT SCIENCE 2019; 10:454. [PMID: 31031789 PMCID: PMC6474313 DOI: 10.3389/fpls.2019.00454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/26/2019] [Indexed: 05/20/2023]
Abstract
The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.
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Affiliation(s)
- Mohsen Hajheidari
- Botanical Institute, Cologne Biocenter, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Csaba Koncz
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Biological Research Center, Institute of Plant Biology, Hungarian Academy of Sciences, Szeged, Hungary
| | - Marcel Bucher
- Botanical Institute, Cologne Biocenter, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
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7
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Meyer KA, Marques-Bonet T, Sestan N. Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences. Mol Biol Evol 2017; 34:1217-1229. [PMID: 28204568 PMCID: PMC5400397 DOI: 10.1093/molbev/msx076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Previous studies have found that genes which are differentially expressed within the developing human brain disproportionately neighbor conserved noncoding sequences (CNSs) that have an elevated substitution rate in humans and in other species. One explanation for this general association of differential expression with accelerated CNSs is that genes with pre-existing patterns of differential expression have been preferentially targeted by species-specific regulatory changes. Here we provide support for an alternative explanation: genes that neighbor a greater number of CNSs have a higher probability of differential expression and a higher probability of neighboring a CNS with lineage-specific acceleration. Thus, neighboring an accelerated element from any species signals that a gene likely neighbors many CNSs. We extend the analyses beyond the prenatal time points considered in previous studies to demonstrate that this association persists across developmental and adult periods. Examining differential expression between non-neural tissues suggests that the relationship between the number of CNSs a gene neighbors and its differential expression status may be particularly strong for expression differences among brain regions. In addition, by considering this relationship, we highlight a recently defined set of putative human-specific gain-of-function sequences that, even after adjusting for the number of CNSs neighbored by genes, shows a positive relationship with upregulation in the brain compared with other tissues examined.
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Affiliation(s)
- Kyle A. Meyer
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT
- Departments of Genetics and Psychiatry, Section of Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT
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8
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Pérez-Rico YA, Boeva V, Mallory AC, Bitetti A, Majello S, Barillot E, Shkumatava A. Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Genome Res 2016; 27:259-268. [PMID: 27965291 PMCID: PMC5287231 DOI: 10.1101/gr.203679.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/09/2016] [Indexed: 12/11/2022]
Abstract
Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ∼42% of zebrafish SEs were located in close proximity to orthologs that also were associated with SEs in mouse and human. Compared to their nonassociated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish annotations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.
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Affiliation(s)
- Yuvia A Pérez-Rico
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.,INSERM, U900, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Valentina Boeva
- INSERM, U900, F-75005, Paris, France.,Institut Curie, Mines ParisTech, PSL Research University, F-75005, Paris, France.,Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France
| | - Allison C Mallory
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
| | - Angelo Bitetti
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Sara Majello
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
| | - Emmanuel Barillot
- INSERM, U900, F-75005, Paris, France.,Institut Curie, Mines ParisTech, PSL Research University, F-75005, Paris, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
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9
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Long HK, Prescott SL, Wysocka J. Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution. Cell 2016; 167:1170-1187. [PMID: 27863239 PMCID: PMC5123704 DOI: 10.1016/j.cell.2016.09.018] [Citation(s) in RCA: 564] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/24/2016] [Accepted: 09/07/2016] [Indexed: 12/27/2022]
Abstract
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally precise gene-expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation. We discuss intricate relationships between distinct elements within complex regulatory landscapes and consider their potential impact on specificity and robustness of transcriptional regulation.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sara L Prescott
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
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10
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Chen L, Guo W, Ren L, Yang M, Zhao Y, Guo Z, Yi H, Li M, Hu Y, Long X, Sun B, Li J, Zhai S, Zhang T, Tian S, Meng Q, Yu N, Zhu D, Tang G, Tang Q, Ren L, Liu K, Zhang S, Che T, Yu Z, Wu N, Jing L, Zhang R, Cong T, Chen S, Zhao Y, Zhang Y, Bai X, Guo Y, Zhao L, Zhang F, Zhao H, Zhang L, Hou Z, Zhao J, Li J, Zhang L, Sun W, Zou X, Wang T, Ge L, Liu Z, Hu X, Wang J, Yang S, Li N. A de novo silencer causes elimination of MITF-M expression and profound hearing loss in pigs. BMC Biol 2016; 14:52. [PMID: 27349893 PMCID: PMC4922063 DOI: 10.1186/s12915-016-0273-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/10/2016] [Indexed: 12/18/2022] Open
Abstract
Background Genesis of novel gene regulatory modules is largely responsible for morphological and functional evolution. De novo generation of novel cis-regulatory elements (CREs) is much rarer than genomic events that alter existing CREs such as transposition, promoter switching or co-option. Only one case of de novo generation has been reported to date, in fish and without involvement of phenotype alteration. Yet, this event likely occurs in other animals and helps drive genetic/phenotypic variation. Results Using a porcine model of spontaneous hearing loss not previously characterized we performed gene mapping and mutation screening to determine the genetic foundation of the phenotype. We identified a mutation in the non-regulatory region of the melanocyte-specific promoter of microphthalmia-associated transcription factor (MITF) gene that generated a novel silencer. The consequent elimination of expression of the MITF-M isoform led to early degeneration of the intermediate cells of the cochlear stria vascularis and profound hearing loss, as well as depigmentation, all of which resemble the typical phenotype of Waardenburg syndrome in humans. The mutation exclusively affected MITF-M and no other isoforms. The essential function of Mitf-m in hearing development was further validated using a knock-out mouse model. Conclusions Elimination of the MITF-M isoform alone is sufficient to cause deafness and depigmentation. To our knowledge, this study provides the first evidence of a de novo CRE in mammals that produces a systemic functional effect. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0273-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.,Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Weiwei Guo
