Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii .

Autor:	Holm I; Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France., Nardini L; Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France., Pain A; 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., Bischoff E; Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France., Anderson CE; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States., Zongo S; Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso., Guelbeogo WM; Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso., Sagnon N; Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso., Gohl DM; University of Minnesota Genomics Center, Minneapolis, MN, United States.; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States., Nowling RJ; Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering (MSOE), Milwaukee, WI, United States., Vernick KD; Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France., Riehle MM; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in genetics [Front Genet] 2022 Jan 10; Vol. 12, pp. 785934. Date of Electronic Publication: 2022 Jan 10 (Print Publication: 2021).
DOI:	10.3389/fgene.2021.785934
Abstrakt:	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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Holm, Nardini, Pain, Bischoff, Anderson, Zongo, Guelbeogo, Sagnon, Gohl, Nowling, Vernick and Riehle.)
Databáze:	MEDLINE
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