INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues ofArabidopsis

Abstract

Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.

Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis

“…Interestingly, after being packaged so compactly it manages in such a way that their distal regulatory elements remain accessible to their target gene for their regulation. Chromatin-chromatin interaction has been identified as an important mechanism for such regulation ( Li et al, 2012 ; Sun et al, 2020 ; Yadav et al, 2021 ). A distal element can specifically interact with its target gene situated on the same or different chromosome by looping ( Dean, 2011 ).…”

Endosperm–Embryo Communications: Recent Advances and Perspectives

“…For example, it was shown that the timing of endosperm cellularization is epigenetically controlled [21]. Another study points out that the endosperm adopts a distinct high-order chromatin structure that differs from other cell types in other plant tissues [39]. It was speculated that genomic imprinting due to such unique arrangement in the endosperm chromatin structure allows the onset of gene activation of several important regulators prior to that of embryo [39].…”

“…Another study points out that the endosperm adopts a distinct high-order chromatin structure that differs from other cell types in other plant tissues [39]. It was speculated that genomic imprinting due to such unique arrangement in the endosperm chromatin structure allows the onset of gene activation of several important regulators prior to that of embryo [39]. However, understanding the detailed molecular mechanisms of the embryo-endosperm interaction requires more investigation.…”

Genome Maintenance Mechanisms at the Chromatin Level

“…The major obstacle has been technical difficulties in determining the chromatin state in plant cells. However, recent advanced techniques, such as high-throughput chromosome conformation method (Hi-C) and modification-specific intracellular antibodies (mintbodies), allow for the high-resolution detection of the chromatin structure and chromatin modifications in plants as well as in animals [ 108 , 115 , 116 ]. Further studies will identify the epigenetic factors involved in genome maintenance and local DNA repair/recombination processes through their interaction with repair machinery and cell-cycle regulators, thereby providing a new perspective on DDR mechanisms.…”