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Deem KD, Halfon MS, Tomoyasu Y. A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species. Sci Rep 2024; 14:10078. [PMID: 38698030 PMCID: PMC11066043 DOI: 10.1038/s41598-024-60432-9] [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: 01/24/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
Comparative analyses between traditional model organisms, such as the fruit fly Drosophila melanogaster, and more recent model organisms, such as the red flour beetle Tribolium castaneum, have provided a wealth of insight into conserved and diverged aspects of gene regulation. While the study of trans-regulatory components is relatively straightforward, the study of cis-regulatory elements (CREs, or enhancers) remains challenging outside of Drosophila. A central component of this challenge has been finding a core promoter suitable for enhancer-reporter assays in diverse insect species. Previously, we demonstrated that a Drosophila Synthetic Core Promoter (DSCP) functions in a cross-species manner in Drosophila and Tribolium. Given the over 300 million years of divergence between the Diptera and Coleoptera, we reasoned that DSCP-based reporter constructs will be useful when studying cis-regulation in a variety of insect models across the holometabola and possibly beyond. To this end, we sought to create a suite of new DSCP-based reporter vectors, leveraging dual compatibility with piggyBac and PhiC31-integration, the 3xP3 universal eye marker, GATEWAY cloning, different colors of reporters and markers, as well as Gal4-UAS binary expression. While all constructs functioned properly with a Tc-nub enhancer in Drosophila, complications arose with tissue-specific Gal4-UAS binary expression in Tribolium. Nevertheless, the functionality of these constructs across multiple holometabolous orders suggests a high potential compatibility with a variety of other insects. In addition, we present the piggyLANDR (piggyBac-LoxP AttP Neutralizable Destination Reporter) platform for the establishment of proper PhiC31 landing sites free from position effects. As a proof-of-principle, we demonstrated the workflow for piggyLANDR in Drosophila. The potential utility of these tools ranges from molecular biology research to pest and disease-vector management, and will help advance the study of gene regulation beyond traditional insect models.
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Affiliation(s)
- Kevin D Deem
- Department of Biology, Miami University, Oxford, OH, 45056, USA
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY, 14203, USA
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2
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Kapil S, Sobti RC, Kaur T. Prediction and analysis of cis-regulatory elements in Dorsal and Ventral patterning genes of Tribolium castaneum and its comparison with Drosophila melanogaster. Mol Cell Biochem 2024; 479:109-125. [PMID: 37004638 DOI: 10.1007/s11010-023-04712-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Abstract
Insect embryonic development and morphology are characterized by their anterior-posterior and dorsal-ventral (DV) patterning. In Drosophila embryos, DV patterning is mediated by a dorsal protein gradient which activates twist and snail proteins, the important regulators of DV patterning. To activate or repress gene expression, some regulatory proteins bind in clusters to their target gene at sites known as cis-regulatory elements or enhancers. To understand how variations in gene expression in different lineages might lead to different phenotypes, it is necessary to understand enhancers and their evolution. Drosophila melanogaster has been widely studied to understand the interactions between transcription factors and the transcription factor binding sites. Tribolium castaneum is an upcoming model animal which is catching the interest of biologists and the research on the enhancer mechanisms in the insect's axes patterning is still in infancy. Therefore, the current study was designed to compare the enhancers of DV patterning in the two insect species. The sequences of ten proteins involved in DV patterning of D. melanogaster were obtained from Flybase. The protein sequences of T. castaneum orthologous to those obtained from D. melanogaster were acquired from NCBI BLAST, and these were then converted to DNA sequences which were modified by adding 20 kb sequences both upstream and downstream to the gene. These modified sequences were used for further analysis. Bioinformatics tools (Cluster-Buster and MCAST) were used to search for clusters of binding sites (enhancers) in the modified DV genes. The results obtained showed that the transcription factors in Drosophila melanogaster and Tribolium castaneum are nearly identical; however, the number of binding sites varies between the two species, indicating transcription factor binding site evolution, as predicted by two different computational tools. It was observed that dorsal, twist, snail, zelda, and Supressor of Hairless are the transcription factors responsible for the regulation of DV patterning in the two insect species.
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Affiliation(s)
- Subham Kapil
- Department of Zoology, DAV University, Jalandhar, India
| | | | - Tejinder Kaur
- Department of Zoology, DAV University, Jalandhar, India.
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3
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Nowling RJ, Njoya K, Peters JG, Riehle MM. Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique. Front Cell Infect Microbiol 2023; 13:1182567. [PMID: 37600946 PMCID: PMC10433755 DOI: 10.3389/fcimb.2023.1182567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Various sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion. Some of these techniques rely on indirect markers such as histone modifications (ChIP-seq with histone antibodies) or chromatin accessibility (ATAC-seq, DNase-seq, FAIRE-seq), while other techniques use direct measures such as episomal assays measuring the enhancer properties of DNA sequences (STARR-seq) and direct measurement of the binding of transcription factors (ChIP-seq with transcription factor-specific antibodies). The activities of cis-regulatory elements such as enhancers, promoters, and repressors are determined by their sequence and secondary processes such as chromatin accessibility, DNA methylation, and bound histone markers. Methods Here, machine learning models are employed to evaluate the accuracy with which cis-regulatory elements identified by various commonly used sequencing techniques can be predicted by their underlying sequence alone to distinguish between cis-regulatory activity that is reflective of sequence content versus secondary processes. Results and discussion Models trained and evaluated on D. melanogaster sequences identified through DNase-seq and STARR-seq are significantly more accurate than models trained on sequences identified by H3K4me1, H3K4me3, and H3K27ac ChIP-seq, FAIRE-seq, and ATAC-seq. These results suggest that the activity detected by DNase-seq and STARR-seq can be largely explained by underlying DNA sequence, independent of secondary processes. Experimentally, a subset of DNase-seq and H3K4me1 ChIP-seq sequences were tested for enhancer activity using luciferase assays and compared with previous tests performed on STARR-seq sequences. The experimental data indicated that STARR-seq sequences are substantially enriched for enhancer-specific activity, while the DNase-seq and H3K4me1 ChIP-seq sequences are not. Taken together, these results indicate that the DNase-seq approach identifies a broad class of regulatory elements of which enhancers are a subset and the associated data are appropriate for training models for detecting regulatory activity from sequence alone, STARR-seq data are best for training enhancer-specific sequence models, and H3K4me1 ChIP-seq data are not well suited for training and evaluating sequence-based models for cis-regulatory element prediction.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI, United States
| | - Kimani Njoya
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - John G. Peters
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI, United States
| | - Michelle M. Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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Yamashita T, Ohde T, Nakamura T, Ishimaru Y, Watanabe T, Tomonari S, Nakamura Y, Noji S, Mito T. Involvement of the scalloped gene in morphogenesis of the wing margin via regulating cell growth in a hemimetabolous insect Gryllus bimaculatus. Dev Growth Differ 2023; 65:348-359. [PMID: 37310211 DOI: 10.1111/dgd.12869] [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: 12/22/2022] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023]
Abstract
The acquisition of wings was a key event in insect evolution. As hemimetabolous insects were the first group to acquire functional wings, establishing the mechanisms of wing formation in this group could provide useful insights into their evolution. In this study, we aimed to elucidate the expression and function of the gene scalloped (sd), which is involved in wing formation in Drosophila melanogaster, and in Gryllus bimaculatus mainly during postembryonic development. Expression analysis showed that sd is expressed in the tergal edge, legs, antennae, labrum, and cerci during embryogenesis and in the distal margin of the wing pads from at least the sixth instar in the mid to late stages. Because sd knockout caused early lethality, nymphal RNA interference experiments were performed. Malformations were observed in the wings, ovipositor, and antennae. By analyzing the effects on wing morphology, it was revealed that sd is mainly involved in the formation of the margin, possibly through the regulation of cell proliferation. In conclusion, sd might regulate the local growth of wing pads and influence wing margin morphology in Gryllus.
