Genome-wide high-throughput chromosome conformation capture analysis reveals hierarchical chromatin interactions during early somatic embryogenesis

作者：Yan Chen, Dejian Xie, Xiangwei Ma, Xiaodong Xue, Mengyu Liu, Xuechen Xiao, Chunwang Lai, Xiaoping Xu, Xiaohui Chen, Yukun Chen, Zihao Zhang, Xu XuHan, Zhongxiong Lai, Yuling Lin · 发表于：PLANT PHYSIOLOGY · 年份：2023 · DOI：10.1093/plphys/kiad348 · 被引用次数：14 · 研究领域：Chromosomal and Genetic Variations、Plant tissue culture and regeneration、Plant Molecular Biology Research

Somatic embryogenesis (SE), like zygotic embryo development, is a progressive process. Early SE is the beginning of a switch from a somatic to an embryogenic state and is an important stage for initiating chromatin reprogramming of SE. Previous studies suggest that changes in chromatin accessibility occur during early SE, although information on the 3D structure of chromatin is not yet available. Here, we present a chromosome-level genome assembly of longan (Dimocarpus longan) using PacBio combined with high-through chromosome conformation capture scaffolding, which resulted in a 446 Mb genome assembly anchored onto 15 scaffolds. During early SE, chromatin was concentrated and then decondensed, and a large number of long terminal repeat retrotransposons (LTR-RTs) were enriched in the local chromatin interaction region, suggesting LTR-RTs were involved in chromatin reorganization. Early SE was accompanied by the transformation from A to B compartments, and the interactions between B compartments were enhanced. Results from chromatin accessibility, monomethylation of histone H3 at lysine 4 (H3K4me1) modification, and transcription analyses further revealed a gene regulatory network for cell wall thickening during SE. Particularly, we found that the H3K4me1 differential peak binding motif showed abnormal activation of ethylene response factor transcription factors and participation in SE. The chromosome-level genomic and multiomics analyses revealed the 3D conformation of chroma...