1
|
Wang J, Chen G, Yu X, Zhou X, Zhang Y, Wu Y, Tong J. Transcriptome analyses reveal differentially expressed genes associated with development of the palatal organ in bighead carp (Hypophthalmichthys nobilis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY PART D: GENOMICS AND PROTEOMICS 2023; 46:101072. [PMID: 36990038 DOI: 10.1016/j.cbd.2023.101072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/12/2023] [Accepted: 03/11/2023] [Indexed: 03/28/2023]
Abstract
The palatal organ is a filter-feeding related organ and occupies a considerable proportion of the head of bighead carp (Hypophthalmichthys nobilis), a large cyprinid fish intensive aquaculture in Asia. In this study, we performed RNA-seq of the palatal organ during growth periods of two (M2), six (M6) and 15 (M15) months of age after hatching. The numbers of differentially expressed genes (DEGs) were 1384, 481 and 1837 for M2 VS M6, M6 VS M15 and M2 VS M15 respectively. The following signaling pathways of energy metabolism and cytoskeleton function were enriched, including ECM-receptor interaction, Cardiac muscle contraction, Steroid biosynthesis and PPAR signaling pathway. Several members of collagen family (col1a1, col2a1, col6a2, col6a3, col9a2), Laminin gamma 1 (lamc1), integrin alpha 1 (itga1), Fatty acid binding protein 2 (fads2) and lipoprotein lipase (lpl), and Protein tyrosine kinase 7 (Ptk7) are candidate genes for growth and development of basic tissues of the palatal organ. Furthermore, taste-related genes such as fgfrl1, fgf8a, fsta and notch1a were also identified, which may be involved in the development of taste buds of the palatal organ. The transcriptome data obtained in this study provide insights into the understanding functions and development mechanisms of palatal organ, and potential candidate genes that may be related to the genetic modulation of head size of bighead carp.
Collapse
Affiliation(s)
- Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geng Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaoyu Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yanhong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| |
Collapse
|
2
|
Wang W, Wang D, Li X, Ai W, Wang X, Wang H. Toxicity mechanisms regulating bone differentiation and development defects following abnormal expressions of miR-30c targeted by triclosan in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158040. [PMID: 35973548 DOI: 10.1016/j.scitotenv.2022.158040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/06/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
As a ubiquitous environmental estrogen-disrupting chemical, triclosan (TCS) can induce severe osteotoxicity; however, the underlying molecular mechanisms remain uncertain. Herein, we evaluated the toxic effects of TCS on the development of cartilage and osteogenesis in 5-dpf zebrafish. Under TCS exposure from 62.5 to 250 μg/L, several osteodevelopmental malformations were observed, such as defect of craniofacial cartilage, pharyngeal arch cartilage dysplasia, and impairments on skeletal mineralization. Further, the morphology of mature chondrocytes became swollen and deformed, their number decreased, nucleus displacement occurred, and most immature chondrocytes were crowded at both ends of ceratobranchial. SEM observation of larval caudal fin revealed that, the layer of collagen fibers and the mineralized calcium nodules were significantly decreased, with the collagen fibers becoming shorter upon TCS exposure. The activity of bone-derived alkaline phosphatase significantly reduced, and marker functional genes related to cartilage and osteoblast development were abnormally expressed. RNA-seq and bioinformatics analysis indicated, that changes in marker genes intimately related to the negative regulation of miR-30c-5p overexpression targeted by TCS, and the up-regulation of miR-30c induced bone developmental defects by inhibiting the bone morphogenetic protein (BMP) signaling pathway. These findings were confirmed by artificially intervening the expression of miR-30c and using BMP pathway agonists in vivo. In sum, TCS induced osteototoxicity by targeting miR-30c up-regulation and interfering in the BMP signaling pathway. These findings enhance mechanistic understanding of TCS-induced spontaneous bone disorders and bone metastatic diseases. Further research is necessary to monitor chronic TCS-exposure levels in surrounding environments and develop relevant safety precautions based on TCS environmental risk.
