microRNA是一種非轉譯的小RNA，長度約有21-23 核苷酸，在真核生物體內的基因表現上扮演具有相當重要的角色。在miRBase收錄的資料庫中，約有一百多個不同物種的miRNA的資訊。其中人類miRNA的資料有885筆、雞的miRNA的資料有520筆 、小鼠的miRNA的資料有689筆。相較於這些物種來說，豬這個物種所發現的miRNA非常的稀少，僅有77筆。豬在畜產業一直是重要的經濟物種，但顯然miRNA的資料上相對來說是較少的，故可知還有許多值得研究的空間。因此在本研究中，我們希望利用電腦分析的方式，在二種不同來源的豬的序列資料中找尋新穎的豬的miRNA。這兩個不同來源的豬的序列資料，一是來自於台灣畜禽基因體計畫中所取得胚胎時期的cDNA序列，另一是線上所釋放豬全基因體序列資料。在第一部份的研究裡，胚胎時期的cDNA序列是來自於4細胞期、8細胞期、桑椹胚期及囊胚期等4個階段。在原始來源裡有56,739筆的cDNA序列，經過了品質及移除載體序列後，以46,435筆序列進行資料分析。在排除了含有其它非編碼RNA (tRNA、rRNA、snoRNA)的序列資料後，將剩下的28,292 cDNA序列與mature miRNA的序列進行比對。我們共發現72條豬的cDNA的序列對應到34種在哺乳動物中的mature miRNA。再進一步將這72條cDNA的序列與對應的precursor miRNA進行配對後，最終找出了4條新穎的豬的miRNA。在第二部份的研究裡，豬基因體序列資料則是由NCBI及Ensembl所下載。在5.5x109的鹼基裡，我們利用BLAST將人類已知的mature miRNA與precursor miRNA對豬的基因體序列資料進行分析比對，得到300條推論的豬的precursor miRNA。藉著預測這些推論的豬的precursor miRNA二級結構，及利用synteny資訊進一步篩選後，我們得到286條的precursor miRNA，對應到387條mature miRNA。移除47條豬已知的precursor miRNA與50條mature miRNA，一共得到337條的mature miRNA。利用二個不同的資料來源，經過我們一步步的篩選所預測的結果，本研究中總共得到了243條precursor miRNA與341條mature miRNA是目前未被定義的。我們相信這些研究結果可以提供給實驗室人員未來研究影響基因表現量的因素，應該對豬的基因體研究提供一些有用的新資訊。

MicroRNA (miRNA) is a class of small 21-23 nucleotide (nt) RNAs that plays a crucial role in gene expression in eukaryotes. The newly released miRNA database (miRBase 13.0) contains 77 pig precursor miRNAs that code for 74 distinct miRNAs. Compared with mouse (689 miRNAs), human (885 miRNAs), or chicken (520 miRNAs), the total number of pig miRNA is much lower than other species. It suggests there are still many unidentified miRNAs in the pig. The objective of this study is to uncover miRNA in the pig genome by using computational analyses. Two different datasets were used in this study: (1) cDNA sequences from different stages of pig embryos (ie., 4-cell, 8-cell, morula and blastocyst), and (2) whole genome sequences downloaded from NCBI and Ensembl databases. The first dataset comprises 56,739 originally assembled cDNA sequences. Several control criteria were applied to filter out vector and low quality sequences and result in 46,435 cDNAs for further analysis. Finally, 28,292 cDNAs were subjected for identification of novel pig miRNA after exclusion of other type of non-coding RNAs (ie., tRNA, rRNA, and snRNA). The search yields 72 pig cDNAs that matched to 34 known mammalian mature miRNAs. Further compare with precursor miRNA from matched mature miRNA resulted in 4 novel pig miRNAs. For the second dataset, a total of 5.5x109 base pairs of pig genome sequences were used in BLAST search for known human mature miRNA, and followed by BLAST against human precursor miRNA sequences to obtain putative pig miRNAs. To further analyze putative pig miRNA, potential hairpin structure of pig pre-miRNA sequences were constructed and compare with the structure of known human pre-miRNAs from the miRBase. Finally we applied synteny comparison between human and pig genomes to further validate putative pig miRNAs. The serial analyses identified 387 pig miRNA. Among then, 337 are new miRNA in the pig genome. Altogether, we have identified 341 novel pig miRNA using computational approaches. These newly identified pig miRNA would facilitate laboratory to select miRNA target genes for future investigations.

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