環單磷酸腺苷受體蛋白相依非編碼小片段核醣核酸在大腸桿菌中的網路建構

Construction of cAMP-CRP dependent Small Non-coding RNAs Networks in Escherichia coli

黃熙淵(Hsi-Yuan Huang)

指導教授 ： 黃憲達

國立交通大學/生物科技學院/生物資訊及系統生物研究所/博士(2011年)

https://doi.org/10.6842/NCTU.2011.00669

摘要

非編碼小片段核醣核酸 (sRNAs) 常因應環境刺激而改變表現量，進而影響標的基因 (Targets) 的蛋白合成與活性。到目前為止，大腸桿菌就包含了80多個非編碼小片段核醣核酸。發現的非編碼小片段核醣核酸受環境與轉錄因子所調控，並有著多樣的生理角色。為了加速非編碼小片段核醣核酸的相關研究，如合成與功能，進而應用於基因網路的建構，非編碼小片段核醣核酸與轉錄因子及標的基因的連結是必需的。此研究以環單磷酸腺苷受體蛋白(cAMP-CRP)調控的非編碼小片段核醣核酸為例子。首先，我們從文獻與已知資料庫收集所有非編碼小片段核醣核酸的資料，接著透過序列分析找出環單磷酸腺苷受體蛋白相依非編碼小片段核醣核酸，並分析其標的基因，最後完成環單磷酸腺苷受體蛋白相依非編碼小片段核醣核酸在大腸桿菌中的網路建構。

關鍵字

大腸桿菌 ； HASH(0xbc4df74) ； 環單磷酸腺苷受體蛋白 ； HASH(0xbc4e064) ； 非編碼小片段核醣核酸

並列摘要

Small non-coding RNAs (sRNAs) carry out a variety of biological functions and affect protein synthesis and protein activities in prokaryotes. Recently, ~80 small RNAs have been found in Escherichia coli. The synthesis of the sRNAs is induced by various conditions and regulators and they would have a variety of physiological roles. To speed up the processes in studying sRNA synthesis and sRNA functions and improve current approaches to gene regulatory network modeling, it is necessary to link these sRNAs to regulators and targets. Here, we use cAMP-CRP related sRNAs as an example and hope to construct the cAMP-CRP dependent small non-coding RNAs networks. Therefore, we collect sRNAs from literatures and public data resource and integrated related information of sRNAs and gene expression profiles. Then, the improved approaches were undertaken to identify CRP regulatory sites in the promoter regions of sRNAs and to identify the targets of sRNAs. Finally, the cAMP-CRP dependent sRNAs Networks are constructed based on this information and existing biological knowledge.

並列關鍵字

Escherichia coli ； HASH(0xbc4e1cc) ； cAMP-CRP ； HASH(0xbc4e298) ； Small Non-coding RNAs ； HASH(0xbc4ed08) ； sRNAs

參考文獻

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