Function of the IncRNA transcriptome in lung development and regeneration

 描述(申请人提供)：肺部疾病是西方世界发病率和死亡率的第三大原因。过去20年的密集研究表明，许多对肺发育至关重要的通路在成人疾病状态下重新激活。最近，非编码RNA被证明在调节肺发育中发挥关键作用。此外，许多miRNAs的表达在成人疾病状态下是不受调控的，这表明在修复/再生/疾病进展中可能起到作用。这导致了一种假设，即非编码RNA转录组可能构成一组核心调控因子，促进损伤后和疾病重塑期间的发育和适当的修复/再生。长非编码RNA(LncRNAs)被认为在调节基因表达方面发挥关键作用，最近的研究表明，它调节从维持多能性到调节神经、眼睛和心脏发育的各种发育过程。LncRNAs通常被定义为不编码多肽的大于200个碱基对的RNA转录本。许多lncRNA是多聚腺苷化的，含有多个外显子-内含子结构。一些lncRNA与蛋白质编码基因重叠，而另一些则以独立的转录本存在于基因之间。LncRNAs的功能机制尚不清楚，但一些研究表明，它们可以作用于顺式或反式，抑制或增强基因的表达，可能是通过与染色质重塑复合体，如多梳抑制物复合体2(PRC2)的相互作用实现的。这表明lncRNAs在定义和调节表观遗传格局以控制基因表达方面发挥了作用。我们最近使用RNAseq和ChIPseq分析对胚胎和成人肺中表达的lncRNAs进行了高通量基因组筛选。在这个屏幕中，我们选择关注基因间的lncRNAs，因为它们在调节基因转录方面具有先前报道的重要性。我们利用这些数据确定了一个包含363个lncRNA的肺LncRNA转录组，这些转录组可能在肺部生物学中发挥关键作用。该数据库为鉴定和鉴定新的和重要的肺基因转录和发育调控因子提供了新的资源。我们的初步数据显示，肺中的lncRNAs经常在转录因子和信号分子附近转录，这些信号分子对肺发育和体内平衡至关重要，包括Nkx2.1、Foxf1和Foxa2，其表达模式与这些基因相似。特别是，我们发现与Nkx2.1(Nanci)相关的一个新的lncRNA作用于Nkx2.1的上游，调节肺基因的表达。这些发现将对我们理解非编码转录组在肺部发育、疾病和修复/再生中的作用产生广泛的影响。

 DESCRIPTION (provided by applicant): Pulmonary disease is the number three cause of morbidity and mortality in the Western world. Intense investigation over the last two decades has shown that many of the pathways critical for lung development are reactivated in adult disease states. Recently, non-coding RNAs have been demonstrated to play key roles in regulating lung development. Moreover, expression of many miRNAs is disregulated in adult disease states suggesting a potential role in repair/regeneration/diseases progression. This has led to the hypothesis that the non-coding RNA transcriptome may constitute a core set of regulatory factors that promote both development and proper repair/regeneration after injury and during disease remodeling in the lung. Long non-coding RNAs (lncRNAs) are thought to play key roles in regulating gene expression and, in recent studies, have been shown to regulate various developmental processes from maintaining pluripotency to regulating neural, eye, and cardiac development. LncRNAs are generally defined as RNA transcripts greater than 200 basepairs that do not encode for a polypeptide. Many lncRNAs are polyadenylated and contain multiple exon-intron structures. Some lncRNAs overlap with protein coding genes while others exists as independent transcripts between genes. The mechanism by which lncRNAs function is unclear but several studies suggest they can act either in cis or trans to either repress or enhance gene expression, possibly through interactions with chromatin remodeling complexes such as polycomb repressor complex 2 (PRC2). This suggests a role for lncRNAs in defining and modulating the epigenetic landscape to control gene expression. We have recently performed a high throughout genomic screen for lncRNAs expressed in the embryonic and adult lung using RNAseq and ChIPseq analysis. In this screen, we have chosen to focus on intergenic lncRNAs given their previously reported importance in regulating gene transcription. We have used these data to identify a lung lncRNA transcriptome containing 363 lncRNAs that likely play critical roles in lung biology. This database of lung lncRNAs provides a novel resource to identify and characterize new and important regulators of lung gene transcription and development. Our preliminary data shows that lung lncRNAs are often transcribed near transcription factors and signaling molecules critically important for lung development and homeostasis including Nkx2.1, Foxf1, and Foxa2 and are expressed in patterns similar to these genes. In particular, we show that a novel lncRNA associated with Nkx2.1 (NANCI) acts upstream of Nkx2.1 to regulate lung gene expression. These findings will have a broad impact on our understanding of the non-coding transcriptome in pulmonary development, disease and repair/regeneration.