Gene Expression Atlas of Schistosoma Mansoni - Part I

This data set (part I of two) was obtained from the RNA-Seq analysis of transcriptomes of adult <i>Schistosoma mansoni </i>and their gonads. All genes represented by transcripts identified in the analysis were given by their Smp numbers. In addition to the average transcript amounts (Reads per Kilobase Million (RPKM), Y-axis) and occurrence, log₂ ratios were given as well as adjusted <i>P</i> values of pairing-, gender,- and tissue-related expression patterns.Custom codes to generate the data are given in a separate file. <br>Abbreviations used for the bar plots (X-axis) are:<br>bM (bisex males), paired males; sM (single-sex males), unpaired males; bF (bisex females), paired females; sF (single-sex females), unpaired females; bT, testis of bM; sT, testis of sM; bO, ovary of bM; sO, ovary of sO. <br

Sma-miR-277 and sma-miR-4989 belong to a gene cluster.

<p>(A) The genomic locus in Chromosome 4 of sma-miR-277 and sma-miR-4989 suggests they belong to a gene cluster. The average distance between genes (represented by coloured boxes) is 109 bases. Here the mature miRNAs (sma-miR2-277 and sma-miR-4989) and passenger miRNAs are represented with coverage plot and aligned reads from one of the small RNA libraries. (B) Predicted stem-loop structures for sma-miR-277 and sma-miR-4989 –individual cases. Mature miRNAs are located in the 3’-end of the hairpin. (C) Due to the cluster organisation of sma-miR-277/sma-miR-4989, it is likely that they are transcribed as one precursor RNA molecule. This figure represents the predicted stem-loop structure for sma-miR-277/sma-miR-4989 when arising from a larger transcript.</p

Sma-miR-277 family predicted targets downregulated in developing female parasites.

<p>Fold change expression (Log₂) of high confidence targets of sma-miR-277 family during the development of male and female worms in two conditions: paired (solid line red) and unpaired (dashed green). Black lines represent the mean expression of genes in paired (solid black line) and unpaired (dashed black line) worms.</p

Sma-miR-4989 is expressed in the cells surrounding the oesophagus and cells of the tegument in adult worms.

<p>Whole mount <i>in situ</i> hybridisation for (A) <i>cathepsin B</i>, (B) sma-miR-124a-3p (<i>124a</i>), and (C) sma-miR-4989. (D) Fluorescence <i>in situ</i> hybridisation showing the colocalization of sma-miR-4989 with four co-expressed tegument-specific mRNAs (<i>calpain</i>, <i>npp-5</i>, <i>annexin</i> and <i>gtp-4</i>). Nuclei are stained with DAPI and shown in blue. Anterior of worms is to the left in A-C. Scale Bars: A-C 100 μm; D 10 μm.</p

MiRNA target prediction based on both miRNA-unaware and miRNA-guided approaches.

<p>(A) Sylamer enrichment landscape plots for 7mers in male (top) and female (bottom) expression data. The x-axis represents a list of transcripts, ranked from more expressed in juveniles to more expressed in adults. The y-axis represents the significance values acquired for each 7mer at each position in the ranked list of transcripts. Coloured boxes represent the fraction of transcripts significantly (adjusted p-value < 0.01) differentially expressed between juvenile and adult worm as found using DESeq2. These transcripts were subsequently filtered based on the presence of the 7mers TGCATTT or GCATTTA as found by Sylamer. The resulting sets are referred to as Male and Female Sylamer genes. (B) Venn Diagram showing the intersection of Male and Female Sylamer genes with schistosome-conserved miRNA targets as found using TargetScan with conservation + miRanda. The overlap represents transcripts with highly conserved sma-miR-277 target sites across the three <i>Schistosome</i> spp (S. <i>mansoni</i>, <i>S</i>. <i>haematobium</i> and S. <i>japonicum</i>) that are also significantly down regulated during worm development.</p

High confidence targets of the sma-miR-277 family identified with a combined approach (Sylamer, miRanda and TargetScan with conservation).

<p>F = female; M = male.</p

Sma-miR-4989 is significantly up-regulated during male and female maturation.

<p>Fold change expression of sma-miR-4989 during development of juvenile to adult worms in male (blue bars) and females (red bars) as measured by RT-qPCR. Samples were collected at the time points (days post infection) indicated in the x-axis from murine hosts infected with pooled (mixed sex) cercariae. Each barplot represents the mean of three biological replicates. T-tests were performed between 49 d.p.i. and 28 d.p.i. and were both significant with p-value ≤ 0.01. Error bars show the standard error of the mean, based on three biological replicates.</p