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Moudgil A, Sobti RC, Kaur T. In-silico identification and comparison of transcription factor binding sites cluster in anterior-posterior patterning genes in Drosophila melanogaster and Tribolium castaneum. PLoS One 2023; 18:e0290035. [PMID: 37590227 PMCID: PMC10434971 DOI: 10.1371/journal.pone.0290035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
The cis-regulatory data that help in transcriptional regulation is arranged into modular pieces of a few hundred base pairs called CRMs (cis-regulatory modules) and numerous binding sites for multiple transcription factors are prominent characteristics of these cis-regulatory modules. The present study was designed to localize transcription factor binding site (TFBS) clusters on twelve Anterior-posterior (A-P) genes in Tribolium castaneum and compare them to their orthologous gene enhancers in Drosophila melanogaster. Out of the twelve A-P patterning genes, six were gap genes (Kruppel, Knirps, Tailless, Hunchback, Giant, and Caudal) and six were pair rule genes (Hairy, Runt, Even-skipped, Fushi-tarazu, Paired, and Odd-skipped). The genes along with 20 kb upstream and downstream regions were scanned for TFBS clusters using the Motif Cluster Alignment Search Tool (MCAST), a bioinformatics tool that looks for set of nucleotide sequences for statistically significant clusters of non-overlapping occurrence of a given set of motifs. The motifs used in the current study were Hunchback, Caudal, Giant, Kruppel, Knirps, and Even-skipped. The results of the MCAST analysis revealed the maximum number of TFBS for Hunchback, Knirps, Caudal, and Kruppel in both D. melanogaster and T. castaneum, while Bicoid TFBS clusters were found only in D. melanogaster. The size of all the predicted TFBS clusters was less than 1kb in both insect species. These sequences revealed more transversional sites (Tv) than transitional sites (Ti) and the average Ti/Tv ratio was 0.75.
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Affiliation(s)
- Anshika Moudgil
- Department of Zoology, DAV University, Jalandhar, Punjab, India
| | | | - Tejinder Kaur
- Department of Zoology, DAV University, Jalandhar, Punjab, India
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Xu R, Dai F, Wu H, Jiao R, He F, Ma J. Shaping the scaling characteristics of gap gene expression patterns in Drosophila. Heliyon 2023; 9:e13623. [PMID: 36879745 PMCID: PMC9984453 DOI: 10.1016/j.heliyon.2023.e13623] [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: 09/23/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
How patterns are formed to scale with tissue size remains an unresolved problem. Here we investigate embryonic patterns of gap gene expression along the anterior-posterior (AP) axis in Drosophila. We use embryos that greatly differ in length and, importantly, possess distinct length-scaling characteristics of the Bicoid (Bcd) gradient. We systematically analyze the dynamic movements of gap gene expression boundaries in relation to both embryo length and Bcd input as a function of time. We document the process through which such dynamic movements drive both an emergence of a global scaling landscape and evolution of boundary-specific scaling characteristics. We show that, despite initial differences in pattern scaling characteristics that mimic those of Bcd in the anterior, such characteristics of final patterns converge. Our study thus partitions the contributions of Bcd input and regulatory dynamics inherent to the AP patterning network in shaping embryonic pattern's scaling characteristics.
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Affiliation(s)
- Ruoqing Xu
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Fei Dai
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Honggang Wu
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 510182, China
- Key Laboratory of Interdisciplinary Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 510182, China
- Key Laboratory of Interdisciplinary Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng He
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Corresponding author. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
| | - Jun Ma
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang, China
- Corresponding author. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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Dutta S, Patel AL, Keenan SE, Shvartsman SY. From complex datasets to predictive models of embryonic development. NATURE COMPUTATIONAL SCIENCE 2021; 1:516-520. [PMID: 38217248 DOI: 10.1038/s43588-021-00110-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/12/2021] [Indexed: 01/15/2024]
Abstract
Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here, we use data from our work on signal-dependent gene repression in the Drosophila embryo to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.
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Affiliation(s)
- Sayantan Dutta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Aleena L Patel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Stanislav Y Shvartsman
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Center of Computational Biology, Flatiron Institute, New York, NY, USA.
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Kalay G, Atallah J, Sierra NC, Tang AM, Crofton AE, Murugesan MK, Wykoff-Clary S, Lott SE. Evolution of larval segment position across 12 Drosophila species. Evolution 2019; 74:1409-1422. [PMID: 31886902 PMCID: PMC7496318 DOI: 10.1111/evo.13911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/25/2022]
Abstract
Many developmental traits that are critical to the survival of the organism are also robust. These robust traits are resistant to phenotypic change in the face of variation. This presents a challenge to evolution. In this article, we asked whether and how a well‐established robust trait, Drosophila segment patterning, changed over the evolutionary history of the genus. We compared segment position scaled to body length at the first‐instar larval stage among 12 Drosophila species. We found that relative segment position has changed many times across the phylogeny. Changes were frequent, but primarily small in magnitude. Phylogenetic analysis demonstrated that rates of change in segment position are variable along the Drosophila phylogenetic tree, and that these changes can occur in short evolutionary timescales. Correlation between position shifts of segments decreased as the distance between two segments increased, suggesting local control of segment position. The posterior‐most abdominal segment showed the highest magnitude of change on average, had the highest rate of evolution between species, and appeared to be evolving more independently as compared to the rest of the segments. This segment was exceptionally elongated in the cactophilic species in our dataset, raising questions as to whether this change may be adaptive.
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Affiliation(s)
- Gizem Kalay
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Joel Atallah
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616.,current address: Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148
| | - Noemie C Sierra
- Earth and Planetary Sciences Department, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Austin M Tang
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Amanda E Crofton
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Mohan K Murugesan
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Sherri Wykoff-Clary
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Susan E Lott
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
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An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:3961-3972. [PMID: 31619460 PMCID: PMC6893207 DOI: 10.1534/g3.119.400788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have identified network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in whole Drosophila melanogaster male terminalia followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the male terminalia are highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (https://flyterminalia.pitt.edu/) as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.
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