Meta-analysis of the pathogenLeishmania donovani’s transcriptome reveals multiple modes of regulation including two reciprocally regulated gene modules

Abstract

ABSTRACTLeishmania donovanicauses a neglected tropical disease called visceral leishmaniasis. Additionally, leishmaniasis also manifests opportunistically, under conditions of immune compromise. The continued non-availability of effectively curative interventions (drugs or vaccines) against this disease necessitates a deeper knowledge ofLeishmaniabiology in order to evolve novel strategies against the disease. We have used a meta-analysis approach to analyseLeishmania’s composite genetic network rather than investigating individual candidate genes. We performed Weighted Gene Co-expression Network Analysis (WGCNA) on publicly availableLeishmania donovanitranscriptome data to identify co-regulatory genetic modules. This clustering ofLeishmania donovanitranscriptomes revealed that genes fall in 30 distinct co-regulated modules with 32 to 3012 genes. In order to analyse the distribution of genes inLeishmaniagene modules, we queried the enrichment or depletion of various annotation-qualifiers in the modules. We observed that several modules are specifically and individually enriched or depleted for annotation qualifiers derived from GO-annotation and KEGG-pathways and are differentially associated with life-phases and experimental conditions. Additionally, modules are also enriched or depleted for sequence based genetic features such as chromosomal location, location on co-transcriptional segment, rank of transcript from initiation of transcription, skewed usage of known RNA Binding Protein motifs. Classification of uncharacterized transcripts into co-regulatory modules provides insights in their probable characteristics, aiding future empirical investigation. Strikingly, two of the modules have reciprocal features including individual associations with logarithmic or stationary growth phases ofLeishmania, two important life-phases that simulate the vector-dwelling pro-cyclic and the pre-infective meta-cyclic forms. Collectively, our analyses ofLeishmaniaco-regulated gene modules is suggestive of additional regulatory modes over the mere differential mRNA stabilization.