The regulatory genome of the malaria vector <i>Anopheles gambiae</i>: integrating chromatin accessibility and gene expression

Ruiz, José Luis; Ranford-Cartwright, Lisa; Gómez-Díaz, Elena

doi:10.1093/nargab/lqaa113

Cited by 16 publications

(35 citation statements)

References 97 publications

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“…The largest overlap with STARR-seq candidate enhancers occurred with the 19,321 H3K27ac ChIP-seq peaks, which are indicative of active enhancers and promoters, because 22.8% of the 3,288 A. coluzzii STARR-seq peaks overlapped with the H3K27ac ChIP-seq peaks. STARR-seq candidate enhancer peaks were also compared with data collected by ATAC-seq on midguts and salivary glands from malaria-infected A. gambiae samples ( Ruiz et al, 2021 ). Of the 3,288 A. coluzzii STARR-seq peaks, 33.6 and 35.3% overlapped with ATAC-seq peaks identified from midguts and salivary gland samples, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…H3K27ac, H3K4me3, H3K9ac, and H3K9me3 ChIP-seq peak boundaries from uninfected A. gambiae samples were downloaded from Supplementary Table S3 of ( Ruiz et al, 2019 ) and saved as four BED files containing the chromosome and peak position for each type of ChIP-seq experiment. ATAC-seq peaks for salivary glands and midguts from malaria-infected A. gambiae ( Ruiz et al, 2021 ) were downloaded from NIH GEO repository GSE152924. The ATAC-seq peaks were separated by tissue and saved as BED files containing the chromosome, and peak position information.…”

Section: Methodsmentioning

confidence: 99%

“…midguts and salivary glands from malaria-infected A. gambiae samples (Ruiz et al, 2021). Of the 3,288 A. coluzzii STARR-seq peaks, 33.6 and 35.3% overlapped with ATAC-seq peaks identified from midguts and salivary gland samples, respectively.…”

Section: Comparison Of Candidate Enhancers With Chip-seq Atac-seq and Computationally Predicted Peaksmentioning

confidence: 95%

“…In contrast, indirect approaches identify enhancers as correlates of genomic regions differing in their chromatin accessibility or histone modification markers. The indirect strategies such as ChIP-seq and ATAC-seq ( Gomez-Diaz et al, 2017 ; Ruiz et al, 2019 ; Farley et al, 2021 ; Ruiz et al, 2021 ) infer enhancer presence based on chromatin properties such as chromatin accessibility and histone modifications, but do not directly or functionally test or confirm enhancer activity. Methods used to survey histone signatures and chromatin accessibility may also detect transcriptional silencers, insulators and other features in addition to enhancers, and the functional category of detected elements is not necessarily distinguishable without additional work, for example direct functional assays.…”

Section: Introductionmentioning

confidence: 99%

“…STARR-seq has been implemented in Drosophila melanogaster ( Arnold et al, 2014 ), plants ( Benoit, 2020 ) and human ( Arnold et al, 2013 ), but has not been used in mosquitoes. Complementary approaches examining chromatin accessibility including FAIRE-seq ( Perez-Zamorano et al, 2017 ) and ATAC-seq ( Ruiz et al, 2021 ) have been used in Anopheles mosquitoes, as well as experiments for computational prediction of enhancers ( Asma and Halfon, 2019 ; Schember and Halfon, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Comparison Of Candidate Enhancers With Chip-seq Atac-seq and Computationally Predicted Peaksmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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Sex-, Tissue- and Stage-Specific Transgene Expression

Nolan¹,

Hammond²

2022

Transgenic Insects

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Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms

Lowe¹,

Wojciechowski

Ellis

et al. 2022

Nucleic Acids Research

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The honey bee genome has the capacity to produce three phenotypically distinct organisms (two diploid female castes: queen and worker, and a haploid male drone). Previous studies have implicated metabolic flux acting via epigenetic regulation in directing nutrition-driven phenotypic plasticity in the honey bee. However, the cis-acting DNA regulatory elements that establish tissue and polyphenism -specific epigenomes and gene expression programmes, remain unclear. Using a high resolution multiomic approach including assay for transposase-accessible chromatin by sequencing (ATAC-seq), RNA-seq and ChIP-seq, we produce the first genome-wide maps of the regulatory landscape across all three adult honey bee phenotypes identifying > 5000 regulatory regions in queen, 7500 in worker and 6500 in drone, with the vast majority of these sites located within intronic regions. These regions are defined by positive enrichment of H3K27ac and depletion of H3K4me3 and show a positive correlation with gene expression. Using ATAC-seq footprinting we determine queen, worker and drone -specific transcription factor occupancy and uncover novel phenotype-specific regulatory networks identifying two key nuclear receptors that have previously been implicated in caste-determination and adult behavioural maturation in honey bees; ecdysone receptor and ultraspiracle. Collectively, this study provides novel insights into key gene regulatory networks that are associated with these distinct polyphenisms in the honey bee.

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The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression

Cited by 16 publications

References 97 publications

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

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

Sex-, Tissue- and Stage-Specific Transgene Expression

Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms

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