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Grants
- 17H03945 Ministry of Education, Culture, Sports, Science and Technology
- 19H02970 Ministry of Education, Culture, Sports, Science and Technology
- 19K06691 Ministry of Education, Culture, Sports, Science and Technology
- 20K21436 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Takahisa Yamashita
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima, Japan
| | - Takahiro Ohde
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Taro Nakamura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Yoshiyasu Ishimaru
- Graduate School of Sciences and Technology for Innovation, Tokushima University, Tokushima, Japan
| | - Takahito Watanabe
- Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Sayuri Tomonari
- Technical Support Department, Tokushima University, Tokushima, Japan
| | - Yuki Nakamura
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima, Japan
| | - Sumihare Noji
- Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Taro Mito
- Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
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5
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Wellmeyer B, Böhringer AC, Rösner J, Merzendorfer H. Analyses of ecdysteroid transporters in the fat body of Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2023. [PMID: 36892191 DOI: 10.1111/imb.12839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
The control of insect moulting and metamorphosis involves ecdysteroids that orchestrate the execution of developmental genetic programs by binding to dimeric hormone receptors consisting of the ecdysone receptor (EcR) and ultraspiracle (USP). In insects, the main ecdysteroids comprise ecdysone (E), which is synthesized in the prothoracic gland and secreted into the haemolymph, and 20-hydroxyecdysone (20E), which is considered the active form by binding to the nuclear receptor of the target cell. While biosynthesis of ecdysteroids has been studied in detail in different insects, the transport systems involved in guiding these steroid hormones across cellular membranes have just recently begun to be studied. By analysing RNAi phenotypes in the red flour beetle, Tribolium castaneum, we have identified three transporter genes, TcABCG-8A, TcABCG-4D and TcOATP4-C1, whose silencing results in phenotypes similar to that observed when the ecdysone receptor gene TcEcRA is silenced, that is, abortive moulting and abnormal development of adult compound eyes during the larval stage. The genes of all three transporters are expressed at higher levels in the larval fat body of T. castaneum. We analysed potential functions of these transporters by combining RNAi and mass spectrometry. However, the analysis of gene functions is challenged by mutual RNAi effects indicating interdependent gene regulation. Based on our findings, we propose that TcABCG-8A, TcABCG-4D and TcOATP4-C1 participate in the ecdysteroid transport in fat body cells, which are involved in E → 20E conversion catalysed by the P450 enzyme TcShade.
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Affiliation(s)
- Benedikt Wellmeyer
- Department of Chemistry-Biology, University of Siegen, Siegen, 57068, Germany
| | | | - Janin Rösner
- Department of Chemistry-Biology, University of Siegen, Siegen, 57068, Germany
| | - Hans Merzendorfer
- Department of Chemistry-Biology, University of Siegen, Siegen, 57068, Germany
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6
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Linz DM, Hara Y, Deem KD, Kuraku S, Hayashi S, Tomoyasu Y. Transcriptomic exploration of the Coleopteran wings reveals insight into the evolution of novel structures associated with the beetle elytron. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:197-213. [PMID: 36617687 PMCID: PMC10107685 DOI: 10.1002/jez.b.23188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 01/10/2023]
Abstract
The acquisition of novel traits is central to organismal evolution, yet the molecular mechanisms underlying this process are elusive. The beetle forewings (elytra) are evolutionarily modified to serve as a protective shield, providing a unique opportunity to study these mechanisms. In the past, the orthologs of genes within the wing gene network from Drosophila studies served as the starting point when studying the evolution of elytra (candidate genes). Although effective, candidate gene lists are finite and only explore genes conserved across species. To go beyond candidate genes, we used RNA sequencing and explored the wing transcriptomes of two Coleopteran species, the red flour beetle (Tribolium castaneum) and the Japanese stag beetle (Dorcus hopei). Our analysis revealed sets of genes enriched in Tribolium elytra (57 genes) and genes unique to the hindwings, which possess more "typical" insect wing morphologies (29 genes). Over a third of the hindwing-enriched genes were "candidate genes" whose functions were previously analyzed in Tribolium, demonstrating the robustness of our sequencing. Although the overlap was limited, transcriptomic comparison between the beetle species found a common set of genes, including key wing genes, enriched in either elytra or hindwings. Our RNA interference analysis for elytron-enriched genes in Tribolium uncovered novel genes with roles in forming various aspects of morphology that are unique to elytra, such as pigmentation, hardening, sensory development, and vein formation. Our analyses deepen our understanding of how gene network evolution facilitated the emergence of the elytron, a unique structure critical to the evolutionary success of beetles.
