Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus

Abstract

Changes in gene activity through epigenetic alterations induced by early environmental challenges during embryogenesis are known to impact the phenotype, health, and disease risk of animals. Learning how environmental cues translate into persisting epigenetic memory may open new doors to improve robustness and resilience of developing animals. It has previously been shown that the heat tolerance of male broiler chickens was improved by cyclically elevating egg incubation temperature. The embryonic thermal manipulation enhanced gene expression response in muscle (P. major) when animals were heat challenged at slaughter age, 35 days post-hatch. However, the molecular mechanisms underlying this phenomenon remain unknown. Here, we investigated the genome-wide distribution, in hypothalamus and muscle tissues, of two histone post-translational modifications, H3K4me3 and H3K27me3, known to contribute to environmental memory in eukaryotes. We found 785 H3K4me3 and 148 H3K27me3 differential peaks in the hypothalamus, encompassing genes involved in neurodevelopmental, metabolic, and gene regulation functions. Interestingly, few differences were identified in the muscle tissue for which differential gene expression was previously described. These results demonstrate that the response to embryonic thermal manipulation (TM) in chicken is mediated, at least in part, by epigenetic changes in the hypothalamus that may contribute to the later-life thermal acclimation.

Keywords: chicken; epigenetic; histone post-translational modification; reprogramming; thermal manipulation.

Figure 1

Characteristics of differential peaks. (A) Percentage of ChIP-seq H3K4me3 differential peaks across genomic features in hypothalamus relative to all differential peaks, obtained using GenomeFeatures. Promoter and downstream regions were defined upstream of Transcription Start and End Sites (TSS and TES, respectively), respectively. (B) Barplot showing the ratio for each feature between the percentage of differential peaks (DP) per feature relative to all DP and the percentage of all peaks per feature vs. all peaks for H3K4me3 in hypothalamus. The color legend is the same as in Figure 1A . (C) Venn diagram showing the number of genes containing a DP that are specific or common for H3K4me3 (K4) and H3K27me3 (K27) marks in hypothalamus (HT) and muscle (M) tissues. (D) Box plot of H3K4me3 relative enrichment to input at CRY2, CDKL5, OCLN, and RGS4 loci in Control (blue) and TM (red) replicates. Box boundaries represent the first and third quartiles. The median is indicated by the bold horizontal line dividing the interquartile range. Upper and lower ticks indicate the 10th and 90th percentiles. Corresponding p-values are indicated at the top of each graph

Figure 2

Functional analysis of hypothalamus and muscle genes bearing H3K4me3 and H3K27me3 differential peaks.The clustering heatmap plot of functional sets of gene ontology (GO) terms was obtained using ViSEAGO. From left to right are shown the major processes, the conditions defining the clusters (histone marks, tissues) defining the clusters, the cluster number, a heat map with the number of GO terms in each set and a dendrogram based on BMA semantic similarity distance and Ward’s clustering criterion.