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lili Ren
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Yaofeng Zhao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Zongyi Guo
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Haijin Yi
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Yiqing Hu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xi Long
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Boyuan Sun
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Jinxiu Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Suoqiang Zhai
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Tinghuan Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Qingyong Meng
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Ning Yu
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Dan Zhu
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Liming Ren
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Ke Liu
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Shihua Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Zhengquan Yu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Nan Wu
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lan Jing
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Ran Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Tao Cong
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Siqing Chen
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Yiqiang Zhao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yue Zhang
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaoqing Bai
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Ying Guo
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Lidong Zhao
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Fengming Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Hui Zhao
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Liang Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Zhaohui Hou
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiugang Zhao
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Jianan Li
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lijuan Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Wei Sun
- Department of Communicative Disorders and Sciences, Center for Hearing and Deafness, State University of New York at Buffalo, Buffalo, New York, USA
| | - Xiangang Zou
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Tao Wang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Liangpeng Ge
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Zuohua Liu
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Xiaoxiang Hu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Jingyong Wang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
| | - Shiming Yang
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
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11
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Abstract
Reversible covalent histone modifications are known to influence spatiotemporal patterns of gene transcription during development. Here I review recent advances in the development and use of methods to analyze the distribution and functions of histone modifications in zebrafish chromatin. I discuss the roles of dynamic histone modification patterns at the promoters and enhancers of genes during the process of zygotic gene activation at blastula stages and the interplay between the molecular machinery responsible for histone modifications, chromatin remodeling and DNA methylation. Interactions are also described between developmentally regulated enhancer sequences and modified histones. A detailed method for chromatin immunoprecipitation using antibodies is provided, and I describe the use of high-throughput whole genome sequencing technology to generate DNA sequence data from chromatin immunoprecipitates. I also discuss computational approaches to integrating DNA sequence data obtained from chromatin immunoprecipitates with annotated reference genome sequences, transcriptome and methylome sequence data, transcription factor binding motif databases, and gene ontologies and describe the types of software tools currently available for visualizing the results.
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Affiliation(s)
- V T Cunliffe
- University of Sheffield, Sheffield, United Kingdom.
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12
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Davis A, Reubens MC, Stellwag EJ. Functional and Comparative Genomics of Hoxa2 Gene cis-Regulatory Elements: Evidence for Evolutionary Modification of Ancestral Core Element Activity. J Dev Biol 2016; 4:jdb4020015. [PMID: 29615583 PMCID: PMC5831782 DOI: 10.3390/jdb4020015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hoxa2 is an evolutionarily conserved developmental regulatory gene that functions to specify rhombomere (r) and pharyngeal arch (PA) identities throughout the Osteichthyes. Japanese medaka (Oryzias latipes) hoxa2a, like orthologous Hoxa2 genes from other osteichthyans, is expressed during embryogenesis in r2–7 and PA2-7, whereas the paralogous medaka pseudogene, ψhoxa2b, is expressed in noncanonical Hoxa2 domains, including the pectoral fin buds. To understand the evolution of cis-regulatory element (CRE) control of gene expression, we conducted eGFP reporter gene expression studies with extensive functional mapping of several conserved CREs upstream of medaka hoxa2a and ψhoxa2b in transient and stable-line transgenic medaka embryos. The CREs tested were previously shown to contribute to directing mouse Hoxa2 gene expression in r3, r5, and PA2-4. Our results reveal the presence of sequence elements embedded in the medaka hoxa2a and ψhoxa2b upstream enhancer regions (UERs) that mediate expression in r4 and the PAs (hoxa2a r4/CNCC element) or in r3–7 and the PAs ψhoxa2b r3–7/CNCC element), respectively. Further, these elements were shown to be highly conserved among osteichthyans, which suggests that the r4 specifying element embedded in the UER of Hoxa2 is a deeply rooted rhombomere specifying element and the activity of this element has been modified by the evolution of flanking sequences that redirect its activity to alternative developmental compartments.
