Decoding chromatin-associated RNA (caRNA) interaction networks: from genome-wide dynamic capture to epigenetic...

Chromatin-associated RNAs (caRNAs) serve as central hubs for regulation within the cell nucleus and are involved in key biological processes such as transcriptional homeostasis, chromatin remodeling, and transgenerational inheritance. In recent years, the development of various genome-wide RNA-chromatin interaction capture technologies has made it possible to resolve the spatial interaction networks between caRNAs and chromatin with high precision. This paper systematically reviews the concepts, functions, and interaction patterns of caRNA, and provides a comprehensive overview of the principles, characteristics, technical biases, and applicable scenarios in the fields of targeted and non-targeted identification technologies. Building on this foundation, this paper conducts a comparative analysis of caRNA regulatory mechanisms in animals and plants across four functional dimensions: the organization of three-dimensional chromatin topology, RNA modification-mediated epigenetic regulatory switches, the transmission of environmental and transgenerational signals, and the pathological mechanisms associated with caRNA network dysregulation. Through this comparative analysis, this paper reveals the common characteristics of caRNA-mediated functional regulation in animals and plants, as well as lineage-specific adaptive strategies, and discusses the challenges and future directions in this field regarding single-cell resolution, AI-assisted data analysis, and translational applications.