長鏈非編碼RNA (long non-coding RNA，lncRNA)在許多生物過程中都有重要調控功能，雖然目前已有許多植物lncRNA被發掘，但大部分的調控機制仍然不清楚。由於探討lncRNA與編碼基因之間的共表現關係有助於了解lncRNA的調控功能，因此在本研究的第一部分，我們建構了一個植物lncRNA的表現譜資料庫JustRNA。目前收錄了來自80種植物的1,024,354 條lncRNAs，表現量資料的部分則是針對六個模式植物收錄了825種情況的3,692組次世代定序資料。除了基本的表現量查詢，JustRNA也提供功能性分析幫助了解lncRNA的調控機制。透過基因組相關性分析和微小RNA標的分析可以建構lncRNA的調控網路，找出可能會和lncRNA有交互作用的鄰近基因和微小RNA。接著進行共表現分析並建構這群基因的共表現網路，將能提高交互作用的可信度。另一方面，JustRNA還整合了轉錄因子和組蛋白修飾的染色質免疫沉澱定序資料，藉此探討lncRNA上游的轉錄調控機制。對於植物lncRNA有興趣的學者將能利用JustRNA獲得調控關係的重要資訊。目前JustRNA資料庫可由以下網址免費取得: http://JustRNA.itps.ncku.edu.tw。本研究的第二部分我們提出了探討lncRNA的分析流程，並實際應用在熱逆境的研究上。由於全球暖化可能會對農作物造成熱逆境的傷害，因此了解lncRNA在長期高溫效應中的調控機制是很重要的課題。為模擬長期高溫效應，我們將阿拉伯芥種植在28 ℃與其最適生長溫度23 ℃進行次世代轉錄體定序的比較分析。根據定序資料的分析結果，lncRNA和編碼基因之間的基因特徵存在明顯差異，可惜這些基因特徵無法用於區別與長期熱效應相關或是沒有改變的lncRNA。為了進一步了解與長期熱效應相關的lncRNA可能的調控功能，我們利用JustRNA調控網路的功能分析這些lncRNA。在共表現網路中，擁有最多交互作用的lncRNA AT2G05215.1 有三個在基因組上鄰近的基因同時也參與在長期熱反應，因此這四個基因很適合做進一步的研究。總結來說，本研究建立了一個植物專屬的lncRNA資料庫，並提出一個探討lncRNA調控特性的分析流程，這將有助於科學家更有效的研究植物lncRNA。

Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. In the first part of this study, the JustRNA, an expression profiling resource for plant lncRNAs was developed. The platform currently contains 1,024,354 lncRNA annotations for 80 plant species. In addition, it includes 3,692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw. In the second part of this study, analysis pipelines for investigation of lncRNAs were proposed and applied to heat stress research. Global warming could cause heat stress on agricultural crops and thus it is necessary to explore the regulatory mechanisms of lncRNAs involved in long-term high-temperature effects. To simulate these effects, we conducted a comparative analysis of the next-generation transcriptome sequencing of Arabidopsis thaliana grown at 28°C and its optimal growth temperature of 23°C. Results of gene feature comparison demonstrated significant different between lncRNAs and protein-coding genes. However, the features could not be used to distinguish between long-term high-temperature effects and no change lncRNAs. Further functional analyses were carried out for long-term high-temperature effects related lncRNAs with “Network Search” of JustRNA. A lncRNAs AT2G05215.1 with the most interactions was observed to co-expressed with three nearby genes which were also involved in long-term high-temperature effects. Therefore, they could be good candidate for further investigation. Overall, this study developed a database for plant lncRNAs and proposed analysis pipelines for discovering regulatory properties. We believe that these will be helpful for scientists to efficiently study insight into plant lncRNAs.

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