Collapse
Affiliation(s)
- Weiwei Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Danting Wang
- Department of Transfusion, The West China Hospital, Sichuan University, 37 Guoxue Lane, Wuhou District, Chengdu 610041, China
| | - Xin Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Weiming Ai
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xuedong Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Huili Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| |
Collapse
|
3
|
Parker HJ, Bronner ME, Krumlauf R. The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates. Bioessays 2016; 38:526-38. [PMID: 27027928 DOI: 10.1002/bies.201600010] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression.
Collapse
Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, USA
| |
Collapse
|
4
|
An autonomous CEBPA enhancer specific for myeloid-lineage priming and neutrophilic differentiation. Blood 2016; 127:2991-3003. [PMID: 26966090 DOI: 10.1182/blood-2016-01-695759] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/02/2016] [Indexed: 12/24/2022] Open
Abstract
Neutrophilic differentiation is dependent on CCAAT enhancer-binding protein α (C/EBPα), a transcription factor expressed in multiple organs including the bone marrow. Using functional genomic technologies in combination with clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 genome editing and in vivo mouse modeling, we show that CEBPA is located in a 170-kb topological-associated domain that contains 14 potential enhancers. Of these, 1 enhancer located +42 kb from CEBPA is active and engages with the CEBPA promoter in myeloid cells only. Germ line deletion of the homologous enhancer in mice in vivo reduces Cebpa levels exclusively in hematopoietic stem cells (HSCs) and myeloid-primed progenitor cells leading to severe defects in the granulocytic lineage, without affecting any other Cebpa-expressing organ studied. The enhancer-deleted progenitor cells lose their myeloid transcription program and are blocked in differentiation. Deletion of the enhancer also causes loss of HSC maintenance. We conclude that a single +42-kb enhancer is essential for CEBPA expression in myeloid cells only.
Collapse
|
5
|
Hox Function Is Required for the Development and Maintenance of the Drosophila Feeding Motor Unit. Cell Rep 2016; 14:850-860. [DOI: 10.1016/j.celrep.2015.12.077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/18/2015] [Accepted: 12/15/2015] [Indexed: 11/24/2022] Open
|
6
|
Shu LP, Zhou ZW, Zhou T, Deng M, Dong M, Chen Y, Fu YF, Jin Y, Zhou SF, He ZX. Ectopic expression of Hoxb4a in hemangioblasts promotes hematopoietic development in early embryogenesis of zebrafish. Clin Exp Pharmacol Physiol 2016; 42:1275-86. [PMID: 26743678 DOI: 10.1111/1440-1681.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/15/2015] [Accepted: 08/24/2015] [Indexed: 12/12/2022]
Abstract
Hemangioblast, including primitive hematopoietic progenitor cells, play an important role in hematopoietic development, however, the underlying mechanism for the propagation of hematopoietic progenitor cells remains elusive. A variety of regulatory molecules activated in early embryonic development play a critical role in the maintenance of function of hematopoietic progenitor cells. Homeobox transcription factors are an important class of early embryonic developmental regulators determining hematopoietic development. However, the effect of homeobox protein Hox-B4 (HOXB4) ectopic expression on the development of hemangioblasts has not been fully addressed. This study aimed to investigate the role of Hoxb4a, an ortholog gene of HOXB4 in zebrafish, in the hematopoietic development in zebrafish. A transgenic zebrafish line was established with Cre-loxP system that stably overexpressed enhanced green fluorescent protein (EGFP)-tagged Hoxb4a protein under the control of hemangioblast-specific lmo2 promoter. Overexpression of Hoxb4a in the development of hemangioblasts resulted in a considerable increase in the number of stem cell leukemia (scl) and lmo2-positive primitive hematopoietic progenitor cells occurring in the posterior intermediate cell mass (ICM). Interestingly, Hoxb4a overexpression also disrupted the development of myelomonocytes in the anterior yolk sac and the posterior ICM, without affecting erythropoiesis in the posterior ICM. Taken together, these results indicate that Hoxb4a favours the development of hematopoietic progenitor cells originated from hemangioblasts in vivo.