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Affiliation(s)
- Adam Davis
- Department of Biology and Physical Sciences, Gordon State College, Barnesville, GA 30204, USA.
| | - Michael C Reubens
- The Scripps Research Institute, 10550 N, Torrey Pines Road, MB3, La Jolla, CA 92037, USA.
| | - Edmund J Stellwag
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA.
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13
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Rodríguez-Mega E, Piñeyro-Nelson A, Gutierrez C, García-Ponce B, Sánchez MDLP, Zluhan-Martínez E, Álvarez-Buylla ER, Garay-Arroyo A. Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach. Dev Dyn 2015; 244:1074-1095. [PMID: 25733163 DOI: 10.1002/dvdy.24268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/24/2015] [Accepted: 02/24/2015] [Indexed: 12/20/2022] Open
Abstract
A growing body of evidence suggests that alterations in transcriptional regulation of genes involved in modulating development are an important part of phenotypic evolution, and this can be documented among species and within populations. While the effects of differential transcriptional regulation in organismal development have been preferentially studied in animal systems, this phenomenon has also been addressed in plants. In this review, we summarize evidence for cis-regulatory mutations, trans-regulatory changes and epigenetic modifications as molecular events underlying important phenotypic alterations, and thus shaping the evolution of plant development. We postulate that a mechanistic understanding of why such molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks that consider the concerted action of genetic and nongenetic components, and that also incorporate the restrictions underlying the genotype to phenotype mapping process. Developmental Dynamics 244:1074-1095, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Emiliano Rodríguez-Mega
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Alma Piñeyro-Nelson
- Department of Plant and Microbial Biology, University of California, Berkeley, California
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - María De La Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México.,Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
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14
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Parker HJ, Sauka-Spengler T, Bronner M, Elgar G. A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancers. PLoS One 2014; 9:e85492. [PMID: 24416417 PMCID: PMC3887057 DOI: 10.1371/journal.pone.0085492] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/05/2013] [Indexed: 11/27/2022] Open
Abstract
The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.
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Affiliation(s)
- Hugo J. Parker
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Tatjana Sauka-Spengler
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Marianne Bronner
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Greg Elgar
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- * E-mail:
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15
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Rubinstein M, de Souza FSJ. Evolution of transcriptional enhancers and animal diversity. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130017. [PMID: 24218630 DOI: 10.1098/rstb.2013.0017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Deciphering the genetic bases that drive animal diversity is one of the major challenges of modern biology. Although four decades ago it was proposed that animal evolution was mainly driven by changes in cis-regulatory DNA elements controlling gene expression rather than in protein-coding sequences, only now are powerful bioinformatics and experimental approaches available to accelerate studies into how the evolution of transcriptional enhancers contributes to novel forms and functions. In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time. We discuss past and current methods used to identify cell-type-specific enhancers and provide examples of how enhancers originate de novo, change and are lost in particular lineages. We then focus in the central part of this Theme Issue on analysing examples of how the molecular evolution of enhancers may change form and function. Throughout this introduction, we present the main findings of the articles, reviews and perspectives contributed to this Theme Issue that together illustrate some of the great advances and current frontiers in the field.
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Affiliation(s)
- Marcelo Rubinstein
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, , C1428ADN Buenos Aires, Argentina
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16
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Irimia M, Maeso I, Roy SW, Fraser HB. Ancient cis-regulatory constraints and the evolution of genome architecture. Trends Genet 2013; 29:521-8. [PMID: 23791467 DOI: 10.1016/j.tig.2013.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/02/2013] [Accepted: 05/15/2013] [Indexed: 01/18/2023]
Abstract
The order of genes along metazoan chromosomes has generally been thought to be largely random, with few implications for organismal function. However, two recent studies, reporting hundreds of pairs of genes that have remained linked in diverse metazoan species over hundreds of millions of years of evolution, suggest widespread functional implications for gene order. These associations appear to largely reflect cis-regulatory constraints, with either (i) multiple genes sharing transcriptional regulatory elements, or (ii) regulatory elements for a developmental gene being found within a neighboring 'bystander' gene (known as a genomic regulatory block). We discuss implications, questions raised, and new research directions arising from these studies, as well as evidence for similar phenomena in other eukaryotic groups.
