Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection

Abstract

BackgroundInfection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and, in particular, of the epigenetic basis for these changes. We have examined genome-wide distribution maps of H3K27ac, H3K9ac, H3K9me3 and H3K4me3 by ChIP-seq and the transcriptome by RNA-seq, of midguts from Anopheles gambiae mosquitoes blood-fed uninfected and infected with natural isolates of the human malaria parasite Plasmodium falciparum in Burkina Faso.ResultsWe report 15,916 regions containing differential histone modification enrichment between infected and uninfected, of which 8339 locate at promoters and/or intersect with genes. The functional annotation of these regions allowed us to identify infection-responsive genes showing differential enrichment in various histone modifications, such as CLIP proteases, antimicrobial peptides-encoding genes, and genes related to melanization responses and the complement system. Further, the motif analysis of regions differentially enriched in various histone modifications predicts binding sites that might be involved in the cis-regulation of these regions, such as Deaf1, Pangolin and Dorsal transcription factors (TFs). Some of these TFs are known to regulate immunity gene expression in Drosophila and are involved in the Notch and JAK/STAT signaling pathways.ConclusionsThe analysis of malaria infection-induced chromatin changes in mosquitoes is important not only to identify regulatory elements and genes underlying mosquito responses to P. falciparum infection, but also for possible applications to the genetic manipulation of mosquitoes and to other mosquito-borne systems.Electronic supplementary materialThe online version of this article (10.1186/s13072-018-0250-9) contains supplementary material, which is available to authorized users.

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

“…Normalized counts were comparable between infections and higher in SGs (Supplementary Figure S5D). We also observed high correlation (~75%) between the RNA-seq data in this study and data from our previous study (42) (Supplementary Figure S5E). We categorized normalized counts in high, medium or low groups as described above (Hmisc::cut2 R function).…”

“…To test such a relationship between chromatin accessibility and epigenetic states, we examined ATAC-seq signal relative to ChIP-seq peaks for various hPTMs that we obtained from our previous study on P. falciparum-infected and non-infected An. gambiae midguts (42). ATAC-seq nucleosome-free signals appeared more enriched (compared to a random distribution) at peaks of H3K9ac, H3K27ac, and to a lesser extent H3K4me3, and depleted at H3K9me3 peaks (Supplementary Figure S1G).…”

“…Among the target genes with a THS annotated, we found 241 important immune-related genes such as stat2, rel2 and members of the TEP family (62) ( Supplementary Table S4), as well as 671 genes that we reported in an earlier study as Plasmodium-responsive by comparing P. falciparuminfected and non-infected An. gambiae midguts (42). These include, for example, genes encoding CLIP serine proteases, argonaute 1 and the defensin DEF1 (Supplementary Table S4).…”

“…There was also a significant positive correlation between the changes in accessibility and the differential expression of the annotated genes (Spearman test: rho 0.60, P < 0.001) ( Figure 4D). The lrim1 gene (AGAP006348), that encodes for a leucine-rich immune protein, is a good example of a Plasmodium-responsive gene (42), that has an experimentally validated enhancer and that was differentially accessible between tissues. Here, we observed the gene to be more highly expressed in SGs, and this was associated with a DiffBind region upstream of the promoter, which was more accessible in SGs, and that coincided with the enhancer experimentally validated by others (44) ( Figure 4E).…”

Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii

“…Enhancer discovery in mosquitoes is limited to a few previous studies using indirect methods based on detection of chromatin properties to infer enhancer locations 32–34 . However, almost nothing is known about mosquito enhancer genetic variation and influence on vector phenotypes, and thus it is necessary to first develop the baseline criteria to distinguish and study enhancers in A. coluzzii .…”