Collapse
Affiliation(s)
- Li-Ping Shu
- Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Centre & Sino-US Joint Laboratory for Medical Sciences, Laboratory Animal Centre, Guiyang Medical University, Guiyang, China
| | - Zhi-Wei Zhou
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ting Zhou
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Min Deng
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mei Dong
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yi Chen
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yan-Fang Fu
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yi Jin
- Laboratory of Development and Diseases and Key Laboratory of Stem Cell Biology and State Key Laboratory for Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine and Shanghai Institute of Hematology (SIH), Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shu-Feng Zhou
- Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Centre & Sino-US Joint Laboratory for Medical Sciences, Laboratory Animal Centre, Guiyang Medical University, Guiyang, China.,Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Zhi-Xu He
- Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Centre & Sino-US Joint Laboratory for Medical Sciences, Laboratory Animal Centre, Guiyang Medical University, Guiyang, China
| |
Collapse
|
7
|
Ishibashi M, Mechaly AS, Becker TS, Rinkwitz S. Using zebrafish transgenesis to test human genomic sequences for specific enhancer activity. Methods 2013; 62:216-25. [PMID: 23542551 DOI: 10.1016/j.ymeth.2013.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 03/15/2013] [Accepted: 03/19/2013] [Indexed: 01/09/2023] Open
Abstract
We detail an approach for the identification of human tissue-specific transcriptional enhancers involving three steps: delineation of search space around a locus or target gene, in silico identification and size definition of putative candidate sequences, and testing through several independent genomic insertions in a transgenic zebrafish reporter assay. Candidate sequences are defined through evolutionary conservation, transcription factor binding and chromatin marks (e.g. ENCODE data) and are amplified from genomic DNA, cloned into basal promoter:fluorescent protein reporter vectors based on the Tol2 transposon system and are microinjected into fertilized zebrafish eggs. After raising injected founders to sexual maturity, fluorescent screening identifies positive founder fish whose offspring undergo a detailed expression analysis to determine tissue specificity and reproducibility of specific enhancers.
Collapse
Affiliation(s)
- Minaka Ishibashi
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, 100 Mallet Street, Camperdown 2050, Australia
| | | | | | | |
Collapse
|
8
|
Angotzi AR, Mungpakdee S, Stefansson S, Male R, Chourrout D. Involvement of Prop1 homeobox gene in the early development of fish pituitary gland. Gen Comp Endocrinol 2011; 171:332-40. [PMID: 21362424 DOI: 10.1016/j.ygcen.2011.02.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 11/22/2022]
Abstract
When mutated in mammals, paired-like homeobox Prop1 gene produces highly variable pituitary phenotypes with impaired regulation of Pit1 and eventually defective synthesis of Pit1-regulated pituitary hormones. Here we have identified fish prop1 orthologs, confirmed their pituitary-specific expression, and blocked the splicing of zebrafish prop1 transcripts using morpholino oligonucleotides. Very early steps of the gland formation seemed unaffected based on morphology and expression of early placodal marker pitx. Prop1 knock-down reduced the expression of pit1, prl (prolactin) and gh (growth hormone), as expected if the function of Prop1 is conserved throughout vertebrates. Less expectedly, lim3 was down regulated. This gene is expressed from early stages of vertebrate pituitary development but is not known to be Prop1-dependent. In situ hybridizations on prop1 morphants using probes for the pan pituitary gene pitx3 and for the hormone gene markers prl, gh and tshβ, revealed abnormal shape, growth and cellular organization of the developed adenohypophysis. Strikingly, the effects of prop1 knock-down on adenohypophysis morphology and gene expression were gradually reversed during late development, despite persistent splice-blocking of transcripts. Therefore, prop1 function appears to be conserved between mammals and fish, at least for the mediation of hormonal cell type differentiation via pit1, but the existence of other fish-specific pathways downstream of prop1 are suggested by our observations.
