Abstract
Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits. However, the pattern of three-dimensional chromatin interactions remains unclear in plants. Here we report the generation of chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data and the construction of extensive H3K4me3- and H3K27ac-centered chromatin interaction maps in maize. Results show that the interacting patterns between proximal and distal regulatory regions of genes are highly complex and dynamic. Genes with chromatin interactions have higher expression levels than those without interactions. Genes with proximal-proximal interactions prefer to be transcriptionally coordinated. Tissue-specific proximal–distal interactions are associated with tissue-specific expression of genes. Interactions between proximal and distal regulatory regions further interweave into organized network communities that are enriched in specific biological functions. The high-resolution chromatin interaction maps will help to understand the transcription regulation of genes associated with complex agronomic traits of maize.
Highlights
Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), an approach through enriching particular subset of interactions associated with chromatin modification or protein of interest, has the power of discovering specific protein-centered chromatin interactions at high resolution (
Our analysis provides a three-dimensional perspective to explore the regulatory mechanism of genes related to complex agronomic traits in maize
Summary
High-resolution maps of chromatin interaction in maize. To map the three-dimensional chromatin interactions associated with gene expression in maize, we adopted the existing ChIAPET protocol[7]. There was high reproducibility between replicates as indicated by the repeatability of biological replicates at different levels, including library reads and peaks of chromatin interaction PETs (Supplementary Fig. 1). We identified 13,999 H3K4me3-related and 20,979 H3K27ac-related high-confidence (false discovery rate (FDR)
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