Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response

Abstract

The innate immune response of Anopheles gambiae involves the transcriptional upregulation of effector genes. Therefore, the cis-regulatory sequences and their cognate binding factors play essential roles in the mosquito’s immune response. However, the genetic control of the mosquito’s innate immune response is not yet fully understood. To gain further insight on the elements, the factors and the potential mechanisms involved, an open chromatin profiling was carried out on A. gambiae-derived immune-responsive cells. Here, we report the identification of cis-regulatory sites, immunity-related transcription factor binding sites, and cis-regulatory modules. A de novo motif discovery carried out on this set of cis-regulatory sequences identified immunity-related motifs and cis-regulatory modules. These modules contain motifs that are similar to binding sites for REL-, STAT-, lola- and Deaf1-type transcription factors. Sequence motifs similar to the binding sites for GAGA were found within a cis-regulatory module, together with immunity-related transcription factor binding sites. The presence of Deaf1- and lola-type binding sites, along with REL- and STAT-type binding sites, suggests that the immunity function of these two factors could have been conserved both in Drosophila and Anopheles gambiae.

Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection

“…As a validation of our strategy to predict regulatory sites and TF binding, we reported the overlap between FAIRE-seq peaks determined in A. gambiae hemocytes in a previous study [27], with histone modifications ChIP-seq peaks in malaria-infected tissues. Even if the experimental conditions and cell types in the two studies are not comparable, we found 9136 MACS2 ChIP-seq peaks and 2690 diffReps regions (10% and 17% of the total, respectively) that intersected with FAIRE-seq peaks.…”

“…Cis-regulatory elements are implicated in the control of gene expression because they contain specific DNA sequences that are binding sites for transcription factors and other chromatin remodelers, and often appear enriched in certain histone modifications. These elements are well mapped in Drosophila [48], but very few have been identified in mosquitoes [27, 49]. The analysis of differential ChIP-seq peaks located at promoters or gene bodies identified significant enrichment in binding sites that match consensus sequences of TFs previously described in Drosophila , including transcription factor deformed epidermal autoregulatory factor-1 (Deaf1) [50].…”

“…In a previous study, we characterized genome-wide occupancy patterns of various histone modifications and established a link between hPTMs and gene expression profiles in midguts and salivary glands of the human malaria vector A. gambiae [26]. In addition, recent reports revealed the role of various transcription factors, such as REL2, lola and Deaf1, in A. gambiae immune defenses [27, 28]. These findings have set the stage for additional studies aimed at understanding how the chromatin landscape is altered in P. falciparum -infected mosquito tissues and what are the molecular players involved in these malaria-induced responses.…”

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

“…aegypti and An. gambiae tissues (39,40). Among the differentially-expressed genes that seem to be regulated by differentially accessible CREs and that contain the above motifs, we found examples of immune-related genes (62), such as srpn6 or gam1, and genes that we identified in our previous study as Plasmodiumresponsive (42), such as the defensin def1.…”

“…aegypti and An. gambiae mosquitoes by FAIRE-seq (39)(40)(41). Chromatin accessibility at regulatory sites is generally of open CREs at introns respective to promoters, and vice versa: genes with higher intronic content contain more intronic THSs, and moreover, chromatin accessibility at these regions also correlates with higher accessibility of the cognate promoters and higher gene expression.…”