プレゼンテーション演習

平成26年8月5日にお茶の水女子大学で行われた「三大学連携 機関リポジトリ研修会」におけるプレゼンテーション資

Additional file 1 of METHimpute: imputation-guided construction of complete methylomes from WGBS data

Figures S1-S12. (PDF 1832 kb

Life cycle of the human parasite <i>Schistosoma mansoni</i> including the five developmental stages presented in this work.

<p>The life cycle starts when eggs are in contact with freshwater and release a free-swimming larva, the miracidium. Miracidia seek out an intermediate host, a freshwater snail of the <i>Biomphalaria</i> genus, penetrate the tegument and transform into primary sporocysts. Sporocysts multiply asexually for approximately ten days and then mature into secondary sporocysts, which generate hundreds of cercariae, a second type of free-swimming larva. Cercariae actively seek a definitive mammalian host (rodent, primate or human) and penetrate the dermis of the host, reaching the vascular system. Schistosomula follow a complex maturation process, ultimately leading to adult worms. Male and female worms form pairs and migrate toward mesenteric veins, where a single female can lay approximately one-hundred eggs per day.</p

Description of frequency and covered chromatin state (kb) in miracidia, Sp1, cercariae, schistosomula and adults for H3K4me3, H3K27me3 or both (bivalent state), genome-wide and at TSS (Transcription Start Site of genes).

<p>Description of frequency and covered chromatin state (kb) in miracidia, Sp1, cercariae, schistosomula and adults for H3K4me3, H3K27me3 or both (bivalent state), genome-wide and at TSS (Transcription Start Site of genes).</p

Details of the antibodies used for ChIP-Seq.

<p>Details of the antibodies used for ChIP-Seq.</p

Description of the large differentially enriched regions (ranges, 10–100 kb) between cercariae and adults for each histone mark combination, as well as the number of annotated genes present in these regions and the number of regions without any coding genes (and their cumulated length).

<p>tRNAs genes were excluded from the gene counts. We also calculated the total length of these regions for each mark.</p

Description of the distributions of peaks (0.3–10 kb) between cercariae and adults for each histone mark.

<p>TSS = Transcription Start Site of genes. Multiple = H3K4me3 + H3K27me3 + H4K40me1 at the same locus. * In the case of H4K20me1, most of the marks were wide and often covering a large part of the gene, if not the whole gene.</p

Histone methyltransferase inhibitors block miracidium to primary sprorocyst transformation.

<p>Each treatment was set up in triplicate and parasites were cultured in CBSS with 1% DMSO at a controlled temperature of 26°C (in the dark). An ANOVA followed by <i>post hoc</i> analysis with Tukey’s multiple comparison test was performed to infer statistical significance; *p<0.005. <b>A</b>. Effect of 0.4 μM of A366, 2 μM of A366 and DMSO (negative control). <b>B</b>. Effect of 0.4 μM of GSK343, 0.4 μM of GSK343 and DMSO (negative control). <b>C.</b> Photomicrographs of miracidia to sporocyst transition in the presence of histone methyltransferase inhibitors. Miracidia transformed in the presence of DMSO (negative control) show normal transformation into sporocysts, but fail to lose their ciliated plates and do not develop into primary sporocysts in the presence of of A366 and GSK343 (10 μM). Representative images were acquired at low power (10X objective).</p

Parameters used in chromstaR for the detection of ‘peaks’ (300 bp to 10 kb wide).

<p><i>Bin size</i>: Size (in bp) in which the genome was fragmented to analyze the histone mark distribution. <i>Differential score</i>: value generated by chromstaR which provide an estimation on how divergent two bins are (0 = no difference, 1 = extremely different). <i>Minimum read count</i>: minimum number of reads which must be mapped inside a bin in order to take it into consideration. Minimum region length: minimum size (in bp) of consecutive adjacent bins with a different chromatin profile between samples. <i>False discovery rate</i> = minimum value to eliminate false positives. <i>Gap</i> = size of gaps which are allowed between two bins or group of bins with a different chromatin profile between samples. This is important, as gaps (where no reads are present) are frequent on <i>S</i>. <i>mansoni</i> genome. The reason for that is only uniquely mapped reads are used, but 47.73% of the genome is repetitive [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007066#ppat.1007066.ref036" target="_blank">36</a>].</p

Gene ontology overrepresentation depending on the type of chromatin enrichment.

<p>In short regions, we removed genes that had also been identified in the long region analysis. Symbol code: *Panther Pathways, ** = Biological Process, *** = Molecular Function, **** = Protein Class. Short regions: 300 bp– 10 kb. Long regions: 10 kb– 100 kb.</p