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Affiliation(s)
- David M Linz
- Department of Biology, Miami University, Oxford, Ohio, USA
| | - Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Kevin D Deem
- Department of Biology, Miami University, Oxford, Ohio, USA
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Shigeo Hayashi
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.,Department of Biology, Kobe University Graduate School of Science, Kobe, Hyogo, Japan
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7
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Rylee JC, Nin‐Velez A, Mahato S, Helms KJ, Wade MJ, Zentner GE, Zelhof AC. Generating and testing the efficacy of transgenic Cas9 in Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2022; 31:543-550. [PMID: 35429082 PMCID: PMC9544626 DOI: 10.1111/imb.12778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/22/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
CRISPR/Cas9 genome editing has now expanded to many insect species, including Tribolium castaneum. However, compared to Drosophila melanogaster, the CRISPR toolkit of T. castaneum is limited. A particularly apparent gap is the lack of Cas9 transgenic animals, which generally offer higher editing efficiency. We address this by creating and testing transgenic beetles expressing Cas9. We generated two different constructs bearing basal heat shock promoter-driven Cas9, two distinct 3' UTRs, and one containing Cas9 fused to EGFP by a T2A peptide. Analyses of Cas9 activity in each transgenic line demonstrated that both designs are capable of inducing CRISPR- mediated changes in the genome in the absence of heat induction. Overall, these resources enhance the accessibility of CRISPR/Cas9 genome editing for the Tribolium research community and provide a benchmark against which to compare future transgenic Cas9 lines.
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Affiliation(s)
| | - Alexandra Nin‐Velez
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
- Present address:
Lilly and Company Corporate CenterIndianapolisIndianaUSA
| | - Simpla Mahato
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
| | | | - Michael J. Wade
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
| | - Gabriel E. Zentner
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
- Present address:
eGenesis, Inc.CambridgeMassachusettsUSA
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8
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Klingler M, Bucher G. The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. EvoDevo 2022; 13:14. [PMID: 35854352 PMCID: PMC9295526 DOI: 10.1186/s13227-022-00201-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
The red flour beetle Tribolium castaneum has emerged as an important insect model system for a variety of topics. With respect to studying gene function, it is second only to the vinegar fly D. melanogaster. The RNAi response in T. castaneum is exceptionally strong and systemic, and it appears to target all cell types and processes. Uniquely for emerging model organisms, T. castaneum offers the opportunity of performing time- and cost-efficient large-scale RNAi screening, based on commercially available dsRNAs targeting all genes, which are simply injected into the body cavity. Well established transgenic and genome editing approaches are met by ease of husbandry and a relatively short generation time. Consequently, a number of transgenic tools like UAS/Gal4, Cre/Lox, imaging lines and enhancer trap lines are already available. T. castaneum has been a genetic experimental system for decades and now has become a workhorse for molecular and reverse genetics as well as in vivo imaging. Many aspects of development and general biology are more insect-typical in this beetle compared to D. melanogaster. Thus, studying beetle orthologs of well-described fly genes has allowed macro-evolutionary comparisons in developmental processes such as axis formation, body segmentation, and appendage, head and brain development. Transgenic approaches have opened new ways for in vivo imaging. Moreover, this emerging model system is the first choice for research on processes that are not represented in the fly, or are difficult to study there, e.g. extraembryonic tissues, cryptonephridial organs, stink gland function, or dsRNA-based pesticides.
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Affiliation(s)
- Martin Klingler
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Staudtstr. 5, 91058, Erlangen, Germany.
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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9
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Sun DA, Bredeson JV, Bruce HS, Patel NH. Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis. Development 2022; 149:275484. [PMID: 35608283 DOI: 10.1242/dev.200793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
Abstract
Emerging research organisms enable the study of biology that cannot be addressed using classical 'model' organisms. New data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-seq to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis and limb development. In addition, we use short- and long-read RNA-seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.
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Affiliation(s)
- Dennis A Sun
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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10
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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings. Proc Natl Acad Sci U S A 2022; 119:2108661119. [PMID: 35169073 PMCID: PMC8872758 DOI: 10.1073/pnas.2108661119] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Where do butterfly eyespots come from? One of the long-standing questions in the field of evolution concerns addressing where novel complex traits come from. Here we show that butterfly eyespots, a novel complex trait, likely originated from the redeployment of a preexisting gene-regulatory network regulating antennae, legs, and wings, to novel locations on the wing. Butterfly eyespots are beautiful novel traits with an unknown developmental origin. Here we show that eyespots likely originated via cooption of parts of an ancestral appendage gene-regulatory network (GRN) to novel locations on the wing. Using comparative transcriptome analysis, we show that eyespots cluster most closely with antennae, relative to multiple other tissues. Furthermore, three genes essential for eyespot development, Distal-less (Dll), spalt (sal), and Antennapedia (Antp), share similar regulatory connections as those observed in the antennal GRN. CRISPR knockout of cis-regulatory elements (CREs) for Dll and sal led to the loss of eyespots, antennae, legs, and also wings, demonstrating that these CREs are highly pleiotropic. We conclude that eyespots likely reused an ancient GRN for their development, a network also previously implicated in the development of antennae, legs, and wings.
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11
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Shen X, Peng Y, Song H, Wang J, Zhao J, Tang P, Han Z, Wang K. Key factors determining competitions between double-stranded RNAs in Tribolium castaneum. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 181:105009. [PMID: 35082032 DOI: 10.1016/j.pestbp.2021.105009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Combinatorial delivery of different double-stranded RNAs (dsRNAs) can result in competitive inhibition in insect pests and remains one of the obstacles in the way of future applications of the RNA interference (RNAi)-based pest control. In this study, we attempted to discover the basic competition characteristics between dsRNAs and provided insight into the solutions of competitive inhibition. RNAi sensitive insect species Tribolium castaneum were treated, and competitions between dsRNA fragments influencing the effectiveness of RNAi response could be measured. A chimeric dsRNA strategy for conjugating different dsRNA fragments into a single molecule and a nanoparticle carbon quantum dots-mediated dsRNA delivery were confirmed as efficient methods to knock down multiple target genes simultaneously. Furthermore, in vitro assays were conducted for determining the accumulation speed of serially diluted and incubated dsRNA in the midgut tissues. Our data showed that the accumulation of dsRNAs of different treated amounts was 0.25 μg ≈ 0.5 μg > 1 μg ≥ 2 μg > 4 μg, indicating that accumulation speed would be affected by treated dsRNA. Overall, our results strongly suggest that endocytic components influencing cellular uptake might be oversaturated when an excess amount of dsRNAs were treated, thereby causing competitive inhibition of target genes.
