Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes.

Genome Biology
K. JordanEduard Akhunov

Abstract

Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs' chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located w...Continue Reading

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Methods Mentioned

BETA
histone acetylation
MNase digest
immunoprecipitation
MNase
MNase-seq
DNA-seq
PCR
chip

Software Mentioned

Bedtools
Illumina NGSC Toolkit
BedOps suite
HISAT2
iSeg
CACTA

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