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Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts. Life (Basel) 2023; 13:life13030708. [PMID: 36983865 PMCID: PMC10054693 DOI: 10.3390/life13030708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
An important question in evolutionary biology is whether (and in what ways) genotype–phenotype (GP) map biases can influence evolutionary trajectories. Untangling the relative roles of natural selection and biases (and other factors) in shaping phenotypes can be difficult. Because the RNA secondary structure (SS) can be analyzed in detail mathematically and computationally, is biologically relevant, and a wealth of bioinformatic data are available, it offers a good model system for studying the role of bias. For quite short RNA (length L≤126), it has recently been shown that natural and random RNA types are structurally very similar, suggesting that bias strongly constrains evolutionary dynamics. Here, we extend these results with emphasis on much larger RNA with lengths up to 3000 nucleotides. By examining both abstract shapes and structural motif frequencies (i.e., the number of helices, bonds, bulges, junctions, and loops), we find that large natural and random structures are also very similar, especially when contrasted to typical structures sampled from the spaces of all possible RNA structures. Our motif frequency study yields another result, where the frequencies of different motifs can be used in machine learning algorithms to classify random and natural RNA with high accuracy, especially for longer RNA (e.g., ROC AUC 0.86 for L = 1000). The most important motifs for classification are the number of bulges, loops, and bonds. This finding may be useful in using SS to detect candidates for functional RNA within ‘junk’ DNA regions.
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Giraldo-Calderón GI, Harb OS, Kelly SA, Rund SS, Roos DS, McDowell MA. VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100860. [PMID: 34864248 PMCID: PMC9133010 DOI: 10.1016/j.cois.2021.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 06/12/2023]
Abstract
VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse 'omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.
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Affiliation(s)
- Gloria I Giraldo-Calderón
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA; Dept. Ciencias Biológicas & Dept. Ciencias Básicas Médicas, Universidad Icesi, Calle 18 No 122-135, Cali, Colombia
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Sarah A Kelly
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Samuel Sc Rund
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA.
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3
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Holm I, Nardini L, Pain A, Bischoff E, Anderson CE, Zongo S, Guelbeogo WM, Sagnon N, Gohl DM, Nowling RJ, Vernick KD, Riehle MM. Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii. Front Genet 2022; 12:785934. [PMID: 35082832 PMCID: PMC8784733 DOI: 10.3389/fgene.2021.785934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences. Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.
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Affiliation(s)
- Inge Holm
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Luisa Nardini
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Adrien Pain
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France.,Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique, Paris, France
| | - Emmanuel Bischoff
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Cameron E Anderson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Soumanaba Zongo
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso
| | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN, United States.,Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Ronald J Nowling
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering (MSOE), Milwaukee, WI, United States
| | - Kenneth D Vernick
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Michelle M Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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Mao W, Zeng Q, She L, Yuan H, Luo Y, Wang R, She Y, Wang W, Wang C, Pan X. Wolbachia Utilizes lncRNAs to Activate the Anti-Dengue Toll Pathway and Balance Reactive Oxygen Species Stress in Aedes aegypti Through a Competitive Endogenous RNA Network. Front Cell Infect Microbiol 2022; 11:823403. [PMID: 35127567 PMCID: PMC8814319 DOI: 10.3389/fcimb.2021.823403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNA), a class of RNA molecules without protein coding potential, are more than 200 nucleotides in length and widely present in a variety of species. Although increasing progress in regard to the determination of lncRNA function has been made in vertebrates, Aedes aegypti lncRNAs were only identified recently and the functions of few lncRNAs have been annotated so far. Herein, the genome-wide alteration of the lncRNA expression profile trigged by Wolbachia wAlbB infection was investigated by comparing A. aegypti Aag2 cells and W-Aag2 cells infected with Wolbachia wAlbB. Based on lncRNA sequencing, 3035 differentially expressed lncRNAs (DE lncRNAs) in total were identified upon Wolbachia infection, which were further validated by quantitative PCR. The constructed co-expression network of DE lncRNAs and mRNAs revealed that Wolbachia-induced DE lncRNAs were highly enriched in the oxidative phosphorylation pathway via trans-activity, according to the KEGG pathway enrichment analyses. In addition, the established competitive endogenous RNA (ceRNA) network identifies the DE lncRNAs enriched in cellular oxidant detoxification based on GO enrichment analysis. Furthermore, silencing of aae-lnc-7598, the significantly up-regulated lncRNA with the highest fold change induced by Wolbachia, caused a significant reduction of antioxidant catalase 1B (CAT1B) gene expression as well as the enhancement of mitochondrial reactive oxygen species (ROS) production in living cells. These findings indicate that Wolbachia manipulates lncRNA to balance intracellular ROS stress and ensure its endosymbiosis in host A. aegypti. Notably, the function assay demonstrated that aae-lnc-0165 suppressed by Wolbachia could induce expression of the REL1 gene, the key regulator of downstream Toll pathway, through the sequence-specific binding of aae-miR-980-5p, which contributes to the activation of Toll pathway. Moreover, the depletion of aae-lnc-0165 caused the suppression of mitochondrial ROS levels in living cells. Our data reveal that Wolbachia activates the anti-dengue Toll pathway through a lncRNA-ceRNA pattern. Taken together, our finding suggested that Wolbachia utilizes lncRNAs to activate host anti-dengue Toll pathway via a ceRNA network. Moreover, Wolbachia employs lncRNAs to ensure ROS homeostasis for ROS-based anti-dengue defense through either trans-regulation or the ceRNA network. This study identifies novel potential molecular biomarkers for prevention and control of epidemic dengue.
