随着长非编码RNA（lncRNA）在多个物种中的系统鉴定，其在基因信息传递过程中的调控作用机制正在被大量发现。lncRNA的表达模式、结构、功能等方面具有高度的复杂性，且往往存在组织与细胞特异性。研究表明，小鼠干细胞中超过60%的lncRNA可能与编码基因在基因组上形成异向转录（divergent transcription）基因对，但该异向转录单元的组织特异性鉴定标准尚不成熟，其功能及调控机制亦不完全清楚。本项目将以模式动物小鼠为研究对象，整合CAGE、H3K4me3 ChIP-seq、RNA-seq等多维数据，对各主要组织类型中的lncRNA/mRNA异向转录基因对进行系统鉴定，并研究该类lncRNA的生成及其对其它编码基因表达的调控。总之，本项目将首次提出lncRNA/mRNA异向转录单元这一功能元件在小鼠中组织特异性的全面注释，并系统地总结分析其生成过程及调控功能的网络模型。

Many noncoding RNA, especially long noncoding RNA (lncRNA) species, have been identified in a large number of model organisms and human. It has been frequently reported that lncRNAs play indispensable roles in regulating major cellular activities and important phenotypes, mostly by taking parts in the network of genetic information transferring. Nevertheless, our understanding about origin and regulation of lncRNA in individual cell types is still poor, and systematic research on lncRNA is still limited, due to strong context-dependency and extensive complexity of expressions, structures, regulations, and functions of lncRNAs. .The proposed research project will focus on a specific type, also a major type, of lncRNAs, i.e., lncRNA genes which are divergently transcribed at promoters of active protein-coding genes. Divergent transcription is frequently observed in Eukaryotic cells as transcriptions at many promoters are bi-directional. Recent literatures reported that in mouse and human embryonic cells, a large fraction of lncRNAs are originated from divergent transcription at promoters of protein coding genes, forming lncRNA/mRNA gene pairs. Given the strong context-dependency of lncRNAs, active divergent transcription gene pairs identified in one cellular context may not necessarily exist in other contexts. In addition, the context-dependent biogenesis, regulation, and functions of such lncRNA/mRNA divergent transcription gene pairs remain unclear. To address these questions, we propose to perform the following studies: 1) Identification of tissue-specific lncRNA/mRNA divergent transcription. We will develop a screening pipeline to identify tissue-specific active lncRNA/mRNA divergent transcription gene pairs in major tissue types of Mus musculus, by integrating multiple evidence from different types of high-throughput profiling data, such as RNA-seq, CAGE from FANTOM, and H3K4me3 ChIP-seq from ENCODE. 2) lncRNA biogenesis. For the lncRNA/mRNA gene pairs, we will categorize different patterns of lncRNA expression as relative to the pairing mRNA in different tissue contexts, and identify upstream regulators that determine these specific expression patterns, using systems biology approaches. 3) lncRNA functions. We will apply well-established algorithms on lncRNA and mRNA expression profiles, to identify functions of lncRNAs on the transcription of protein coding genes, followed by experimental validations and detailed mechanistic studies on selected lncRNAs. In summary, the proposed research will generate the first comprehensive index of tissue-specific active lncRNA/mRNA divergent transcription gene pairs, followed by systematic analysis of lncRNA biogenesis regulation and biological functions. Considering the high conservation of lncRNA/mRNA divergent transcription between mouse and human, our results will also provide valuable insights about identification, regulation, and functions of lncRNA/mRNA divergent transcription gene pairs in human.