Project description:To reveal the correlation between epigenomic diversity and genomic SNVs, we first identified SNPs between T4 with other eleven Trichinella species. In total, we obtained 5,395,250 common SNVs across the twelve Trichinella species.
Project description:This experiment used ChIP-seq technology to create a genome-wide profile of histone marks in normal human pancreatic islets. In the current work we analyzed two histone marks associated with gene expression (H3K4me3, H3K4me1) and marks associated with gene repression (H3K27me3). Each mark was anayzed using samples obtained from four donors (n=4). Chromatin Immunoprecipitations (ChIPs) for histone marks were performed using specific anti-histone antibodies. Enrichment of each sample was calulated with respect to its individual input using qPCR. Samples were sequenced with Solexa and sequenced DNA from both Input (n=4) and ChIP (n = 4) samples were aligned to the NCBI Genome Build 36.1 Hg18 to determine regions that were enriched for binding by modified histones. ArrayExpress Release Date: 2010-02-17 Publication Title: Genome-wide analysis of histone modifications in human pancreatic islets Publication Author List: Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, Liu C, Naji A, Kaestner KH Person Roles: submitter Person Last Name: Bhandare Person First Name: Reena Person Email: bhandare@mail.med.upenn.edu Person Phone: Person Address: 771 Clinical Research Building, 415 Curie Blvd, Philadelphia, PA, 19104 Person Affiliation: Department of Genetics, University of Pennsylvania
Project description:As the most studied type of epigenetic modifications found in many taxa, DNA methylation has been confirmed to play a crucial role in transposon silencing, transcriptional regulation and thus phenotypic variation, as well as rapid adaption to changing environments. To fully understand the methylome variation in Trichinella, here, we report 12 single-base resolution methylomes of three life stages using WGBS. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel. Moreover, we also reveal associations between methylation divergence and genetic basis, including nucleotide variant and structural variation.