Collapse
Affiliation(s)
- Anna Rita Angotzi
- Sars, International Centre for Marine Molecular Biology, University of Bergen, High Technology Centre, Thormoehlensgt 55, N-5008 Bergen, Norway
| | | | | | | | | |
Collapse
|
9
|
Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes. Dev Biol 2010; 340:269-82. [PMID: 20144609 DOI: 10.1016/j.ydbio.2010.01.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 01/17/2010] [Accepted: 01/30/2010] [Indexed: 01/30/2023]
Abstract
Hox genes are key regulators of anterior-posterior axis patterning and have a major role in hindbrain development. The zebrafish Hox4 paralogs have strong overlapping activities in hindbrain rhombomeres 7 and 8, in the spinal cord and in the pharyngeal arches. With the aim to predict enhancers that act on the hoxa4a, hoxb4a, hoxc4a and hoxd4a genes, we used sequence conservation around the Hox4 genes to analyze all fish:human conserved non-coding sequences by reporter assays in stable zebrafish transgenesis. Thirty-four elements were functionally tested in GFP reporter gene constructs and more than 100 F1 lines were analyzed to establish a correlation between sequence conservation and cis-regulatory function, constituting a catalog of Hox4 CNEs. Sixteen tissue-specific enhancers could be identified. Multiple alignments of the CNEs revealed paralogous cis-regulatory sequences, however, the CNE sequence similarities were found not to correlate with tissue specificity. To identify ancestral enhancers that direct Hox4 gene activity, genome sequence alignments of mammals, teleosts, horn shark and the cephalochordate amphioxus, which is the most basal extant chordate possessing a single prototypical Hox cluster, were performed. Three elements were identified and two of them exhibited regulatory activity in transgenic zebrafish, however revealing no specificity. Our data show that the approach to identify cis-regulatory sequences by genome sequence alignments and subsequent testing in zebrafish transgenesis can be used to define enhancers within the Hox clusters and that these have significantly diverged in their function during evolution.
Collapse
|
10
|
Jiménez-Delgado S, Pascual-Anaya J, Garcia-Fernàndez J. Implications of duplicated cis-regulatory elements in the evolution of metazoans: the DDI model or how simplicity begets novelty. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:266-75. [PMID: 19651705 DOI: 10.1093/bfgp/elp029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The discovery that most regulatory genes were conserved among animals from distant phyla challenged the ideas that gene duplication and divergence of homologous coding sequences were the basis for major morphological changes in metazoan evolution. In recent years, however, the interest for the roles, conservation and changes of non-coding sequences grew-up in parallel with genome sequencing projects. Presently, many independent studies are highlighting the importance that subtle changes in cis-regulatory regions had in the evolution of morphology trough the Animal Kingdom. Here we will show and discuss some of these studies, and underscore the future of cis-Evo-Devo research. Nevertheless, we would also explore how gene duplication, which includes duplication of regulatory regions, may have been critical for spatial or temporal co-option of new regulatory networks, causing the deployment of new transcriptome scenarios, and how these induced morphological changes were critical for the evolution of new forms. Forty years after Susumu Ohno famous sentence 'natural selection merely modifies, while redundancy creates', we suggest the alternative: 'natural selection modifies, while redundancy of cis-regulatory elements innovates', and propose the Duplication-Degeneration-Innovation model to explain the increased evolvability of duplicated cis-regulatory regions. Paradoxically, making regulation simpler by subfunctionalization paved the path for future complexity or, in other words, 'to make it simple to make it complex'.
