tRNA屬於small ncRNA(小型非編碼核糖核酸, small non-coding RNA)的一種，其 tRNA的分子降解產物tRFs (tRNA-derived small RNA fragments)為tRNA之非隨機產生的碎片，在tRFs被新一代定序技術(NGS)發現後，許多生物學者開始對其進行研究。但tRF的真正功能特性都並未確定，且尚未擁有命名法，生物學家猜測tRF會引發核醣核酸干擾基因表達現象(RNAi現象, RNA interference)，以此途徑來沉默基因。然而tRF與內源基因的調控機制尚未明朗，以往的生物實驗要找出這類型的標靶序列，必須經過許多生物實驗的試誤，試誤法耗費的時間、人力與金錢成本十分龐大。若可以先使用生物學上的規則來做預測，找出較有可能的配對後再進行實驗，必會為大幅降低實驗成本並且更容易切中目標。
本研究根據本實驗室過往在線蟲piRNA與mRNA標靶研究上的基礎，並參考目前學界對於tRF的相關研究結果，嘗試建立一假說。假設tRF會與某特定蛋白質結合並對其他RNA產生調控作用。利用合作者提供的線蟲中與PRG-1蛋白結合的CLIP資料及線蟲的CLASH資料，針對此假說加上實驗資料，設計出一套完整的tRF預測流程，找出會與PRG-1結合之tRF，並開發tRF標靶預測工具，預測所有RNA基因序列的tRF標靶位置區域，並將預測結果整理建立tRF-RNA交互作用資料庫，提供兩種搜尋模式讓使用者根據不同需求可選擇不同搜尋方法，搜尋結果包括tRF-RNA標靶對的詳細資訊，並以視覺化的方式呈現標靶位置預測圖給使用者。最後根據這些已知的資訊更進一步的探討會與PRG-1結合之tRF的和piRNA之間是否有類似的性質，以及挑選出數個有極高可信度的tRF-RNA標靶對，利於生物學家做更進一步的實驗證實。
tRFBase資料庫網址:
http://cosbi6.ee.ncku.edu.tw/tRFBase/
關鍵字:線蟲、tRF、基因沉默、標靶位置預測

tRNA is a kind of small ncRNA, tRFs are non-randomly generated fragments of tRNA, after tRFs were found by Next Generation Sequencing Technology, many biologists began researching it. But tRF’s characteristic and function are not being confirmed, and it doesn’t have nomenclature, biologists conjectured that tRF will trigger RNAi pathway, and to silence gene. However, the regulatory mechanisms of tRF and endogenous genes are not clear now, if biologist went to find out those tRF-RNA target pairs, only can use trial and error method, it expend a lot of time, manpower and money. So, if we can make prediction by biological rules first, then find most likely pairs to do the experiment, this way can reduce the cost of experiment and find target pairs easily.
This study is based on the research results of worm piRNA-mRNA target pairs in our laboratory, and refer to the current research results on tRF. We assume tRF will bind with specific protein and regulate other RNA. Use the CLIP-Seq and CLASH data provided by cooperator and experiment data. We design a pipeline to find tRF bind with PRG-1. Further, we develop a prediction tool to find all tRF-RNA target pairs on all RNA sequences. Finally, we build a database about tRF-RNA interaction. We provide two search mode for user, search result include tRF-RNA target pairs information, and visualize the target position for user. At the end of this study, we explore whether there is a similar property between which tRF can bind with PRG-1 and piRNA, then pick some high reliability target pairs, which will help biologists to do further experimental confirmation.
tRFBase is available at : http://cosbi6.ee.ncku.edu.tw/tRFBase/
Key words: C. elegans, tRF, targeting-site prediction, silent mutations

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