Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments

文献类型： 外文期刊

第一作者： Shao, Dan

作者： Shao, Dan;Yang, Yu;Shao, Dan;Shi, Shourong;Tong, Haibing

作者机构：

关键词： three-dimensional genome; chicken; topologically associated domains; A; B compartments; extreme environments

期刊名称：GENES （ 影响因子：4.141； 五年影响因子：4.474 ）

ISSN：

年卷期： 2022 年 13 卷 12 期

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收录情况： SCI

摘要： The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation.

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