Collapse
Affiliation(s)
- Senda Jiménez-Delgado
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
| | | | | |
Collapse
|
11
|
Ma LH, Punnamoottil B, Rinkwitz S, Baker R. Mosaic hoxb4a neuronal pleiotropism in zebrafish caudal hindbrain. PLoS One 2009; 4:e5944. [PMID: 19536294 PMCID: PMC2693931 DOI: 10.1371/journal.pone.0005944] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 05/12/2009] [Indexed: 12/26/2022] Open
Abstract
To better understand how individual genes and experience influence behavior, the role of a single homeotic unit, hoxb4a, was comprehensively analyzed in vivo by clonal and retrograde fluorescent labeling of caudal hindbrain neurons in a zebrafish enhancer-trap YFP line. A quantitative spatiotemporal neuronal atlas showed hoxb4a activity to be highly variable and mosaic in rhombomere 7–8 reticular, motoneuronal and precerebellar nuclei with expression decreasing differentially in all subgroups through juvenile stages. The extensive Hox mosaicism and widespread pleiotropism demonstrate that the same transcriptional protein plays a role in the development of circuits that drive behaviors from autonomic through motor function including cerebellar regulation. We propose that the continuous presence of hoxb4a positive neurons may provide a developmental plasticity for behavior-specific circuits to accommodate experience- and growth-related changes. Hence, the ubiquitous hoxb4a pleitropism and modularity likely offer an adaptable transcriptional element for circuit modification during both growth and evolution.
Collapse
Affiliation(s)
- Leung-Hang Ma
- Department of Physiology and Neuroscience, New York University Medical Center, New York, New York, United States of America
| | - Beena Punnamoottil
- Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - Silke Rinkwitz
- Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - Robert Baker
- Department of Physiology and Neuroscience, New York University Medical Center, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
12
|
Regulation of mir-196b by MLL and its overexpression by MLL fusions contributes to immortalization. Blood 2009; 113:3314-22. [PMID: 19188669 DOI: 10.1182/blood-2008-04-154310] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene produce chimeric proteins that cause abnormal expression of a subset of HOX genes and leukemia development. Here, we show that MLL normally regulates expression of mir-196b, a hematopoietic microRNA located within the HoxA cluster, in a pattern similar to that of the surrounding 5' Hox genes, Hoxa9 and Hoxa10, during embryonic stem (ES) cell differentiation. Within the hematopoietic lineage, mir-196b is most abundant in short-term hematopoietic stem cells and is down-regulated in more differentiated hematopoietic cells. Leukemogenic MLL fusion proteins cause overexpression of mir-196b, while treatment of MLL-AF9 transformed bone marrow cells with mir-196-specific antagomir abrogates their replating potential in methylcellulose. This demonstrates that mir-196b function is necessary for MLL fusion-mediated immortalization. Furthermore, overexpression of mir-196b was found specifically in patients with MLL associated leukemias as determined from analysis of 55 primary leukemia samples. Overexpression of mir-196b in bone marrow progenitor cells leads to increased proliferative capacity and survival, as well as a partial block in differentiation. Our results suggest a mechanism whereby increased expression of mir-196b by MLL fusion proteins significantly contributes to leukemia development.
Collapse
|
13
|
Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, Becker TS. Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol 2008; 327:526-40. [PMID: 19073165 DOI: 10.1016/j.ydbio.2008.10.044] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 10/02/2008] [Accepted: 10/28/2008] [Indexed: 01/01/2023]
Abstract
Pan-vertebrate developmental cis-regulatory elements are discernible as highly conserved noncoding elements (HCNEs) and are often dispersed over large areas around the pleiotropic genes whose expression they control. On the loci of two developmental transcription factor genes, SOX3 and PAX6, we demonstrate that HCNEs conserved between human and zebrafish can be systematically and reliably tested for their regulatory function in multiple stable transgenes in zebrafish, and their genomic reach estimated with confidence using synteny conservation and HCNE density along these loci. HCNEs of both human and zebrafish function as specific developmental enhancers in zebrafish. We show that human HCNEs result in expression patterns in zebrafish equivalent to those in mouse, establishing zebrafish as a suitable model for large-scale testing of human developmental enhancers. Orthologous human and zebrafish enhancers underwent functional evolution within their sequence and often directed related but non-identical expression patterns. Despite an evolutionary distance of 450 million years, one pax6 HCNE drove expression in identical areas when comparing zebrafish vs. human HCNEs. HCNEs from the same area often drive overlapping patterns, suggesting that multiple regulatory inputs are required to achieve robust and precise complex expression patterns exhibited by developmental genes.
