25 research outputs found
Additional file 2: Table S1. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
Overrepresentation hypergeometric test on Hypermethylated-DMRs and Hypomethylated-DMRs. (XLSX 9Â kb
Per què PsycINFO? (guia per als alumnes del 1er. Curs del Grau de Psicologia) [vídeo]. Setembre 2014
Orthologous genes identified between I. batatas (Sp1) and I. trifida (Sp2). (XLSX 394 KB
Additional file 8: Figure S5. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
IGV view of a hypermethylated-DMR (A) and a hypomethylated (B). (TIFF 173Â kb
Additional file 5: Table S3. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
Hypermethylated- and hypomethylated-DMRs flanking within 2000Â bp of annotated genes. (XLSX 204Â kb
Additional file 4: Table S2. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
GO analysis of hypermethylated- and hypomethylated-DMRs. (XLSX 824Â kb
Pathways illustrating the network of genomic loci involved with (A & B) Regions undergoing increase in 5mC content and (C & D) decrease in 5mC contents, upon simulated microgravity.
<p>Pathways illustrating the network of genomic loci involved with (A & B) Regions undergoing increase in 5mC content and (C & D) decrease in 5mC contents, upon simulated microgravity.</p
Pathways illustrating the network of genomic loci involved with (A & B) Regions undergoing increase in 5hmC content and (C & D) differential gene expression.
<p>Pathways illustrating the network of genomic loci involved with (A & B) Regions undergoing increase in 5hmC content and (C & D) differential gene expression.</p
Schematic illustration of the bioinformatics pipeline for MeDIP-seq, hMeDIP-seq and RNA-seq analysis used in our study to understand the DNA methylation and hydroxymethylation and gene expression patterns induced by simulated microgravity.
<p>All steps were done in parallel in TK6 subjected to “simulated” microgravity and static controls under the influence of Earth’s gravitational force.</p
A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells
<div><p>Cells alter their gene expression in response to exposure to various environmental changes. Epigenetic mechanisms such as DNA methylation are believed to regulate the alterations in gene expression patterns. <i>In vitro</i> and <i>in vivo</i> studies have documented changes in cellular proliferation, cytoskeletal remodeling, signal transduction, bone mineralization and immune deficiency under the influence of microgravity conditions experienced in space. However microgravity induced changes in the epigenome have not been well characterized. In this study we have used Next-generation Sequencing (NGS) to profile ground-based “simulated” microgravity induced changes on DNA methylation (5-methylcytosine or 5mC), hydroxymethylation (5-hydroxymethylcytosine or 5hmC), and simultaneous gene expression in cultured human lymphoblastoid cells. Our results indicate that simulated microgravity induced alterations in the methylome (~60% of the differentially methylated regions or DMRs are hypomethylated and ~92% of the differentially hydroxymethylated regions or DHMRs are hyperhydroxymethylated). Simulated microgravity also induced differential expression in 370 transcripts that were associated with crucial biological processes such as oxidative stress response, carbohydrate metabolism and regulation of transcription. While we were not able to obtain any global trend correlating the changes of methylation/ hydroxylation with gene expression, we have been able to profile the simulated microgravity induced changes of 5mC over some of the differentially expressed genes that includes five genes undergoing differential methylation over their promoters and twenty five genes undergoing differential methylation over their gene-bodies. To the best of our knowledge, this is the first NGS-based study to profile epigenomic patterns induced by short time exposure of simulated microgravity and we believe that our findings can be a valuable resource for future explorations.</p></div
Peak signals visualized on common bean chromosomes by using Genome Viewer.
<p>Comparative visualization of a representative region on chromosome 11 in rust-inoculated common bean at 12 hai with mock-inoculated sample as background for H3K9<sub>me2</sub> and H4K12<sub>ac</sub> modifications using Integrative Genomics Viewer (IGV).</p