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Affiliation(s)
- Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
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17
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Goode DK, Elgar G. Capturing the regulatory interactions of eukaryote genomes. Brief Funct Genomics 2012; 12:142-60. [PMID: 23117864 DOI: 10.1093/bfgp/els041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A key finding from early genomics research is the remarkable consistency in the number of protein-coding regions across diverse species. This has led many researchers to look to the cis-regulatory elements of genes as the fundamental influence behind evolving gene function and subsequent species diversification. Historically, since these elements are often located in vast intergenic and intronic regions of the genome, their identification has been recalcitrant. Now, with the deluge of whole-genome data from representatives of numerous eukaryotic lineages, various approaches have enabled us to begin to recognize features that characterize regulatory regions of the genome. Here we endeavour to collate these approaches in order to give an overview of the complexities involved in extrapolating regulatory signatures. The resource provided by the escalating richness of whole-genome datasets enables more sophisticated modelling of these regulatory signatures yet at the same time introduces increasing potential for noise. While we are only at the advent of making these discoveries, the next decade promises to be a very exciting and rewarding time for genome researchers.
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Affiliation(s)
- Debbie K Goode
- Cambridge Institute for Medical Research, Deptartment of Haematology, Addenbrooke's Hospital, Hills Road, Cambridge, UK
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18
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Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res 2012; 22:2356-67. [PMID: 22722344 PMCID: PMC3514665 DOI: 10.1101/gr.139725.112] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tightly physically linked in diverse lineages across over 600 million years of evolution. Integrating sequence conservation, gene expression data, gene function, epigenetic marks, and other genomic features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos, which provided further evidence of putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results suggest that ancient genomic functional associations are far more common than previously thought—involving ∼12% of the ancestral bilaterian genome—and that cis-regulatory constraints are crucial in determining metazoan genome architecture.
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Affiliation(s)
- Manuel Irimia
- Department of Biology, Stanford University, Stanford, California 94305, USA
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19
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Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues. Nat Commun 2012; 3:848. [DOI: 10.1038/ncomms1851] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 04/18/2012] [Indexed: 12/24/2022] Open
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20
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Beaster-Jones L. Cis-regulation and conserved non-coding elements in amphioxus. Brief Funct Genomics 2012; 11:118-30. [DOI: 10.1093/bfgp/els006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Chatterjee S, Lufkin T. Regulatory genomics: Insights from the zebrafish. CURRENT TOPICS IN GENETICS 2012; 5:1-10. [PMID: 23440612 PMCID: PMC3577074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The sequencing of many vertebrate species over the last decade has opened up the possibility of using comparative genomics as a powerful tool to elucidate regulatory elements in the vertebrate genome. The zebrafish has played a pivotal role in this process. Its genome has been used in large-scale genome comparisons to locate vertebrate specific regulatory elements and also it has been an excellent model system to test out the predicted DNA sequences for their ability to drive reporter gene expression in vivo. In spite of all the successes there have still been some issues in using the zebrafish as a model system for these kinds of assays. This review will shed some light on the successes and failures of the zebrafish in pushing forward regulatory genomics.