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Affiliation(s)
- Xu Shen
- Collaborative Innovation Center for Modern Grain Circulation and Safety, Joint Laboratory for International Cooperation in Grain Circulation and security, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, Jiangsu, China
| | - Yingchuan Peng
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Huifang Song
- Faculty of Biological Science & Technology, Changzhi University, Changzhi 046011, China
| | - Jinda Wang
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Zhao
- State Tobacco Monopoly Administration Key Laboratory for Green Prevention and Control of Tobacco Diseases and Pests in Huanghuai Tobacco Area, Institute of Tobacco Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Peian Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, Joint Laboratory for International Cooperation in Grain Circulation and security, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, Jiangsu, China
| | - Zhaojun Han
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Kangxu Wang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, Joint Laboratory for International Cooperation in Grain Circulation and security, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, Jiangsu, China; The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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12
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Moqtaderi Z, Brown S, Bender W. Genome-wide oscillations in G + C density and sequence conservation. Genome Res 2021; 31:2050-2057. [PMID: 34649930 PMCID: PMC8559709 DOI: 10.1101/gr.274332.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Eukaryotic genomes typically show a uniform G + C content among chromosomes, but on smaller scales, many species have a G + C density that fluctuates with a characteristic wavelength. This oscillation is evident in many insect species, with wavelengths ranging between 700 bp and 4 kb. Measures of evolutionary conservation oscillate in phase with G + C content, with conserved regions having higher G + C. Loci with large regulatory regions show more regular oscillations; coding sequences and heterochromatic regions show little or no oscillation. There is little oscillation in vertebrate genomes in regions with densely distributed mobile repetitive elements. However, species with few repeats show oscillation in both G + C density and sequence conservation. These oscillations may reflect optimal spacing of cis-regulatory elements.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Susan Brown
- Department of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Welcome Bender
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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13
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Diaz-Cuadros M, Pourquié O, El-Sherif E. Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans. PLoS Genet 2021; 17:e1009812. [PMID: 34648490 PMCID: PMC8516289 DOI: 10.1371/journal.pgen.1009812] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. In this article, we review 2 processes that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. We study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), we elucidate the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ezzat El-Sherif
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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The β 2Tubulin, Rad50-ATPase and enolase cis-regulatory regions mediate male germline expression in Tribolium castaneum. Sci Rep 2021; 11:18131. [PMID: 34518617 PMCID: PMC8438054 DOI: 10.1038/s41598-021-97443-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/19/2021] [Indexed: 11/19/2022] Open
Abstract
Genetics-based pest management processes, including the sterile insect technique, are an effective method for the control of some pest insects. However, current SIT methods are not directly transferable to many important pest insect species due to the lack of genetic sexing strains. Genome editing is revolutionizing the way we conduct genetics in insects, including in Tribolium castaneum, an important genetic model and agricultural pest. We identified orthologues of β2Tubulin, Rad50-ATPase and enolase in T. castaneum. Using RT-PCR, we confirmed that these genes are predominantly expressed in the testis. PiggyBac-based transformation of T. castaneum cis-regulatory regions derived from Tc-β2t, Tc-rad50 or Tc-eno resulted in EGFP expression specifically in the T. castaneum testis. Additionally, we determined that each of these regulatory regions regulates EGFP expression in different cell types of the male gonad. Cis-regulatory regions from Tc-β2t produced EGFP expression throughout spermatogenesis and also in mature sperms; Tc-rad50 resulted in expression only in the haploid spermatid, while Tc-eno expressed EGFP in late spermatogenesis. In summary, the regulatory cis-regions characterized in this study are not only suited to study male gonadal function but could be used for development of transgenic sexing strains that produce one sex in pest control strategies.
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Schember I, Halfon MS. Identification of new Anopheles gambiae transcriptional enhancers using a cross-species prediction approach. INSECT MOLECULAR BIOLOGY 2021; 30:410-419. [PMID: 33866636 PMCID: PMC8266755 DOI: 10.1111/imb.12705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/09/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
The success of transgenic mosquito vector control approaches relies on well-targeted gene expression, requiring the identification and characterization of a diverse set of mosquito promoters and transcriptional enhancers. However, few enhancers have been characterized in Anopheles gambiae to date. Here, we employ the SCRMshaw method we previously developed to predict enhancers in the A. gambiae genome, preferentially targeting vector-relevant tissues such as the salivary glands, midgut and nervous system. We demonstrate a high overall success rate, with at least 8 of 11 (73%) tested sequences validating as enhancers in an in vivo xenotransgenic assay. Four tested sequences drive expression in either the salivary gland or the midgut, making them directly useful for probing the biology of these infection-relevant tissues. The success of our study suggests that computational enhancer prediction should serve as an effective means for identifying A. gambiae enhancers with activity in tissues involved in malaria propagation and transmission.
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Affiliation(s)
- Isabella Schember
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203
- NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203
- Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263
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16
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Asma H, Halfon MS. Annotating the Insect Regulatory Genome. INSECTS 2021; 12:591. [PMID: 34209769 PMCID: PMC8305585 DOI: 10.3390/insects12070591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
Abstract
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods.
