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Prostate H3K4me3 ChIP-seq

ABSTRACT: Exposure to pesticide chlordecone is associated with high risk of prostate cancer.We hypothesised that changes in histone H3K4me3 could be involved in pathological processes in prostate induced by chlordecone. We exposed mice to chlordecone during embryonic development (E6.5-E15.5) and we analysed F1 progeny male epigenetic H3K4me3 marks in prostate tissue, as well as H3K4me3 in the prostate of F3 progeny to reveal the transgenerational effects resulting from the ancestral exposure to CD. We performed ChIP using H3K4me3 commercial antibody (Merck Millipore, 07-473) and pooled prostate tissues from 4 mice. DNA-protein complex was immunoprecipitated, eluted and DNA purified.

ORGANISM(S): Mus musculus

PROVIDER: GSE135199 | GEO | 2021/04/01

REPOSITORIES: GEO

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Histone mark modifications in murine ovary after gestational exposure to chlordecone

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2020-12-04 | E-MTAB-8880 | biostudies-arrayexpress

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Project description:Prostate H3K4me3 ChIP-seq and the transgenerational effects of pesticide chlordecone on prostate

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Transgenerational effect of Chlordecone [ChIP-seq]

Project description:The environmental factors such as pesticides could affect the developmental processes and cause the phenotypic changes. Moreover, the changes could be transferred to a subsequent generation via gametes. In this project we studied whether the pesticide chlordecone could cause the developmental effects and cause the transgenerational inheritance in outbred mouse strain. Mice were treated during development at dose 100 µg/kg/day and the progeny of exposed mice were crossed for three generations. The testes of the third generations males were used for anti-H3K4me3 ChiP-seq analysis. We used two biological replicates for each condition.

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Quantitative analysis of chromatin occupancy (ChIP-Seq) from wild-type mice and Kdm5c KO mice in standard conditions (H3K4me3, H3K4me1, and Kdm5C) or upon novelty exposure (H3K4me3), and control mice and Kdm5c ifKO mice in basal state (H3K4me3).

Project description:Chromatin immunoprecipitation (ChIP) experiments were conducted as previously described (Ito et al, 2013) using anti-H3K4me3 (Millipore, #07-473), anti-H3K4me1 (Abcam, #ab8895), or anti-Kdm5C (Iwase et al., 2016). Hippocampi derived from two different animals were pooled together for each sample and two independent biological replicates per condition were sequenced according to manufacturer instructions in a HiSeq2500 apparatus (Illumina, Inc). Information on library preparation method, size of the libraries, and mapping to reference genome can be found in Supplementary Material accompanying the manuscript. ChIP-seq reads were aligned to the mouse genome (Mus_musculus.GRCm.38.83) using bowtie2 (v2.2.9) (Langmead and Salzberg, 2012) and further processed using samtools (v1.3.1) (Li et al., 2009). Peak calling was performed using MACS2 (v2.1.0) (Zhang et al., 2008) with default parameters except for Kdm5c that were as follows: -q 0.01 --nomodel --extsize 131 --broad --broad-cutoff 0.1. Read counts on aligned bam files were performed using Rsubread (v1.22.3) (Liao et al., 2014). Differential peak methylation analysis for H3K4me3 chromatin mark was performed using DESeq2 (v1.10.0) (Love et al., 2014) of the bioconductor suite (Huber et al., 2015) in the R (v3.3) statistical computing platform. For consideration of differentially methylated regions between conditions, we used adjusted p-value < 0.05 as indicated in the manuscript.

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