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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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Bentovim L, Harden TT, DePace AH. Transcriptional precision and accuracy in development: from measurements to models and mechanisms. Development 2017; 144:3855-3866. [PMID: 29089359 PMCID: PMC5702068 DOI: 10.1242/dev.146563] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During development, genes are transcribed at specific times, locations and levels. In recent years, the emergence of quantitative tools has significantly advanced our ability to measure transcription with high spatiotemporal resolution in vivo. Here, we highlight recent studies that have used these tools to characterize transcription during development, and discuss the mechanisms that contribute to the precision and accuracy of the timing, location and level of transcription. We attempt to disentangle the discrepancies in how physicists and biologists use the term ‘precision' to facilitate interactions using a common language. We also highlight selected examples in which the coupling of mathematical modeling with experimental approaches has provided important mechanistic insights, and call for a more expansive use of mathematical modeling to exploit the wealth of quantitative data and advance our understanding of animal transcription. Summary: This Review highlights how high-resolution quantitative tools and theoretical models have formed our current view of the mechanisms determining precision and accuracy in the timing, location and level of transcription in the Drosophila embryo.
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Affiliation(s)
- Lital Bentovim
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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Guo Q, Huang Y, Zou F, Liu B, Tian M, Ye W, Guo J, Sun X, Zhou D, Sun Y, Ma L, Shen B, Zhu C. The role of miR-2∼13∼71 cluster in resistance to deltamethrin in Culex pipiens pallens. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 84:15-22. [PMID: 28342977 DOI: 10.1016/j.ibmb.2017.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/24/2017] [Accepted: 03/21/2017] [Indexed: 06/06/2023]
Abstract
Excessive and continuous application of deltamethrin has resulted in the development of deltamethrin resistance among mosquitoes, which becomes a major obstacle for mosquito control. In a previous study, differentially expressed miRNAs between deltamethrin-susceptible (DS) strain and deltamethrin-resistant (DR) strain using illumina sequencing in Culex pipiens pallens were identified. In this study, we applied RNAi and the Centers for Disease Control and Prevention (CDC) bottle bioassay to investigate the relationship between miR-2∼13∼71 cluster (miR-2, miR-13 and miR-71) and deltamethrin resistance. We used quantitative real-time PCR (qRT-PCR) to measure expression levels of miR-2∼13∼71 clusters. MiR-2∼13∼71 cluster was down regulated in adult female mosquitoes from the DR strain and played important roles in deltamethrin resistance through regulating target genes, CYP9J35 and CYP325BG3. Knocking down CYP9J35 and CYP325BG3 resulted in decreased mortality of DR mosquitoes. This study provides the first evidence that miRNA clusters are associated with deltamethrin resistance in mosquitoes. Moreover, we investigated the regulatory networks formed between miR-2∼13∼71 cluster and its target genes, which provide a better understanding of the mechanism involved in deltamethrin resistance.
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Affiliation(s)
- Qin Guo
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Yun Huang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Feifei Zou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China; Microbiology and Immunology Department, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, PR China
| | - Bingqian Liu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China; Department of Clinical Laboratory, Subei People's Hospital of Jiangsu Province, Yangzhou, Jiangsu, 225001, PR China
| | - Mengmeng Tian
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Wenyun Ye
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Juxin Guo
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Xueli Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Dan Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Yan Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Lei Ma
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China.
| | - Changliang Zhu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China.
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de Souza Gomes M, Donoghue MTA, Muniyappa M, Pereira RV, Guerra-Sá R, Spillane C. Computational identification and evolutionary relationships of the microRNA gene cluster miR-71/2 in protostomes. J Mol Evol 2013; 76:353-8. [PMID: 23740160 DOI: 10.1007/s00239-013-9563-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 04/24/2013] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20-24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computational approach is used to investigate the extent of evolutionary conservation of the miR-71/2 cluster in animals, and to identify novel miRNAs in the miRNA cluster miR-71/2. The miR-71/2 cluster, consisting of copies of the miR-71 and miR-2 (including miR-13) families, was found to be Protostome-specific. Although, this cluster is highly conserved across the Protostomia, the miR-2 family is completely absent from the Deuterostomia species, while miR-71 is absent from the Vertebrata and Urochordata. The evolutionary conservation and clustering propensity of the miR-71/2 family across the Protostomes could indicate the common functional roles across the member species of the Protostomia.
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Arnone JT, Robbins-Pianka A, Arace JR, Kass-Gergi S, McAlear MA. The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes. BMC Genomics 2012; 13:546. [PMID: 23051624 PMCID: PMC3500266 DOI: 10.1186/1471-2164-13-546] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 10/03/2012] [Indexed: 11/16/2022] Open
Abstract
Background Coordinated cell growth and development requires that cells regulate the expression of large sets of genes in an appropriate manner, and one of the most complex and metabolically demanding pathways that cells must manage is that of ribosome biogenesis. Ribosome biosynthesis depends upon the activity of hundreds of gene products, and it is subject to extensive regulation in response to changing cellular conditions. We previously described an unusual property of the genes that are involved in ribosome biogenesis in yeast; a significant fraction of the genes exist on the chromosomes as immediately adjacent gene pairs. The incidence of gene pairing can be as high as 24% in some species, and the gene pairs are found in all of the possible tandem, divergent, and convergent orientations. Results We investigated co-regulated gene sets in S. cerevisiae beyond those related to ribosome biogenesis, and found that a number of these regulons, including those involved in DNA metabolism, heat shock, and the response to cellular stressors were also significantly enriched for adjacent gene pairs. We found that as a whole, adjacent gene pairs were more tightly co-regulated than unpaired genes, and that the specific gene pairing relationships that were most widely conserved across divergent fungal lineages were correlated with those genes that exhibited the highest levels of transcription. Finally, we investigated the gene positions of ribosome related genes across a widely divergent set of eukaryotes, and found a significant level of adjacent gene pairing well beyond yeast species. Conclusion While it has long been understood that there are connections between genomic organization and transcriptional regulation, this study reveals that the strategy of organizing genes from related, co-regulated pathways into pairs of immediately adjacent genes is widespread, evolutionarily conserved, and functionally significant.
