Genome-wide identification of long range chromatin interactions involved in regulation of gene expression in Arabidopsis thaliana

Eukaryotic gene transcription is a complex and tightly regulated process, controlled by the functional interaction between the genes and its regulatory elements. Recently immense number of long-range chromatin interactions has been reported in human, but barely any information in plants. Here we identified genome-wide cis (intra-chromosomal), trans (inter-chromosomal) and multiple interactions in Arabidopsis thaliana through Hi-C and validated through 3C-PCR assay. We had demonstrated that genes interacting with enhancers are more expressed than the control gene group through in silico analysis and identified the binding sites for the known transcription factors (TFs) and enriched motifs in the interacting fragments. Our finding uncovers the previously unknown long range chromatin interactions in Arabidopsis and provides new insight into the interplay of regulatory elements and promoters.