Characterization Of The Nanci-Nkx2.1 Locus: A Novel Role For Lncrnas In Buffering Transcription Factor Expression

Long noncoding RNAs (lncRNA) are capable of regulating gene transcription and other complex biological processes. However, the role of lncRNAs in vivo, especially within the contexts of lung development and homeostasis, are still poorly understood. In this work, I establish a new paradigm where in a subset of lncRNAs act as rheostats to buffer expression of their neighboring transcription factors (TFs) in vivo. Through analysis of the embryonic and adult lung transcriptome, I identified lncRNAs expressed in the lung and determined that lncRNAs are enriched near TF loci. Furthermore, lncRNAs and their neighboring TFs often share similar expression patterns, suggesting a regulatory relationship between the two genes. To test this hypothesis I used multiple mouse models, molecular, and proteomic techniques to further characterize the regulatory relationship between the lncRNA NANCI and its neighboring TF Nkx2.1, a critical regulator of pulmonary development. These experiments revealed that NANCI acts in cis to promote Nkx2.1 expression at the transcriptional level, while Nkx2.1 directly represses NANCI expression. In Nkx2.1 heterozygotes this negative feedback loop leads to increased expression of NANCI, which is sufficient to normalize Nkx2.1 expression and lung function. However, concurrent in trans mutations of NANCI and Nkx2.1 disrupt the buffering loop between these genes causing persistent Nkx2.1 deficiency. This in turn leads to defective pulmonary development as well as progressive degeneration and reprogramming of the adult lung epithelium. Altogether this work provides insight into regulation of the TF Nkx2.1 and a model for studying the in vivo function of lncRNAs associated with other critical TFs