利用次世代定序技術系統化分析微小非編碼核醣核酸

Abstract

次世代定序技術(NGS)是一個新的定序技術，它是一個能夠快速、大量以及穩定偵測和分析微小非編碼核醣核酸(small non-coding RNA)的表現量的方法。微小非編碼核醣核酸在生物體內主要影響到基因沉默(gene silencing)、DNA甲基化、組蛋白修飾。為了研究微小非編碼核醣核酸的功能，微陣列(microarray)被廣泛的使用。隨著次世代定序的發展，近年來越來越多生物學家利用次世代定序技術來研究微小非編碼核醣核酸的功能。次世代定序比微陣列在分析微小非編碼核醣核酸上更為準確且能發現未知的微小非編碼核醣核酸。次世代定序技術提供生物學家更好的資料品質，但是到目前為止，如何廣泛且完整的分析微小非編碼核醣核酸還未被提出。這個研究的主要目標就是針對次世代定序技術在微小非編碼核醣核酸建立廣泛且完整的分析流程，希望這個系統化的分析流程能夠幫助生物學家快速的分析資 以及獲得更多有用的結果。

Next-generation sequencing (NGS) technology which is a novel sequencing technology offers high-throughput and robust approaches for monitoring and analyzing the expression of small non-coding RNAs. Small non-coding RNAs contain microRNAs (miRNAs) and short interfering RNAs (siRNAs) which play an important role in gene silencing, DNA methylation and heterochromatic histone modifications in animals and plants by targeting mRNAs. Unlike capillary-based sequencing, next-generation sequencing technology produces million of sequences (35~1000 nt) at a time. This offers the quantitative analysis in the small non-coding RNA. Moreover, comparing oligonucleotide microarray, it can be used to not only profile the expression levels of known miRNAs but also discovery novel miRNAs. In the recent years, there are more and more studies applying this sequencing technology to deciphering the function of small non-coding RNAs. However, there are no complete and comprehensive analysis flows for these sequencing data. This work aims at developing the systematic and comprehensive analysis pipeline in small non-coding RNA including animals and plants for next-generation sequencing data. This pipeline can help biologists to easily apply their own NGS data to finding the biological significant small non-coding RNAs, pathways and regulation networks between small non-coding RNAs and their target genes.