研究發育過程轉錄體的網路隨機性與動態生物途徑分析來探討發育過程的演化

Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis

柯逵悅(Kuei-Yueh Ko)

指導教授 ： 阮雪芬

共同指導教授 ： 歐陽彥正(Yen-Jen Oyang)

國立臺灣大學/生命科學院/基因體與系統生物學學位學程/碩士(2017年)

https://doi.org/10.6342/NTU201702130

摘要

發育是經由一系列的分裂、調控、與決定所構成。經過這一系列發育的過程，不同的物種由一顆受精卵成長成形態迥異的個體。科學家試圖提出各種演化發育的模型來描述各個物種發育過程的異同；其中，就以 funnel model 與 hourglass model (發育砂石漏模型) 最為有名。

Funnel model敘述個體發育時，會先從一般共有的特徵一步一步發育出物種特有的特徵。另一方面，hourglass model敘述各個物種在發育時期中有一個時期的相似性會特別高。這一段時期被稱為 phylotypic stage。藉由比較各個物種發育時期的轉錄體，不同研究均指向 hourglass model。儘管有證據指出 phylotypic stage 的存在，然而，這其中的演化上的解釋以及背後的分子機轉仍舊尚未被提出。

在我們的研究中，我們利用網路與生物途徑分析去探討這個問題。利用基因關聯網路與基因表現資料，我們首先量測生物網路在不同發育時期的隨機性。這樣的分析讓我們能夠了解生物網路中的隨機性隨著發育過程的變化。接下來，我們試著計算出各個生物途徑在發育過程的動態變化。希望利用各個物種不同功能的動態變化來深入比較不同物種發育過程。藉由系統性的網路分析觀點，我們的結果提供了另一個觀點來比較不同的胚胎發育。

關鍵字

基因體親緣分層 ； 基因關聯網路 ； 發育砂石漏模型 ； 轉錄體年齡圖譜

並列摘要

Each developmental process consists of a series of divisions, regulations, and decisions. Throughout different series of developmental instructions, a fertilized egg of each species develops into distinct multicellular organism, which may be totally different from each other. Various evo-devo models have been proposed to describe the similarities and differences among developmental processes. The funnel model and hourglass model are the most well-known among them.
The funnel model states that the development proceeds from general features to species-specific patterns. On the other hand, the hourglass model states that higher similarity exists during the formation of body plan among the embryogenesis of different species. The stage with the highest conservation is referred as the phylotypic stage. By comparing the transcriptomic data among different species, several studies have been reported to support the idea of hourglass model. Although pieces of evidence indicate an evolutionary constraint during phylotypic stage, the evolutionary explanation and molecular mechanism behind this phenomenon, however, are not fully understood yet.
In our study, we aimed to tackle the problem via network and pathway analyses. Using the gene association network information and gene expression data, we first measured the stochasticity within the biological network during the developmental process. Such analysis enables us to trace and compare the changes of network randomness among developmental processes of different species. Next, we sketched out the pathway dynamics during developmental process in order to narrow down our study from global network connections to detailed molecular regulations. With the systematic network view of developmental process, our results provided an alternative aspect of comparative embryology.

並列關鍵字

Developmental hourglass ； genomic phylostratigraphy ； gene association network ； network entropy ； functional class scoring

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