Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize

Abstract

Distinct nucleosome (Nuc) architectures decode key regulatory information related to various cellular processes. However, how fragile nucleosomes (FNs) and resistant nucleosomes (RNs), with contrasting sensitivity to MNase cleavage, are reprogrammed in responses to cold treatment (COLD) are completely uncharacterized in plants. To this end, we conducted MNase-seq with light, medium and heavy MNase cleavage combined with multi-omics data analyses, including RNA-seq, chromatin immunoprecipitation sequencing (ChIP-seq), MNase hypersensitivity sequencing (MH-seq) and resequencing data, between COLD and CK. We found that COLD induced reprogramming of a subset of nucleosomes (Nucs) and had distinct impacts on occupancy changes of RNs/FNs in genic and TE regions, and dynamic changes of FNs/RNs as well. FNs/RNs and cold related interchangeable nucleosomes (Nucs) had distinct DNA sequence and epigenetic features, motif enrichment, and sequence diversity during maize evolution. Importantly, FNs and RNs had distinct biological relevance and exhibited differential relationships with gene expression. The position of +1 RNs and the occupancy of +1 FNs may play vital roles in the regulation of gene transcription. Thus, our study sheds new insights into how chromatin structures function in response to cold in plants, therefore providing some potential genomic loci for genome editing based bioengineering improvement of cold resistance.