Collapse
Affiliation(s)
- Pavla Navratilova
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | | | | | | | | | | |
Collapse
|
14
|
Yang W, Ng P, Zhao M, Wong TKF, Yiu SM, Lau YL. Promoter-sharing by different genes in human genome--CPNE1 and RBM12 gene pair as an example. BMC Genomics 2008; 9:456. [PMID: 18831769 PMCID: PMC2568002 DOI: 10.1186/1471-2164-9-456] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 10/03/2008] [Indexed: 11/27/2022] Open
Abstract
Background Regulation of gene expression plays important role in cellular functions. Co-regulation of different genes may indicate functional connection or even physical interaction between gene products. Thus analysis on genomic structures that may affect gene expression regulation could shed light on the functions of genes. Results In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1) and RNA binding motif protein 12 (RBM12), share the most 5' exons and therefore the promoter region in human. Further analysis identified many gene pairs in human genome that share the same promoters and 5' exons but have totally different coding sequences. Analysis of genomic and expressed sequences, either cDNAs or expressed sequence tags (ESTs) for CPNE1 and RBM12, confirmed the conservation of this phenomenon during evolutionary courses. The co-expression of the two genes initiated from the same promoter is confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) in different tissues in both human and mouse. High degrees of sequence conservation among multiple species in the 5'UTR region common to CPNE1 and RBM12 were also identified. Conclusion Promoter and 5'UTR sharing between CPNE1 and RBM12 is observed in human, mouse and zebrafish. Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes. More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.
Collapse
Affiliation(s)
- Wanling Yang
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, PR China.
| | | | | | | | | | | |
Collapse
|
15
|
Pashos EE, Kague E, Fisher S. Evaluation of cis-regulatory function in zebrafish. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:465-73. [PMID: 18820318 DOI: 10.1093/bfgp/eln045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
As increasing numbers of vertebrate genomes are sequenced, comparative genomics offers tremendous promise to unveil mechanisms of transcriptional gene regulation on a large scale. However, the challenge of analysing immense amounts of sequence data and relating primary sequence to function is daunting. Several teleost species occupy crucial niches in the world of comparative genomics, as experimental model organisms of wide utility and living roadmaps of molecular evolution. Extant species have evolved after a teleost-specific genome duplication, and offer the opportunity to examine the evolution of thousands of duplicate gene pairs. Transgenesis in zebrafish is being increasingly employed to functionally examine non-coding sequences, from fish and mammals. Here, we discuss current approaches to the study of gene regulation in teleosts, and the promise of future research.
Collapse
|
16
|
Punnamoottil B, Kikuta H, Pezeron G, Erceg J, Becker TS, Rinkwitz S. Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs. Dev Dyn 2008; 237:2195-208. [DOI: 10.1002/dvdy.21618] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
17
|
Hadzhiev Y, Lang M, Ertzer R, Meyer A, Strähle U, Müller F. Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction. Genome Biol 2008; 8:R106. [PMID: 17559649 PMCID: PMC2394741 DOI: 10.1186/gb-2007-8-6-r106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 05/09/2007] [Accepted: 06/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cis-regulatory modules of developmental genes are targets of evolutionary changes that underlie the morphologic diversity of animals. Little is known about the 'grammar' of interactions between transcription factors and cis-regulatory modules and therefore about the molecular mechanisms that underlie changes in these modules, particularly after gene and genome duplications. We investigated the ar-C midline enhancer of sonic hedgehog (shh) orthologs and paralogs from distantly related vertebrate lineages, from fish to human, including the basal vertebrate Latimeria menadoensis. RESULTS We demonstrate that the sonic hedgehog a (shha) paralogs sonic hedgehog b (tiggy winkle hedgehog; shhb) genes of fishes have a modified ar-C enhancer, which specifies a diverged function at the embryonic midline. We have identified several conserved motifs that are indicative of putative transcription factor binding sites by local alignment of ar-C enhancers of numerous vertebrate sequences. To trace the evolutionary changes among paralog enhancers, phylogenomic reconstruction was carried out and lineage-specific motif changes were identified. The relation between motif composition and observed developmental differences was evaluated through transgenic functional analyses. Altering and exchanging motifs between paralog enhancers resulted in reversal of enhancer specificity in the floor plate and notochord. A model reconstructing enhancer divergence during vertebrate evolution was developed. CONCLUSION Our model suggests that the identified motifs of the ar-C enhancer function as binary switches that are responsible for specific activity between midline tissues, and that these motifs are adjusted during functional diversification of paralogs. The unraveled motif changes can also account for the complex interpretation of activator and repressor input signals within a single enhancer.
