醫(yī)學(xué)數(shù)據(jù)挖掘 miRNA基礎(chǔ)知識(shí)

1、microRNA non-coding RNA, ncRNA不能翻譯成蛋白的功能性RNA分子Housekeeping non-coding RNAtRNAs、 rRNAs、snRNAs Regulatory non-coding RNAsmall non-coding RNAsiRNA、miRNA、piRNA etc.Long non-coding RNA （lncRNA，200 nt ）microRNA的概念microRNA簡(jiǎn)稱miRNA，一類進(jìn)化上保守的內(nèi)源性的非編碼RNA, 長(zhǎng)度約22個(gè)核苷酸，在轉(zhuǎn)錄后層面調(diào)控基因的表達(dá)。非編碼RNA約22調(diào)控基因的表達(dá)內(nèi)源性轉(zhuǎn)錄后proteinmRNA

2、DNA功能表型轉(zhuǎn)錄后調(diào)控轉(zhuǎn)錄調(diào)控MicroRNA和其靶基因3非翻譯區(qū)結(jié)合，導(dǎo)致RNA誘導(dǎo)的沉默復(fù)合體（RNA-induced silencing complex，簡(jiǎn)稱RISC）降解其靶mRNA或阻礙其靶的翻譯。miRNA的生物合成過程mature miRNAPrecursor miRNAPrimary miRNAmiRNA gene轉(zhuǎn)錄剪切剪切miRNA的生物合成過程70-90堿基22堿基幾百幾千堿基miRNA的一般特點(diǎn)序列特點(diǎn)非編碼性成熟的miRNA 5 端為單一磷酸基團(tuán)，3端為羥基,這一特點(diǎn)使它與大多數(shù)寡核苷酸和功能RNA 的降解片段區(qū)別開來；表達(dá)特點(diǎn)miRNA具有時(shí)序性以及組織特異性在特

3、定的時(shí)間，組織中才會(huì)表達(dá)保守型特點(diǎn)在物種間高度通過和靶基因3UTR（3非翻譯區(qū)）結(jié)合導(dǎo)致RNA誘導(dǎo)的沉默復(fù)合體（RNA-induced silencing complex,簡(jiǎn)稱RISC）降解其靶mRNA或阻礙其靶的翻譯。miRNA的作用機(jī)制 RISC剖析重大疾病相關(guān)miRNA的調(diào)控機(jī)制和功能生物學(xué)證實(shí)Target genesmiRNA功能1功能n功能2表型It is clear that miRNAs have many different targets dozens in some cases, hundreds in others but depending on the cells i

4、nvolved, it seems likely that only a small number of them have a crucial role in cancer pathogenesis. nature reviews genetics (2009)microRNA靶基因預(yù)測(cè)算法原理miRNA“種子區(qū)”與mRNA的3UTR序列堿基互補(bǔ)第2-第8堿基miRNA與mRNA形成雙鏈結(jié)構(gòu)的熱力學(xué)穩(wěn)定性靶基因二級(jí)結(jié)構(gòu)和靶點(diǎn)外序列對(duì)靶基因預(yù)測(cè)的影響靶點(diǎn)在多物種間的序列保守性基本步驟在3UTR上探尋和miRNA“種子區(qū)”完全互補(bǔ)的序列；計(jì)算miRNA和這些序列結(jié)合產(chǎn)生的自由能下降值，對(duì)靶點(diǎn)進(jìn)行

5、篩選；對(duì)靶點(diǎn)進(jìn)行物種間序列比對(duì)，利用物種保守性進(jìn)一步篩選。miRNA靶位點(diǎn)預(yù)測(cè)的難點(diǎn)：miRNA與靶位點(diǎn)的不完全互不配對(duì)幾種靶預(yù)測(cè)算法比較miRNAs regulate many key biological processes, by determining how and when genes turn on and off細(xì)胞的生長(zhǎng)，增殖，分化，凋亡器官的建成生物個(gè)體的發(fā)育，繁殖與人類重大疾病相關(guān)Biological functions of miRNAs 基于mRNA、miRNA雙重表達(dá)譜分析復(fù)雜疾病中的miRNA調(diào)控背景miRNAs influence cell proliferat

6、ion and tumorigenesis in a cell-type specific manner, depending on the milieu of target mRNAs that are expressed. It is clear that miRNAs have many different targets dozens in some cases, hundreds in others but depending on the cells involved, it seems likely that only a small number of them have a

7、crucial role in cancer pathogenesis. nature reviews genetics (2009)盡管差異表達(dá)分析方法已經(jīng)識(shí)別了許多疾病miRNA，但是大部分miRNA在疾病中的作用還是未知的miRNAGene 1、Gene 2、Gene 3Gene 4、Gene N功能miRNA表達(dá)譜差異表達(dá)miRNA上調(diào)miRNA下調(diào)miRNAmRNA表達(dá)譜差異表達(dá)mRNA下調(diào)mRNA上調(diào)mRNA預(yù)測(cè)差異表達(dá)miRNA調(diào)控的靶基因預(yù)測(cè)的靶向關(guān)系GO功能注釋/富集預(yù)測(cè)差異表達(dá)miRNA調(diào)控的靶基因數(shù)據(jù)mRNA表達(dá)譜miRNA表達(dá)譜miRNA-mRNA靶向關(guān)系皮爾森相關(guān)系數(shù)

8、注意：miRNA、mRNA表達(dá)譜中樣本順序要一致samplesexpressionmiRNAtargetmiRNAtargetAnti-correlation of microRNA expression and predicted target mRNA. Expression levels of miR-200c and VEGFA in the primary dataset showing anti-correlation in both ccRCC and matched normal kidney tissue.loss of miR-200c function in ccRCC

9、contributes to increase in VEGF levels.Case 1前提假設(shè)miRNAs implicated in a specific tumor phenotype will show aberrant regulation of their target genesA key difference from other methods is that we identified dysregulated network edges (regulations) instead of dysregulated nodes (miRNAs) to assemble di

10、sease-related signatures. IF：5.225in vitro analysis RDH11an oncogene, is located in a high-level amplifications region in tumor cells and specifically expressed in the prostate LRP1 promote the invasion and migration ability of lung cancer cells and glioblastoma cellsis directly regulated by hsa-miR-205 in lung cancer cells SMAD3, a major TGF- signaling transducer miRNA family 的協(xié)同失調(diào)作用包含三個(gè)miRNA家族mir-125, mir-181 和mir-145家族最小的后驗(yàn)概率為77.4% ，表明這些miRNA和前列腺癌相關(guān)這些基因富集的功能有pathways in prostat