2014 October 14 | Mitchell Guttman and John L. Rinn
The article reviews the emerging understanding of the regulatory principles of large non-coding RNAs (ncRNAs). It highlights the diverse functions of ncRNAs, which extend beyond their role as messengers between genes and proteins. The authors discuss the discovery and characterization of various large ncRNAs, such as *H19*, *XIST*, *Airm*, *Tug1*, *NRON*, and *HOTAIR*, and their involvement in processes like X chromosome inactivation, imprinting control, and gene expression regulation. They emphasize the importance of chromatin signatures in identifying ncRNA genes and the role of ncRNAs in modulating chromatin states and transcriptional regulation. The article also explores the concept of cis- and trans-regulatory mechanisms, suggesting that while some ncRNAs may act as cis-regulators, most function as trans-regulators. Additionally, it discusses the formation of RNA-protein interactions and the potential modular nature of large ncRNAs, where discrete domains interact with specific protein complexes to achieve regulatory functions. The authors propose that large ncRNAs can serve as molecular scaffolds, bringing together multiple regulatory components to form complex regulatory circuits. Finally, they outline the challenges and future directions in understanding the modular RNA regulatory code and the potential for synthetic engineering of ncRNAs to achieve specific regulatory roles.The article reviews the emerging understanding of the regulatory principles of large non-coding RNAs (ncRNAs). It highlights the diverse functions of ncRNAs, which extend beyond their role as messengers between genes and proteins. The authors discuss the discovery and characterization of various large ncRNAs, such as *H19*, *XIST*, *Airm*, *Tug1*, *NRON*, and *HOTAIR*, and their involvement in processes like X chromosome inactivation, imprinting control, and gene expression regulation. They emphasize the importance of chromatin signatures in identifying ncRNA genes and the role of ncRNAs in modulating chromatin states and transcriptional regulation. The article also explores the concept of cis- and trans-regulatory mechanisms, suggesting that while some ncRNAs may act as cis-regulators, most function as trans-regulators. Additionally, it discusses the formation of RNA-protein interactions and the potential modular nature of large ncRNAs, where discrete domains interact with specific protein complexes to achieve regulatory functions. The authors propose that large ncRNAs can serve as molecular scaffolds, bringing together multiple regulatory components to form complex regulatory circuits. Finally, they outline the challenges and future directions in understanding the modular RNA regulatory code and the potential for synthetic engineering of ncRNAs to achieve specific regulatory roles.