利用系統生物學的方法研究人類如何透過微小核醣核酸和剪接因子之交亙作用以調控核醣核酸的選擇性剪接

Abstract

核醣核酸選擇性剪接和微小核醣核酸調控機制都扮演著關鍵角色且屬於生物中心法則之後轉錄的過程。對於真核生物來說，兩調控網路機制都是非常重要的，但其中仍有許多生化的代謝路徑尚未被研究透徹。加上最近的研究發現，這兩者具有功能性的交亙作用，可以在特定的組織中産生關鍵性的影響。Makeyev作者群提出了關於在神經系統具有表現特異性的微小核醣核酸miR-124透過與標靶基因PTBP1的結合，導致PTBP1於神經系統中表現被抑制，然而其同源基因PTBP2可以取而代之並進而操縱選擇性剪接之調控網路，如此可以使得下游基因從非神經系統剪接結果之特異性到神經系統剪接結果之特異性的轉變。因此本研究的目標就是在不同的人類組織中找出所有可能具有組織特異性的微小核醣核酸與剪接因子所產生的功能性交亙作用，在此我們稱為調控模組。為了達成目標，我們所提出系統化的方法，主要可以分成三個部份：建構完整剪接因子資料庫、發展數種情境之微小核醣核酸標靶基因的預測、蒐集整合微小核醣核酸和剪接因子於不同的組織中的表現量以正確找尋可能的調控模組。研究結果中，針對具有拮抗作用的剪接因子利用同源基因的註解資訊，在腦相關的組織和賀爾蒙相關的組織中，可以得到可靠的調控模組。以腦組織來說，調控模組中微小核醣核酸hsa-miR-124, hsa-miR-128和hsa-miR-181b可以抑制剪接因子RBMS1，而剪接因子ELAVL3, ELAVL1, ELAVL2和ELAVL4將有可能取代RBMS1來操縱選擇性調控網路。由研究結果可以說明微小核醣核酸可以調控具有拮抗作用的剪接因子在特定的組織中。得到這些可能的調控模組是有利於開啟並了解人類複雜的選擇性剪接調控網路。

RNA splicing factors (SFs) and microRNAs (miRNAs) play crucial roles in post-transcriptional biological processes. The regulatory networks of SF and miRNA are important in eukaryotes but their biological pathways have not yet been fully deciphered. Recent studies have demonstrated the critical effects of functional interactions between SFs and miRNAs, especially in tissue specificity. For instance, Makeyev et al. proposed that the transition from non-nervous system (NS) to NS-specific alternative variants is resulted from neuron-specific microRNA miR-124 targeting to the splicing factor PTBP1; then, its homologous gene PTBP2 can replace the roles of PTBP1 to manipulate the alternative splicing regulatory network. Thus, the aim of this work is to identify all functional interactions between miRNAs and SFs, which are called regulatory modules here, in different tissues. This study proposed a systematic method which contains three major steps: constructing the repository of splicing factors, developing the miRNA target prediction service with different scenarios, and the integration of additional expression profiling of miRNAs and splicing factors for identifying the regulatory modules. This work can identify the regulatory modules by annotating paralogous information to the splicing factors which are antagonized in brain-related and hormone-related tissues. In particular, the regulatory module of hsa-miR-124, hsa-miR-128 and hsa-miR-181b might down-regulate RBMS1 in brain. Then, the up-regulated ELAVL3, ELAVL1, ELAVL2 and ELAVL4 might be possible to replace RBMS1 as the regulators in alternative splicing regulatory networks. The results indicate that miRNA modulates the antagonism of splicing factors in specific tissue. The proposed modules are useful to shed light on realizing human alternative splicing regulatory network.