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

Abstract

Background: 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. Results: 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 within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions: Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors inArabidopsis

“…With the former, transcription factors may already be bound to DNA but do not initiate transcription until their cognate signal activates them; with the latter, changes in chromatin accessibility may be related to long-distance transcriptional activation or facilitate other process such as DNA recombination or repair (54,55). The lack of direct correlation between DEGs and DARs has been previously noted in comparable analyses (56,57). We acknowledge that associating DARs with the closest transcriptional unit may to some extent bias the analysis, since genes can be regulated by distal regulatory elements (24,28,58), but to date there are no methods to directly associate changes in chromatin accessibility and changes in gene expression.…”

Wheat speciation and adaptation: perspectives from reticulate evolution

“…The studies of gene flow in Triticum species at the whole-genome level just got off the ground recently (Cheng et al 2019;Hao et al 2020b;Zhou et al 2020). By combing with massive data from gene expression (Ramírez-González et al 2018), epigenomics, and regulatory elements profiling (Gardiner et al 2015;Jordan et al 2020;Li et al 2019;Wang et al 2021b), answers to these questions will soon be available. The development of chromosome engineering and genome editing makes it possible to introduce target alleles, multi-gene editing, and directed evolution of protein (Cullot et al 2019;Zhu et al 2020).…”

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

“…In the allopolyploid wheat genome, 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 (Jordan et al 2020). In addition, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid wheat chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression (Lu et al 2020).…”

“…Thus, chromatin accessibility changes may provide new insight into the intrinsic nature of the regulation of transcription after plant autopolyploidization. Continuous efforts have focused on studying chromatin accessibility in plant allopolyploids (Jordan et al 2020;Lu et al 2020), implying that chromatin accessibility influences differential gene expression induced by allopolyploidization. However, characterization of open chromatin and investigation of their biological effects in autopolyploidization are lacking.…”