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Affiliation(s)
- Hasiba Asma
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
| | - Marc S. Halfon
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203, USA
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17
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Rösner J, Tietmeyer J, Merzendorfer H. Functional analysis of ABCG and ABCH transporters from the red flour beetle, Tribolium castaneum. PEST MANAGEMENT SCIENCE 2021; 77:2955-2963. [PMID: 33620766 DOI: 10.1002/ps.6332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/21/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND ATP-binding cassette transporter (ABC transporter) subfamilies ABCA-C and ABCG-H have been implicated in insecticide detoxification, mostly based on findings of elevated gene expression in response to insecticide treatment. We previously characterized TcABCA-C genes from the model beetle and pest Tribolium castaneum and demonstrated that TcABCA and TcABCC genes are involved in the elimination of diflubenzuron, because RNA interference (RNAi)-mediated gene silencing increased susceptibility. In this study, we focused on the potential functions of TcABCG and TcABCH genes in insecticide detoxification. RESULTS When we silenced the expression of TcABCG-H genes using RNAi, we noticed a previously unreported developmental RNAi phenotype for TcABCG-4F, which is characterized by 50% mortality and ecdysial arrest during adult moult. When we knocked down the Drosophila brown orthologue TcABCG-XC, we did not obtain apparent eye colour phenotypes but did observe a loss of riboflavin uptake by Malpighian tubules. Next, we determined the expression profiles of all TcABCG-H genes in different tissues and developmental stages and analysed transcript levels in response to treatment with four chemically unrelated insecticides. We found that some genes were specifically upregulated after insecticide treatment. However, when we determined insecticide-induced mortalities in larvae that were treated by double-stranded RNA injection to silence those TcABCG-H genes that were upregulated, we did not observe a significant increase in susceptibility to insecticides. CONCLUSION Our findings suggest that the observed insecticide-dependent induction of TcABCG-H gene expression reflects an unspecific stress response, and hence underlines the significance of functional studies on insecticide detoxification. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Janin Rösner
- Department of Chemistry-Biology, University of Siegen, Siegen, Germany
| | - Johanne Tietmeyer
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Hans Merzendorfer
- Department of Chemistry-Biology, University of Siegen, Siegen, Germany
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18
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Palazzo A, Marsano RM. Transposable elements: a jump toward the future of expression vectors. Crit Rev Biotechnol 2021; 41:792-808. [PMID: 33622117 DOI: 10.1080/07388551.2021.1888067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Expression vectors (EVs) are artificial nucleic acid molecules with a modular structure that allows for the transcription of DNA sequences of interest in either cellular or cell-free environments. These vectors have emerged as cross-disciplinary tools with multiple applications in an expanding Life Sciences market. The cis-regulatory sequences (CRSs) that control the transcription in EVs are typically sourced from either viruses or from characterized genes. However, the recent advancement in transposable elements (TEs) technology provides attractive alternatives that may enable a significant improvement in the design of EVs. Commonly known as "jumping genes," due to their ability to move between genetic loci, TEs are constitutive components of both eukaryotic and prokaryotic genomes. TEs harbor native CRSs that allow the regulated transcription of transposition-related genes. However, some TE-related CRSs display striking characteristics, which provides the opportunity to reconsider TEs as lead actors in the design of EVs. In this article, we provide a synopsis of the transcriptional control elements commonly found in EVs together with an extensive discussion of their advantages and limitations. We also highlight the latest findings that may allow for the implementation of TE-derived sequences in the EVs feasible, possibly improving existing vectors. By introducing this new concept of TEs as a source of regulatory sequences, we aim to stimulate a profitable discussion of the potential advantages and benefits of developing a new generation of EVs based on the use of TE-derived control sequences.
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Affiliation(s)
- Antonio Palazzo
- Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Bari, Italy
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19
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Daimon T, Koyama T, Yamamoto G, Sezutsu H, Mirth CK, Shinoda T. The Number of Larval Molts Is Controlled by Hox in Caterpillars. Curr Biol 2021; 31:884-891.e3. [PMID: 33308417 DOI: 10.1016/j.cub.2020.11.017] [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: 06/02/2020] [Revised: 10/14/2020] [Accepted: 11/05/2020] [Indexed: 11/17/2022]
Abstract
Animals with exoskeletons molt for further growth. In insects, the number of larval (or nymphal) molts varies inter- and intra-specifically, and it is widely accepted that the variation in the number of larval molts is an adaptive response to diverse environmental conditions.1-5 However, the molecular mechanism that underlies the variety and plasticity in the number of larval molts is largely unknown. In the silkworm, Bombyx mori, there are strains that molt three, four, or five times, and these numbers are determined by allelic variation at a single autosomal locus, Moltinism (M).6-9 Here, we demonstrate that the Hox gene Sex combs reduced (Scr) is responsible for the phenotypes of the M locus. Scr is selectively expressed in the larval prothoracic gland (PG), an endocrine organ that produces molting hormones.2Scr represses the biosynthesis of molting hormones in the PG, thereby regulating the incremental increase in body size during each larval instar. Our experiments consistently suggest that the differential expression levels of Scr among the three M alleles result in different growth ratios that ultimately lead to the different number of larval molts. Although the role of Hox genes in conferring segmental identity along the body axis and in molding segment-specific structure later in development has been well established,10-13 the present study identifies an unexpected role of Hox gene in hormone biosynthesis. This new role means that, in addition to shaping segment-specific morphology, Hox genes also drive the evolution of life history traits by regulating animal physiology.
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Affiliation(s)
- Takaaki Daimon
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; National Agricultural and Food Research Organization, Ibaraki 305-8634, Japan; Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-0032, Japan.
| | - Takashi Koyama
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Gaku Yamamoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Sezutsu
- National Agricultural and Food Research Organization, Ibaraki 305-8634, Japan
| | - Christen K Mirth
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Tetsuro Shinoda
- National Agricultural and Food Research Organization, Ibaraki 305-8634, Japan; Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima 960-1296, Japan
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20
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Nowling RJ, Behura SK, Halfon MS, Emrich SJ, Duman-Scheel M. PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map. Hereditas 2021; 158:7. [PMID: 33509290 PMCID: PMC7844911 DOI: 10.1186/s41065-021-00172-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assembly in key areas such as the M/m sex-determining locus. Release of the updated genome assembly has precipitated the need to reprocess historical functional genomic data sets, including cis-regulatory element (CRE) maps that had previously been generated for A. aegypti. RESULTS We re-processed and re-analyzed the A. aegypti whole embryo FAIRE seq data to create an updated embryonic CRE map for the AaegL5 genome. We validated that the new CRE map recapitulates key features of the original AaegL3 CRE map. Further, we built on the improved assembly in the M/m locus to analyze overlaps of open chromatin regions with genes. To support the validation, we created a new method (PeakMatcher) for matching peaks from the same experimental data set across genome assemblies. CONCLUSION Use of PeakMatcher software, which is available publicly under an open-source license, facilitated the release of an updated and validated CRE map, which is available through the NIH GEO. These findings demonstrate that PeakMatcher software will be a useful resource for validation and transferring of previous annotations to updated genome assemblies.