Collapse
Affiliation(s)
- Yavor Hadzhiev
- Laboratory of Developmental Transcription Regulation, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
- Laboratory of Developmental Neurobiology and Genetics, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| | - Michael Lang
- Department of Zoology and Evolution biology, Faculty of Biology, University of Konstanz, Konstanz D-78457, Germany
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
| | - Raymond Ertzer
- Laboratory of Developmental Neurobiology and Genetics, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| | - Axel Meyer
- Department of Zoology and Evolution biology, Faculty of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Uwe Strähle
- Laboratory of Developmental Neurobiology and Genetics, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| | - Ferenc Müller
- Laboratory of Developmental Transcription Regulation, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| |
Collapse
|
18
|
Woltering JM, Durston AJ. MiR-10 represses HoxB1a and HoxB3a in zebrafish. PLoS One 2008; 3:e1396. [PMID: 18167555 PMCID: PMC2148072 DOI: 10.1371/journal.pone.0001396] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Accepted: 12/10/2007] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The Hox genes are involved in patterning the anterior-posterior axis. In addition to the protein coding Hox genes, the miR-10, miR-196 and miR-615 families of microRNA genes are conserved within the vertebrate Hox clusters. The members of the miR-10 family are located at positions associated with Hox-4 paralogues. No function is yet known for this microRNA family but the genomic positions of its members suggest a role in anterior-posterior patterning. METHODOLOGY/PRINCIPAL FINDINGS Using sensor constructs, overexpression and morpholino knockdown, we show in Zebrafish that miR-10 targets HoxB1a and HoxB3a and synergizes with HoxB4 in the repression of these target genes. Overexpression of miR-10 also induces specific phenotypes related to the loss of function of these targets. HoxB1a and HoxB3a have a dominant hindbrain expression domain anterior to that of miR-10 but overlap in a weaker expression domain in the spinal cord. In this latter domain, miR-10 knockdown results in upregulation of the target genes. In the case of a HoxB3a splice variant that includes miR-10c within its primary transcript, we show that the microRNA acts in an autoregulatory fashion. CONCLUSIONS/SIGNIFICANCE We find that miR-10 acts to repress HoxB1a and HoxB3a within the spinal cord and show that this repression works cooperatively with HoxB4. As with the previously described interactions between miR-196 and HoxA7 and Hox-8 paralogues, the target genes are located in close proximity to the microRNA. We present a model in which we postulate a link between the clustering of Hox genes and post-transcriptional gene regulation. We speculate that the high density of transcription units and enhancers within the Hox clusters places constraints on the precision of the transcriptional control that can be achieved within these clusters and requires the involvement of post-transcriptional gene silencing to define functional domains of genes appropriately.
