Study : Modified Hi-C reveals distinct chromatin architecture in endosperm and leaf of Arabidopsis
Modified Hi-C reveals distinct chromatin architecture in endosperm and leaf of Arabidopsis
Higher-order chromatin structure undergoes dramatic changes in response to various developmental and environmental signals, wherein distinct cell types posses specific chromatin organization. High throughput chromatin conformation capture assays (Hi-C) allows study of higher-order chromatin structure; however, it requires a large number of cells. This requirement has so far limited the establishment of cell type-specific higher-order chromatin structure in the plant. To overcome this limitation, we modified the Hi-C protocol (mHi-C) to be applicable to a limited amount of starting material. For this, mHi-C libraries were generated from INTACT-purified endosperm and leaf nuclei. Correlation plots showed that our mHi-C data from INTACT-leaf accurately reiterate chromatin interaction patterns derived from conventional leaf Hi-C data. We further identified compacted structural domains (CSDs) and loose structural domains (LSDs) in leaf and endosperm and their differential patterns revealed distinct higher-order chromatin organization in leaf and endosperm. Our analysis revealed that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We discovered increased chromatin interactions frequencies in the endosperm in comparison to leaf tissue. Using cell-specific Hi-C and INTACT-RNA-seq, on a genome-wide scale higher expression of self-looped interacting genes was observed. It was further identified that interacting intergenic regions act as a negative regulator and influence the gene expression in a specific cells in the plant. Our study provides evidence that the higher-order chromatin structure differs between cell types in plants and these interactions could influence the transcription activity positively as well as negatively. Overall design: Two independent biological replicates of the mHi-C library from Arabidopsis endosperm were generated in order to examine the tissue-specific spatial organization of chromatin. Two additional independent biological replicates from 4-week-old leaves of Arabidopsis were also processed with the purpose of corroborating the data generated by our mHi-C method and comparing them with previously published conventional Hi-C data from leaf.