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Affiliation(s)
- Ronald J Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, 1025 North Broadway, Milwaukee, WI, 53202, USA.
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Marc S Halfon
- Department of Biochemistry, State University of New York at Buffalo, NY, 14203, Buffalo, USA
| | - Scott J Emrich
- Min H. Kao Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, 37996, USA
| | - Molly Duman-Scheel
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, South Bend, IN, 46617, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
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21
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Courtier‐Orgogozo V, Danchin A, Gouyon P, Boëte C. Evaluating the probability of CRISPR-based gene drive contaminating another species. Evol Appl 2020; 13:1888-1905. [PMID: 32908593 PMCID: PMC7463340 DOI: 10.1111/eva.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.
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Affiliation(s)
| | - Antoine Danchin
- Institut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris DescartesParisFrance
| | - Pierre‐Henri Gouyon
- Institut de Systématique, Évolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUAParisFrance
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Tomoyasu Y, Halfon MS. How to study enhancers in non-traditional insect models. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb212241. [PMID: 32034049 DOI: 10.1242/jeb.212241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue- and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse traits. An amazing array of diverse traits seen in insect morphology, physiology and behavior has been the subject of research for centuries. Although enhancer studies in insects outside of Drosophila have been limited, recent advances in functional genomic approaches have begun to make such studies possible in an increasing selection of insect species. Here, instead of comprehensively reviewing currently available technologies for enhancer studies in established model organisms such as Drosophila, we focus on a subset of computational and experimental approaches that are likely applicable to non-Drosophila insects, and discuss the pros and cons of each approach. We discuss the importance of validating enhancer function and evaluate several possible validation methods, such as reporter assays and genome editing. Key points and potential pitfalls when establishing a reporter assay system in non-traditional insect models are also discussed. We close with a discussion of how to advance enhancer studies in insects, both by improving computational approaches and by expanding the genetic toolbox in various insects. Through these discussions, this Review provides a conceptual framework for studying the function and evolution of enhancers in non-traditional insect models.
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Affiliation(s)
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
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23
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Herndon N, Shelton J, Gerischer L, Ioannidis P, Ninova M, Dönitz J, Waterhouse RM, Liang C, Damm C, Siemanowski J, Kitzmann P, Ulrich J, Dippel S, Oberhofer G, Hu Y, Schwirz J, Schacht M, Lehmann S, Montino A, Posnien N, Gurska D, Horn T, Seibert J, Vargas Jentzsch IM, Panfilio KA, Li J, Wimmer EA, Stappert D, Roth S, Schröder R, Park Y, Schoppmeier M, Chung HR, Klingler M, Kittelmann S, Friedrich M, Chen R, Altincicek B, Vilcinskas A, Zdobnov E, Griffiths-Jones S, Ronshaugen M, Stanke M, Brown SJ, Bucher G. Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics 2020; 21:47. [PMID: 31937263 PMCID: PMC6961396 DOI: 10.1186/s12864-019-6394-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
Background The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.
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Affiliation(s)
- Nicolae Herndon
- Department of Computer Science, East Carolina University, Greenville, NC, 27858, USA
| | - Jennifer Shelton
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Lizzy Gerischer
- Institut für Mathematik und Informatik, Universität Greifswald, Greifswald, Germany
| | - Panos Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Maria Ninova
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Jürgen Dönitz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Carsten Damm
- Institut für Informatik, Fakultät für Mathematik und Informatik, Georg-August-Universität Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Janna Siemanowski
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Peter Kitzmann
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Julia Ulrich
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Stefan Dippel
- Göttinger Graduiertenschule fur Neurowissenschaften Biophysik und Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Georg Oberhofer
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Yonggang Hu
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Jonas Schwirz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Magdalena Schacht
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Sabrina Lehmann
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Alice Montino
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Nico Posnien
- Department of Developmental Biology, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Daniela Gurska
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Kristen A Panfilio
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Jianwei Li
- Department Developmental Biology, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Dominik Stappert
- Institute of Zoology: Developmental Biology, University of Cologne, Zülpicher Weg 47b, 50674, Cologne, Germany
| | - Siegfried Roth
- Institute of Zoology: Developmental Biology, University of Cologne, Zülpicher Weg 47b, 50674, Cologne, Germany
| | - Reinhard Schröder
- Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael Schoppmeier
- Department of Biology, Divison of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Ho-Ryun Chung
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnenstraße 63-73, 14195, Berlin, Germany
| | - Martin Klingler
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Sebastian Kittelmann
- Oxford Brookes University, Centre for Functional Genomics, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Markus Friedrich
- Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI, 48202, USA
| | - Rui Chen
- Baylor College of Medicine, Houston, Texas, USA
| | - Boran Altincicek
- Institute of Crop Science and Resource Conservation (INRES-Phytomedicine), Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Evgeny Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Matthew Ronshaugen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Mario Stanke
- Institut für Mathematik und Informatik, Universität Greifswald, Greifswald, Germany.
| | - Sue J Brown
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Gregor Bucher
- Georg-August-Universität Göttingen, Göttingen, Germany.