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Affiliation(s)
- Sumantra Chatterjee
- Stem Cell and Developmental Biology, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
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22
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Chatterjee S, Bourque G, Lufkin T. Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes. BMC DEVELOPMENTAL BIOLOGY 2011; 11:63. [PMID: 22011226 PMCID: PMC3210094 DOI: 10.1186/1471-213x-11-63] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/20/2011] [Indexed: 01/29/2023]
Abstract
BACKGROUND Identifying DNA sequences (enhancers) that direct the precise spatial and temporal expression of developmental control genes remains a significant challenge in the annotation of vertebrate genomes. Locating these sequences, which in many cases lie at a great distance from the transcription start site, has been a major obstacle in deciphering gene regulation. Coupling of comparative genomics with functional validation to locate such regulatory elements has been a successful method in locating many such regulatory elements. But most of these studies looked either at a single gene only or the whole genome without focusing on any particular process. The pressing need is to integrate the tools of comparative genomics with knowledge of developmental biology to validate enhancers for developmental transcription factors in greater detail RESULTS Our results show that near four different genes (nkx3.2, pax9, otx1b and foxa2) in zebrafish, only 20-30% of highly conserved DNA sequences can act as developmental enhancers irrespective of the tissue the gene expresses in. We find that some genes also have multiple conserved enhancers expressing in the same tissue at the same or different time points in development. We also located non-conserved enhancers for two of the genes (pax9 and otx1b). Our modified Bacterial artificial chromosome (BACs) studies for these 4 genes revealed that many of these enhancers work in a synergistic fashion, which cannot be captured by individual DNA constructs and are not conserved at the sequence level. Our detailed biochemical and transgenic analysis revealed Foxa1 binds to the otx1b non-conserved enhancer to direct its activity in forebrain and otic vesicle of zebrafish at 24 hpf. CONCLUSION Our results clearly indicate that high level of functional conservation of genes is not necessarily associated with sequence conservation of its regulatory elements. Moreover certain non conserved DNA elements might have role in gene regulation. The need is to bring together multiple approaches to bear upon individual genes to decipher all its regulatory elements.
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Affiliation(s)
- Sumantra Chatterjee
- Stem Cell and Developmental Biology, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
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23
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Royo JL, Hidalgo C, Roncero Y, Seda MA, Akalin A, Lenhard B, Casares F, Gómez-Skarmeta JL. Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PLoS One 2011; 6:e24824. [PMID: 21935474 PMCID: PMC3172297 DOI: 10.1371/journal.pone.0024824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/18/2011] [Indexed: 12/28/2022] Open
Abstract
Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions.
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Affiliation(s)
- José Luis Royo
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Carmen Hidalgo
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Yolanda Roncero
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - María Angeles Seda
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Altuna Akalin
- Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
| | - Boris Lenhard
- Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
- Sars Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Fernando Casares
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
- * E-mail:
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24
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Functional analysis of conserved non-coding regions around the short stature hox gene (shox) in whole zebrafish embryos. PLoS One 2011; 6:e21498. [PMID: 21731768 PMCID: PMC3123344 DOI: 10.1371/journal.pone.0021498] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/30/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mutations in the SHOX gene are responsible for Leri-Weill Dyschondrosteosis, a disorder characterised by mesomelic limb shortening. Recent investigations into regulatory elements surrounding SHOX have shown that deletions of conserved non-coding elements (CNEs) downstream of the SHOX gene produce a phenotype indistinguishable from Leri-Weill Dyschondrosteosis. As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene. METHODOLOGY/PRINCIPAL FINDINGS Expression of the shox gene in zebrafish was identified using in situ hybridization, with embryos showing expression in the blood, putative heart, hatching gland, brain pharyngeal arch, olfactory epithelium, and fin bud apical ectodermal ridge. By identifying sequences showing 65% identity over at least 40 nucleotides between Fugu, human, dog and opossum we uncovered 35 CNEs around the shox gene. These CNEs were compared with CNEs previously discovered by Sabherwal et al., resulting in the identification of smaller more deeply conserved sub-sequence. Sabherwal et al.'s CNEs were assayed for regulatory function in whole zebrafish embryos resulting in the identification of additional tissues under the regulatory control of these CNEs. CONCLUSION/SIGNIFICANCE Our results using whole zebrafish embryos have provided a more comprehensive picture of the expression pattern of the shox gene, and a better understanding of its regulation via deeply conserved noncoding elements. In particular, we identify additional tissues under the regulatory control of previously identified SHOX CNEs. We also demonstrate the importance of these CNEs in evolution by identifying duplicated shox CNEs and more deeply conserved sub-sequences within already identified CNEs.
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Chatterjee S, Lufkin T. Fishing for function: zebrafish BAC transgenics for functional genomics. MOLECULAR BIOSYSTEMS 2011; 7:2345-51. [PMID: 21647532 DOI: 10.1039/c1mb05116d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transgenics using bacterial artificial chromosomes (BACs) offers a great opportunity to look at gene regulation in a developing embryo. The modified BAC containing a reporter inserted just before the translational start site of the gene of interest allows for the visualization of spatio-temporal gene expression. Though this method has been used in the mouse model extensively, its utility in zebrafish studies is relatively new. This review aims to look at the utility of making BAC transgenics in zebrafish and its applications in functional genomics. We look at the various methods to modify the BAC, some limitations and what the future holds.
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Affiliation(s)
- Sumantra Chatterjee
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore
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