Epigenomic Maps of Bread Wheat Chromosome 3B

In wheat, genome-wide epigenetic studies have long been hampered by the lack of a reference sequence. However, relationships between chromosome structure, gene expression and evolution were recently demonstrated with the publication of the first assembled reference sequence of the largest wheat chromosome 3B (Choulet et al., 2014). Taking advantage of this unique genomic resource, we initiated a project aiming at exploring the epigenetic landscape of this chromosome in order to better understand the organization of euchromatin vs. heterochromatin in a polyploid and highly repetitive genome.

Our strategy relies on a combination of immuno-precipitation targeting methylated DNA and 4 histone-related marks (H3K4me3, H3K4me2, H3K27me3, H3K36me3) with gene sequence capture and high-throughput sequencing. An average of 100 million paired-end reads per biological sample was generated and mapped on homeologous group 3 chromosome sequence assemblies. Paired-end reads mapped only on the 3B were selected for further analyses. Samples precipitated with methylated DNA showed a low coverage of 3%, confirming that genic regions are weakly methylated. A higher coverage of 37% was observed with the epigenetic mark H3K36me3, confirming the association of this mark with exons predominantly present in our captured sequences. Peak calling methods are currently under testing.

The combination of these epigenetic marks will allow us to define chromatin states along the bread wheat chromosome 3B and to investigate the impact of epigenetic marks on gene expression.