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Affiliation(s)
- Wei Mao
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Qin Zeng
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Lingzhi She
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Hao Yuan
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Yuying Luo
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Renke Wang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Yueting She
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Weifeng Wang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Chaojun Wang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
| | - Xiaoling Pan
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, China
- The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, China
- *Correspondence: Xiaoling Pan,
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5
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Amaro IA, Ahmed-Braimah YH, League GP, Pitcher SA, Avila FW, Cruz PC, Harrington LC, Wolfner MF. Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract. BMC Genomics 2021; 22:896. [PMID: 34906087 PMCID: PMC8672594 DOI: 10.1186/s12864-021-08201-0] [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: 08/09/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mating induces behavioral and physiological changes in the arbovirus vector Aedes aegypti, including stimulation of egg development and oviposition, increased survival, and reluctance to re-mate with subsequent males. Transferred seminal fluid proteins and peptides derived from the male accessory glands induce these changes, though the mechanism by which they do this is not known. RESULTS To determine transcriptome changes induced by seminal proteins, we injected extract from male accessory glands and seminal vesicles (MAG extract) into females and examined female lower reproductive tract (LRT) transcriptomes 24 h later, relative to non-injected controls. MAG extract induced 87 transcript-level changes, 31 of which were also seen in a previous study of the LRT 24 h after a natural mating, including 15 genes with transcript-level changes similarly observed in the spermathecae of mated females. The differentially-regulated genes are involved in diverse molecular processes, including immunity, proteolysis, neuronal function, transcription control, or contain predicted small-molecule binding and transport domains. CONCLUSIONS Our results reveal that seminal fluid proteins, specifically, can induce gene expression responses after mating and identify gene targets to further investigate for roles in post-mating responses and potential use in vector control.
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Affiliation(s)
- I Alexandra Amaro
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Garrett P League
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Sylvie A Pitcher
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Frank W Avila
- Max Planck Tandem Group in Mosquito Reproductive Biology, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Priscilla C Cruz
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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Dong S, Dong Y, Simões ML, Dimopoulos G. Mosquito transgenesis for malaria control. Trends Parasitol 2021; 38:54-66. [PMID: 34483052 DOI: 10.1016/j.pt.2021.08.001] [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] [Received: 06/08/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
Malaria is one of the deadliest diseases. Because of the ineffectiveness of current malaria-control methods, several novel mosquito vector-based control strategies have been proposed to supplement existing control strategies. Mosquito transgenesis and gene drive have emerged as promising tools for preventing the spread of malaria by either suppressing mosquito populations by self-destructing mosquitoes or replacing mosquito populations with disease-refractory populations. Here we review the development of mosquito transgenesis and its application for malaria control, highlighting the transgenic expression of antiparasitic effector genes, inactivation of host factor genes, and manipulation of miRNAs and lncRNAs. Overall, from a malaria-control perspective, mosquito transgenesis is not envisioned as a stand-alone approach; rather, its use is proposed as a complement to existing vector-control strategies.
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Affiliation(s)
- Shengzhang Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Maria L Simões
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
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