Collapse
|
19
|
Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol 2007; 8 Suppl 1:S4. [PMID: 18047696 PMCID: PMC2106839 DOI: 10.1186/gb-2007-8-s1-s4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around developmental regulatory genes in which an insertion results in the same global expression pattern, irrespective of exact position. These areas coincide with vertebrate chromosomal segments containing identical gene order; a phenomenon known as conserved synteny and thought to be a vestige of evolution. Genomic comparative studies have found large numbers of highly conserved noncoding elements (HCNEs) spanning these and other loci. HCNEs are thought to act as transcriptional enhancers based on the finding that many of those that have been tested direct tissue specific expression in transient or transgenic assays. Although gene order in hox and other gene clusters has long been known to be conserved because of shared regulatory sequences or overlapping transcriptional units, the chromosomal areas found through insertional hotspots contain only one or a few developmental regulatory genes as well as phylogenetically unrelated genes. We have termed these regions genomic regulatory blocks (GRBs), and show that they underlie the phenomenon of conserved synteny through all sequenced vertebrate genomes. After teleost whole genome duplication, a subset of GRBs were retained in two copies, underwent degenerative changes compared with tetrapod loci that exist as single copy, and that therefore can be viewed as representing the ancestral form. We discuss these findings in light of evolution of vertebrate chromosomal architecture and the identification of human disease mutations.
Collapse
Affiliation(s)
- Hiroshi Kikuta
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormoehlensgate, 5008 Bergen, Norway
| | | | | | | | | |
Collapse
|
20
|
Hoegg S, Boore JL, Kuehl JV, Meyer A. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. BMC Genomics 2007; 8:317. [PMID: 17845724 PMCID: PMC2080641 DOI: 10.1186/1471-2164-8-317] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 09/10/2007] [Indexed: 11/10/2022] Open
Abstract
Background Teleost fish have seven paralogous clusters of Hox genes stemming from two complete genome duplications early in vertebrate evolution, and an additional genome duplication during the evolution of ray-finned fish, followed by the secondary loss of one cluster. Gene duplications on the one hand, and the evolution of regulatory sequences on the other, are thought to be among the most important mechanisms for the evolution of new gene functions. Cichlid fish, the largest family of vertebrates with about 2500 species, are famous examples of speciation and morphological diversity. Since this diversity could be based on regulatory changes, we chose to study the coding as well as putative regulatory regions of their Hox clusters within a comparative genomic framework. Results We sequenced and characterized all seven Hox clusters of Astatotilapia burtoni, a haplochromine cichlid fish. Comparative analyses with data from other teleost fish such as zebrafish, two species of pufferfish, stickleback and medaka were performed. We traced losses of genes and microRNAs of Hox clusters, the medaka lineage seems to have lost more microRNAs than the other fish lineages. We found that each teleost genome studied so far has a unique set of Hox genes. The hoxb7a gene was lost independently several times during teleost evolution, the most recent event being within the radiation of East African cichlid fish. The conserved non-coding sequences (CNS) encompass a surprisingly large part of the clusters, especially in the HoxAa, HoxCa, and HoxDa clusters. Across all clusters, we observe a trend towards an increased content of CNS towards the anterior end. Conclusion The gene content of Hox clusters in teleost fishes is more variable than expected, with each species studied so far having a different set. Although the highest loss rate of Hox genes occurred immediately after whole genome duplications, our analyses showed that gene loss continued and is still ongoing in all teleost lineages. Along with the gene content, the CNS content also varies across clusters. The excess of CNS at the anterior end of clusters could imply a stronger conservation of anterior expression patters than those towards more posterior areas of the embryo.
Collapse
Affiliation(s)
- Simone Hoegg
- Lehrstuhl für Evolutionsbiologie und Zoologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jeffrey L Boore
- Program in Evolutionary Genomics, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, and University of California, Berkeley, California 94720, USA
- SymBio Corporation, 1455 Adams Drive, Menlo Park, CA 94025, and University of California, Berkeley, California 94720, USA
| | - Jennifer V Kuehl
- Program in Evolutionary Genomics, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, and University of California, Berkeley, California 94720, USA
| | - Axel Meyer
- Lehrstuhl für Evolutionsbiologie und Zoologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| |
Collapse
|