Long-range interactions between proximal and distal regulatory regions in maize

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.

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

“…The TE was considered as an enhancer, as shown by a transient in vivo assay [41]. The interactome data support this claim that there was a physical contact between Hopscotch and tb1 gene (Figure 5B) as have also been shown [31]. Interestingly, we also detected a direct physical contact between the tb1-DMR and tb1 gene itself in maize line B73 but missing in teosinte using our newly generated HiChIP data (Figure 5B).…”

“…Li et al, recently profiled genomic regions colocalized with H3K4me3 and H3K27ac, two well-known chromatin marks for promoters and enhancers [49,50], to define the interactome in maize [31]. We leveraged these interactome data to study the relationship between DMRs and physical interactions.…”

“…A MITE transposon insertion in the vgt1 locus was considered as the causal variation for the down regulation of the ZmRAP2.7, which was a transcription factor in the flowering time pathway [58]. Reanalysis of the published ChIP data revealed that the DMR colocalized with H3K27ac, the chromatin activation mark, and there existed a physical interaction between the DMR and vgt1 locus in maize [31] (Figure 4D). To examine the interaction status in teosinte, we then generated HiChIP data for a teosinte sample using the same tissue and antibodies (see materials and methods).…”

“…To isolate the nuclear from cross-linked tissues, we used the methods as described previously [31]. After obtaining the purified nuclear, we resuspended it in 0.5% SDS and used 10% Triton X-100 to quench it, and then performed digestion, incorporation, and proximity ligation reactions as previously described [74].…”

“…Ames 21809) interactome using HiChIP method with two antibodies of H3K4me3 and H3K27ac. Together with the analysis from previously published genome [29], transcriptome [30], methylome [6], and interactome [31] datasets, we estimated epimutation rates and the selection pressure in different timescales, investigated the DNA methylation landscapes and variations, detected differentially methylated regions (DMRs), characterized the genomic features that are related with DMRs, and functionally validated two DMRs that are associated with adaptation-traits. Our results suggested that DNA methylation is likely under weak selection during evolution.…”