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Affiliation(s)
- James T Arnone
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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Dupont PY, Guttin A, Issartel JP, Stepien G. Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genes. BMC Genomics 2012; 13:482. [PMID: 22978616 PMCID: PMC3477019 DOI: 10.1186/1471-2164-13-482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/16/2012] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The analysis of gene promoters is essential to understand the mechanisms of transcriptional regulation required under the effects of physiological processes, nutritional intake or pathologies. In higher eukaryotes, transcriptional regulation implies the recruitment of a set of regulatory proteins that bind on combinations of nucleotide motifs. We developed a computational analysis of promoter nucleotide sequences, to identify co-regulated genes by combining several programs that allowed us to build regulatory models and perform a crossed analysis on several databases. This strategy was tested on a set of four human genes encoding isoforms 1 to 4 of the mitochondrial ADP/ATP carrier ANT. Each isoform has a specific tissue expression profile linked to its role in cellular bioenergetics. RESULTS From their promoter sequence and from the phylogenetic evolution of these ANT genes in mammals, we constructed combinations of specific regulatory elements. These models were screened using the full human genome and databases of promoter sequences from human and several other mammalian species. For each of transcriptionally regulated ANT1, 2 and 4 genes, a set of co-regulated genes was identified and their over-expression was verified in microarray databases. CONCLUSIONS Most of the identified genes encode proteins with a cellular function and specificity in agreement with those of the corresponding ANT isoform. Our in silico study shows that the tissue specific gene expression is mainly driven by promoter regulatory sequences located up to about a thousand base pairs upstream the transcription start site. Moreover, this computational strategy on the study of regulatory pathways should provide, along with transcriptomics and metabolomics, data to construct cellular metabolic networks.
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Affiliation(s)
- Pierre-Yves Dupont
- INRA, UMR 1019, Unité de Nutrition Humaine, 63122, St Genès-Champanelle, France
- Université d'Auvergne, Unité de Nutrition Humaine, Clermont Université, BP 10448, 63000, Clermont-Ferrand, France
| | - Audrey Guttin
- Institut des Neurosciences, Equipe Nanomédecine et Cerveau, Inserm U836, 38700, La Tronche, France
- Université Joseph Fourier 1, Grenoble, 38041, France
- Plate-forme Transcriptome et Protéome Cliniques, Institut de Biologie et Pathologie, CHU Grenoble, 38043, Grenoble, France
| | - Jean-Paul Issartel
- Institut des Neurosciences, Equipe Nanomédecine et Cerveau, Inserm U836, 38700, La Tronche, France
- Université Joseph Fourier 1, Grenoble, 38041, France
- Plate-forme Transcriptome et Protéome Cliniques, Institut de Biologie et Pathologie, CHU Grenoble, 38043, Grenoble, France
- CNRS, 38042, Grenoble, France
| | - Georges Stepien
- INRA, UMR 1019, Unité de Nutrition Humaine, 63122, St Genès-Champanelle, France
- Université d'Auvergne, Unité de Nutrition Humaine, Clermont Université, BP 10448, 63000, Clermont-Ferrand, France
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Jefferson WN, Padilla-Banks E, Phelps JY, Gerrish KE, Williams CJ. Permanent oviduct posteriorization after neonatal exposure to the phytoestrogen genistein. ENVIRONMENTAL HEALTH PERSPECTIVES 2011; 119:1575-1582. [PMID: 21810550 PMCID: PMC3226509 DOI: 10.1289/ehp.1104018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/02/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Preimplantation embryo loss during oviduct transit has been observed in adult mice after a 5-day neonatal exposure to the phytoestrogen genistein (Gen; 50 mg/kg/day). OBJECTIVE We investigated the mechanisms underlying the contribution of the oviduct to infertility. METHODS Female mice were treated on postnatal days 1-5 with corn oil or Gen (50 mg/kg/day). We compared morphology, gene expression, and protein expression in different regions of the reproductive tracts of Gen-treated mice with those of control littermates at several time points. RESULTS Neonatal Gen treatment resulted in substantial changes in expression of genes that modulate neonatal oviduct morphogenesis, including Hoxa (homeobox A cluster), Wnt (wingless-related MMTV integration site), and hedgehog signaling genes. An estrogen receptor antagonist blocked these effects, indicating that they were induced by the estrogenic activity of Gen. Oviducts of adults treated neonatally with Gen had abnormal morphology and were stably "posteriorized," as indicated by altered Hoxa gene patterning during the time of treatment and dramatic, permanent up-regulation of homeobox genes (e.g., Pitx1, Six1) normally expressed only in the cervix and vagina. CONCLUSIONS Neonatal exposure to estrogenic environmental chemicals permanently disrupts oviduct morphogenesis and adult gene expression patterns, and these changes likely contribute to the infertility phenotype.
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Affiliation(s)
- Wendy N Jefferson
- Reproductive Medicine Group, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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