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24
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Farnworth MS, Eckermann KN, Ahmed HMM, Mühlen DS, He B, Bucher G. The Red Flour Beetle as Model for Comparative Neural Development: Genome Editing to Mark Neural Cells in Tribolium Brain Development. Methods Mol Biol 2020; 2047:191-217. [PMID: 31552656 DOI: 10.1007/978-1-4939-9732-9_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated) scientists working with Tribolium castaneum can now generate transgenic lines with site-specific insertions at their region of interest. We present two methods to generate in vivo imaging lines suitable for marking subsets of neurons with fluorescent proteins. The first method relies on homologous recombination and uses a 2A peptide to create a bicistronic mRNA. In such lines, the target and the marker proteins are not fused but produced at equal amounts. This work-intensive method is compared with creating gene-specific enhancer traps that do not rely on homologous recombination. These are faster to generate but reflect the expression of the target gene less precisely. Which method to choose, strongly depends on the aims of each research project and in turn impacts of how neural cells and their development are marked. We describe the necessary steps from designing constructs and guide RNAs to embryonic injection and making homozygous stocks.
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Affiliation(s)
- Max S Farnworth
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany. .,Göttingen Graduate Center for Molecular Biosciences, Neurosciences and Biophysics, Göttingen, Germany.
| | - Kolja N Eckermann
- Göttingen Graduate Center for Molecular Biosciences, Neurosciences and Biophysics, Göttingen, Germany.,Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Hassan M M Ahmed
- Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.,Department of Crop Protection, Faculty of Agriculture, University of Khartoum, Khartoum-North, Khartoum, Sudan
| | - Dominik S Mühlen
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.,Göttingen Graduate Center for Molecular Biosciences, Neurosciences and Biophysics, Göttingen, Germany
| | - Bicheng He
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.
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25
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Nguyen QH, Nguyen-Vo TH, Le NQK, Do TTT, Rahardja S, Nguyen BP. iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks. BMC Genomics 2019; 20:951. [PMID: 31874637 PMCID: PMC6929481 DOI: 10.1186/s12864-019-6336-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength. The benchmark dataset from Liu et al.'s study was used to develop and evaluate the ensemble models. A comparative analysis between iEnhancer-ECNN and existing state-of-the-art methods was done to fairly assess the model performance. RESULTS Our experimental results demonstrates that iEnhancer-ECNN has better performance compared to other state-of-the-art methods using the same dataset. The accuracy of the ensemble model for enhancer identification (layer 1) and enhancer classification (layer 2) are 0.769 and 0.678, respectively. Compared to other related studies, improvements in the Area Under the Receiver Operating Characteristic Curve (AUC), sensitivity, and Matthews's correlation coefficient (MCC) of our models are remarkable, especially for the model of layer 2 with about 11.0%, 46.5%, and 65.0%, respectively. CONCLUSIONS iEnhancer-ECNN outperforms other previously proposed methods with significant improvement in most of the evaluation metrics. Strong growths in the MCC of both layers are highly meaningful in assuring the stability of our models.
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Affiliation(s)
- Quang H Nguyen
- School of Information and Communication Technology, Hanoi University of Science and Technology, 1 Dai Co Viet, Hanoi 100000, Vietnam
| | - Thanh-Hoang Nguyen-Vo
- School of Mathematics and Statistics, Victoria University of Wellington, Gate 7, Kelburn Parade, Wellington, 6142, New Zealand
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, Taipei Medical University, Keelung Road, Da'an Distric, Taipei City, 106, Taiwan (R.O.C.)
| | - Trang T T Do
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam
| | - Susanto Rahardja
- School of Marine Science and Technology, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China.
| | - Binh P Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Gate 7, Kelburn Parade, Wellington, 6142, New Zealand.
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26
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Abstract
ABSTRACT
There is now compelling evidence that many arthropods pattern their segments using a clock-and-wavefront mechanism, analogous to that operating during vertebrate somitogenesis. In this Review, we discuss how the arthropod segmentation clock generates a repeating sequence of pair-rule gene expression, and how this is converted into a segment-polarity pattern by ‘timing factor’ wavefronts associated with axial extension. We argue that the gene regulatory network that patterns segments may be relatively conserved, although the timing of segmentation varies widely, and double-segment periodicity appears to have evolved at least twice. Finally, we describe how the repeated evolution of a simultaneous (Drosophila-like) mode of segmentation within holometabolan insects can be explained by heterochronic shifts in timing factor expression plus extensive pre-patterning of the pair-rule genes.
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Affiliation(s)
- Erik Clark
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Andrew D. Peel
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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27
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Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of Tribolium castaneum. G3-GENES GENOMES GENETICS 2019; 9:2363-2373. [PMID: 31113821 PMCID: PMC6643895 DOI: 10.1534/g3.119.400340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcriptomic studies of Tribolium castaneum have led to significant advances in our understanding of co-regulation and differential expression of genes in development. However, previously used microarray approaches have covered only a subset of known genes. The aim of this study was to investigate gene expression patterns of beetle embryo, germ-line and somatic tissues. We identified 12,302 expressed genes and determined differentially expressed up and down-regulated genes among all samples. For example, 1624 and 3639 genes were differentially increased in expression greater than or equal to twofold change (FDR < 0.01) in testis vs. ovary (virgin female) and ovary vs. embryo (0-5 hr), respectively. Of these, many developmental, somatic and germ-line differentially expressed genes were identified. Furthermore, many maternally deposited transcripts were identified, whose expression either decreased rapidly or persisted during embryogenesis. Genes with the largest change in expression were predominantly decreased during early embryogenesis as compared to ovary or were increased in testis compared to embryo. We also identify zygotic genes induced after fertilization. The genome wide variation in transcript regulation in maternal and zygotic genes could provide additional information on how the anterior posterior axis formation is established in Tribolium embryos as compared to Drosophila Together, our data will facilitate studies of comparative developmental biology as well as help identify candidate genes for identifying cis-elements to drive transgenic constructs.
