Mechanisms regulating lncRNA short and long range signaling

生物学方面的重大技术突破揭示了我们的 了解基因调控和染色质三维结构。在…的核心 了解基因调控是对转录调控、长时间非编码的研究 由增强子转录的RNA(LncRNAs)。而lncRNAs的概念 发挥全基因组的作用，作为转录调节现在被接受，关系 LncRNAs和染色质之间的三维结构尚不清楚。因此，一个中央 生物学中的问题仍然存在：lncRNAs如何与染色质相互作用来建立 染色质三维结构背景下的基因调控网络？ 通过结合使用大规模分析，包括下一代 核酸测序、质谱学蛋白质测序、全基因组 染色体构象和生物信息学，我们现在可以研究它们之间的关系 表观遗传因素、基因调控和染色质三维结构之间的关系。 十多年来，我的实验室一直在研究Evf2的转录调控， 第一个增强子调节的，超服务的lncRNA(冯等人)。2006年，邦德等人。2009年， Berghoff等人。2013年，Cajigas等人。2015年)。总的来说，这些研究确立了一些 关于lncRNAs在基因调控中作用的基本原则，包括 发现单个发育调节的lncRNA控制GABA能中间神经元 发育与成人大脑回路(邦德等人)2009年)。我们之前的工作主要集中在 EVF2对相邻或重叠、Dlx5/6基因间增强子的调控，并报道了 对基因表达、转录因子募集、组蛋白的短期影响 修饰、位点特异性CpG DNA甲基化和直接抑制ATPase和 染色质重塑活动(Bond等人2009年，Berghoff等人。2013年，Cajigas等人。 2015年)。 在这项提案中，我们将结合在 我的实验室在过去的十年里，利用最近的大规模技术，来确定 EVF2基因调控网络与染色质三维结构的关系

Major technological breakthroughs in biology reveal new dimensions in our understanding of gene regulation and chromatin 3-D structure. At the heart of understanding gene regulation are studies of transcription-regulating, long non-coding RNAs (lncRNAs) that are transcribed from enhancers. While the concept that lncRNAs play genome-wide roles as transcriptional regulators is now accepted, the relationship between lncRNAs and chromatin 3-D structure is still unclear. Therefore, a central question in biology remains: How do lncRNAs interact with chromatin to establish gene regulatory networks in the context of chromatin 3-D structure? By using a combination of large-scale analyses, including next-generation nucleic-acid sequencing, mass spectrometry protein sequencing, genome-wide chromosome conformation, and bioinformatics, we can now investigate the relationship between epigenetic factors, gene regulation, and chromatin 3-D structure. For over a decade, my lab has been studying transcriptional regulation by Evf2, the first enhancer-regulating, ultraconserved lncRNA (Feng et al. 2006, Bond et al. 2009, Berghoff et al. 2013, Cajigas et al. 2015). Collectively, these studies establish some fundamental principles regarding the role of lncRNAs in gene regulation, including the finding that a single developmentally regulated lncRNA controls GABAergic interneuron development and adult brain circuitry (Bond et al. 2009). Our previous work focused on Evf2 regulation of adjacent or overlapping, Dlx5/6 intergenic enhancers, and reported short-range effects on gene expression, transcription factor recruitment, histone modifications, site-specific CpG DNA methylation, and direct inhibition of ATPase and chromatin remodeling activities (Bond et al. 2009, Berghoff et al. 2013, Cajigas et al. 2015). In this proposal, we will combine the genetic and biochemical tools developed in my lab over the past decade, with recent large-scale technologies, to determine the relationship between the Evf2 gene regulatory network and chromatin 3-D structure.