Project description:Nucleosome organization is critical for the regulation of gene expression, and genome-scale mapping of nucleosomes has revealed a conserved, highly ordered pattern in nucleosome positioning. Most genome-wide studies have been performed in model organisms and little is known about nucleosome positioning in evolutionarily divergent eukaryotes. We generated a high-resolution nucleosome map of the protozoan parasite Toxoplasma gondii from four high quality MNase-Seq datasets. T. gondii nucleosomes are organised in phase around the transcription start sites (TSSs) with a canonical pattern that is conserved across eukaryotes. Nucleosome occupancy in exons is influenced by several factors, including GC content, length of exons and strength of splice sites. Poly(dA:dT) is enriched at the +1 nucleosome rather than nucleosome-free regions (NFRs) and serves as the key sequence associated with nucleosome formation in T. gondii. Motif analysis of sequences in NFR1, adjacent to the transcription start site, revealed enrichment of DNA-binding motifs recognized by members of the plant-like ApiAP2 transcription factor family that is conserved across Apicomplexa. Genes associated with the two most common motifs are enriched in genes upregulated during two major waves of mRNA accumulation within the cell cycle. Genome-wide peaks from T. gondii assays for transposase-accessible chromatin using sequencing (ATAC-seq) coincide with NFR1, consistent with the enrichment of T. gondii open chromatin regulatory regions localizing to close to transcription initiation sites. Finally, by integrating the map of nucleosome positions with ChIP-seq we suggest that nucleosome positioning and placement of histone variants and histone modifications play roles in splicing of genes in T. gondii.
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum and Toxoplasma gondii. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of T. gondii VEG strain. The aim is to make comparative transcriptional landscape maps of Neospora and Toxoplasma at different time points at different life cycle stages and compare levels of expression of orthologous genes in these two organisms.
Project description:This SuperSeries is composed of the following subset Series: GSE11437: Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array GSE11514: Expression QTL mapping of Toxoplasma gondii genes, Tachyzoite array Keywords: SuperSeries Refer to individual Series
Project description:Expression profile microarray of human foreskin fibroblast cell comparing control untreated HFF cell with HFF cell infected with ME49 strain.Study on Toxoplasma gondii infection of HFF cell LncRNAs expression, for further studies on the differential exprssion of LncRNAs in HFF cell against the infection of Toxoplasma gondii research provide the basic function.
Project description:Two samples, 0hr and 72hr, were used to generate tachyzoite and bradyzoite transcriptional data from tissue-cultured Toxoplasma gondii strain Prugniaud, respectively.