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28
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Asma H, Halfon MS. Computational enhancer prediction: evaluation and improvements. BMC Bioinformatics 2019; 20:174. [PMID: 30953451 PMCID: PMC6451241 DOI: 10.1186/s12859-019-2781-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods for CRM discovery, but it is critical that we develop effective means to evaluate their performance in terms of estimating their sensitivity and specificity. RESULTS We introduce here pCRMeval, a pipeline for in silico evaluation of any enhancer prediction tools that are flexible enough to be applied to the Drosophila melanogaster genome. pCRMeval compares the result of predictions with the extensive existing knowledge of experimentally-validated Drosophila CRMs in order to estimate the precision and relative sensitivity of the prediction method. In the case of supervised prediction methods-when training data composed of validated CRMs are used-pCRMeval can also assess the sensitivity of specific training sets. We demonstrate the utility of pCRMeval through evaluation of our SCRMshaw CRM prediction method and training data. By measuring the impact of different parameters on SCRMshaw performance, as assessed by pCRMeval, we develop a more robust version of SCRMshaw, SCRMshaw_HD, that improves the number of predictions while maintaining sensitivity and specificity. Our analysis also demonstrates that SCRMshaw_HD, when applied to increasingly less well-assembled genomes, maintains its strong predictive power with only a minor drop-off in performance. CONCLUSION Our pCRMeval pipeline provides a general framework for evaluation that can be applied to any CRM prediction method, particularly a supervised method. While we make use of it here primarily to test and improve a particular method for CRM prediction, SCRMshaw, pCRMeval should provide a valuable platform to the research community not only for evaluating individual methods, but also for comparing between competing methods.
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Affiliation(s)
- Hasiba Asma
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA
| | - Marc S Halfon
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA.
- Department of Biochemistry, University at Buffalo-State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA.
- Department of Biological Sciences, University at Buffalo-State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA.
- Department of Biomedical Informatics, University at Buffalo-State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA.
- NY State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY, 14203, USA.
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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29
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Le NQK, Yapp EKY, Ho QT, Nagasundaram N, Ou YY, Yeh HY. iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding. Anal Biochem 2019; 571:53-61. [PMID: 30822398 DOI: 10.1016/j.ab.2019.02.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/17/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
An enhancer is a short (50-1500bp) region of DNA that plays an important role in gene expression and the production of RNA and proteins. Genetic variation in enhancers has been linked to many human diseases, such as cancer, disorder or inflammatory bowel disease. Due to the importance of enhancers in genomics, the classification of enhancers has become a popular area of research in computational biology. Despite the few computational tools employed to address this problem, their resulting performance still requires improvements. In this study, we treat enhancers by the word embeddings, including sub-word information of its biological words, which then serve as features to be fed into a support vector machine algorithm to classify them. We present iEnhancer-5Step, a web server containing two-layer classifiers to identify enhancers and their strength. We are able to attain an independent test accuracy of 79% and 63.5% in the two layers, respectively. Compared to current predictors on the same dataset, our proposed method is able to yield superior performance as compared to the other methods. Moreover, this study provides a basis for further research that can enrich the field of applying natural language processing techniques in biological sequences. iEnhancer-5Step is freely accessible via http://biologydeep.com/fastenc/.
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Affiliation(s)
- Nguyen Quoc Khanh Le
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798, Singapore.
| | - Edward Kien Yee Yapp
- Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, #08-04, Innovis, 138634, Singapore
| | - Quang-Thai Ho
- Department of Computer Science and Engineering, Yuan Ze University, 32003, Taiwan
| | - N Nagasundaram
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798, Singapore
| | - Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, 32003, Taiwan
| | - Hui-Yuan Yeh
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798, Singapore.
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30
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McKay DJ. Using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to Identify Functional Regulatory DNA in Insect Genomes. Methods Mol Biol 2019; 1858:89-97. [PMID: 30414113 DOI: 10.1007/978-1-4939-8775-7_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Differential regulation of gene expression determines cell-type-specific function, making identification of the cis-regulatory elements that control gene expression a central goal of developmental biology. In addition, changes in the sequence of cis-regulatory elements are thought to drive changes in gene expression patterns between species, making comparisons of cis-regulatory element usage important for evolutionary biology as well. Due to the number of extant species and the incredible morphological diversity that they exhibit, insects are favorite model organisms for both developmental and evolutionary biologists alike. However, identifying cis-regulatory elements in insect genomes is challenging. Here, I describe a method termed FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements, followed by high-throughput sequencing) that can be used to identify functional DNA regulatory elements from developing insect tissues, genome-wide.
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Affiliation(s)
- Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Genetics, Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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31
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Clark-Hachtel CM, Moe MR, Tomoyasu Y. Detailed analysis of the prothoracic tissues transforming into wings in the Cephalothorax mutants of the Tribolium beetle. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:352-361. [PMID: 29913217 DOI: 10.1016/j.asd.2018.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
Despite the immense importance of the wing in the evolution and successful radiation of the insect lineages, the origin of this critical structure remains a hotly-debated mystery. Two possible tissues have been identified as an evolutionary origin of wings; the lateral expansion of the dorsal body wall (tergal edge) and structures related to an ancestral proximal leg segment (pleural tissues). Through studying wing-related tissues in the red flour beetle, Tribolium castaneum, we have previously presented evidence in support of a dual origin of insect wings, a third hypothesis proposing that wings evolved from a combination of both tergal and pleural tissues. One key finding came from the investigation of a Cephalothorax (Cx) mutant, in which the ectopic wing characteristic to this mutant was found to be formed from both tergal and pleural contributions. However, the degree of contribution of the two tissues to the wing remains elusive. Here, we took advantage of multiple Cx alleles available in Tribolium, and produced a variety of degrees and types of ectopic wing tissues in their prothoracic segments. Through detailed phenotypic scoring of the Cx phenotypes based on nine categories of mutant traits, along with comprehensive morphological analysis of the ectopic wing tissues, we found that (i) ectopic wing tissues can be formed at various locations in the prothorax, even internally, (ii) the lateral external ectopic wing tissues have tergal origin, while the internal and posterior external ectopic wing tissues appear to be of pleural origin, and (iii) the ectopic wing tissues of both tergal and pleural origin are capable of transforming into wing surface tissues. Collectively, these outcomes suggest that the evolutionary contribution of each tissue to a complete wing may be more complex than the simple binary view that is typically invoked by a dual origin model (i.e. the wing blade from the tergal contribution + musculature and articulation from the pleural contribution).
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Affiliation(s)
| | - Madison R Moe
- Department of Biology, Miami University, 700E High St., Oxford, OH, USA
| | - Yoshinori Tomoyasu
- Department of Biology, Miami University, 700E High St., Oxford, OH, USA.
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