利用脊椎動物cDNA組之同源性比較找出胚早期發育共同表現的基因及其相關功能

Abstract

哺乳類動物早期胚發育時期泛指從受精卵到胚胎埋植入子宮前的發育階段，此階段包括了受精卵在生長、遷移、分化及形態上的變化等，是脊椎動物發育過程中的重要階段之一。公開資料庫中脊椎動物早期胚發育時期之相關基因庫，發現目前大部分物種在胚早期發育時期的研究甚少，某些物種甚至闕如。有鑑於此，本研究旨為利用現存於公開資料庫之脊椎動物胚早期發育的有限資料，找出脊椎動物物種間胚早期發育時期的共同表現基因，並進一步分析其相關功能，期能增加對脊椎動物在胚早期發育階段基因表現的暸解。 利用NCBI（National Center for Biotechnology Information）的UniGene資料庫和TIGR（The Institute for Genomic Research）的Gene Index資料庫分別收集牛（Bos taurus）、小鼠（Mus musculus）、豬（Sus scrofa）和非洲爪蟾（Xenopus laevis）四個物種在早期胚發育時期的基因庫。篩選上述基因庫中四物種之早期胚表現基因序列總數分別為：小鼠：13,705條、牛：2,407條、豬：4,015條和非洲爪蟾：15,329條。藉由序列比對工具BLAST（Basic Local Alignment Search Tool），以小鼠的早期胚表現基因序列資料為基礎對其他三物種之序列資料庫進行序列相似性分析。分析結果將四物種間共同表現基因分為七大群組，其總數分別為：小鼠與牛共同表現者：1,414條、小鼠與豬共同表現者：1,909條、小鼠與非洲爪蟾共同表現者：2,372條、小鼠、牛與豬共同表現者：411條、小鼠、牛與非洲爪蟾共同表現者：602條、小鼠、豬與非洲爪蟾共同表現者：860條和小鼠、豬、牛與非洲爪蟾共同表現者：254條。進一步分析物種間共同表現基因所具備之功能，利用三組共同表現基因：小鼠與豬、小鼠與非洲爪蟾以及小鼠、牛、豬與非洲爪蟾之共同表現者，分別以小鼠之共同表現基因身份為代表進行功能性解析。結果顯示，四個物種之共同表現基因在三大功能分項：生物作用（biological process, P）、分子功能（molecular function, F）和細胞組成（cellular component, C）分析中分別有112（P）、113（F）和105（C）個共同表現基因具有功能性註解；小鼠與豬之共同表現基因在三大功能分項分析中分別有857（P）、926（F）和862（C）個共同表現基因具有功能性註解；小鼠與非洲爪蟾之共同表現基因在三大功能分項分析中分別有1,208（P）、1,281（F）和1,145（C）個共同表現基因具有功能性註解。就生物作用分項分析結果而言，物種間共同表現基因的功能主要以參與代謝過程（meatabolic process）為主；在分子功能方面主要牽涉細胞分子鍵結（molecular binding）；而細胞組成功能分項也顯示共同表現基因的表現主要以細胞內為主。 利用生物資訊比對工具及公開資料庫可針對不同物種間之早期胚表現基因進行同源性比較篩選，所得之結果將有助生物學者廣泛瞭解脊椎動物在早期胚發育過程中的共同表現基因及所具備之相關功能。

The early embryonic stages of mammals are the developmental process from zygote to preimplantation. The stages of embryogenesis are critical for embryonic development in vertebrates. Several key developmental events occurr in these stages, such as cell growth, migration, differentiation, and morphogenesis. In spite of the importance occurring in the early embryogenesis, limited information has been provided by previous studies. For this reason, the purpose of this study is to utilize the public databases to screen those commonly expressed genes with their related functions at early embryonic stages in vertebrates. The UniGene and the Gene Index databases in the National Center for Biotechnology Information (NCBI) and The Institute for Genomic Research (TIGR) were designed to collect and assemble sequences of expressed sequences tags (ESTs) and mRNA. Each assembled entry is a set of transcript sequences that appear to come from the same transcription locus. The numbers of unigene entries and tentative consensuses (TC) of embryos before implantation collected from Bos taurus (Bt), Mus musculus (Mm), Sus scrofa (Ssc) and Xenopus laevis (Xl) were 2,407, 13,705, 4,015, and 15,329, respectively. The analytic results among four species were divided into seven groups. All of the commonly expressed genes were 1,414 for Mm and Bt; 1,909 for Mm and Ssc; 2,372 for Mm and Xl; 411 for Mm, Bt and Ssc; 602 for Mm, Bt and Xl and 860 for Mm, Ssc and Xl. However, there were 254 genes commonly expressed in all these four species. Furthermore, the unigenes of Mm were classified according to the Gene Ontology (GO) by three categories: biological process (P), molecular function (F) and cellular component (C). The results among Mm, Bt, Ssc and Xl showed the entries with GO identifiers were 112 (P), 113 (F) and 105 (C); the results between Mm and Ssc showed the entries with GO identifiers were 857 (P), 926 (F) and 862 (C); the results between Mm and Xl showed the entries with GO identifiers were 1,208 (P), 1,281 (F) and 1,145 (C). For the entries that mapped to biological processes, most of them with their functional annotations were related to metabolic processes. For molecular function, most of the commonly expressed genes were related to some macromolecule or ion binding. In addition, these activated genes are expressed intracellularly at early developmental stages. The commonly expressed genes and their related functions might be annotated using comparison tool among sequence databases of different species. The analytical procedure would assist animal scientists to screen the conserved genes with fundamental roles and functions.