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標題: | 轉錄組分析揭示內含子保留現象廣泛存在於陸地植物中的 NAC 轉錄因子家族 Transcriptomic analysis revealing widespread last intron retention events of the NAC transcription factor family in land plants |
作者: | Chen-Yu Kuan 管晨宇 |
指導教授: | 林盈仲(Ying-Chung Jimmy Lin) |
關鍵字: | 保守內含子保留剪接異構體,陸地植物演化,VNS轉錄因子家族,維管束演化,NAC轉錄因子家族,生命體動態平衡,小分子干擾核糖核酸, Conserved intron retention,Land plant evolution,VNS family,vascular evolution,NAC family,Homeostasis,Small interfering peptide, |
出版年 : | 2019 |
學位: | 碩士 |
摘要: | 維管束發育相關的VNS家族中,存在毛果楊的PtrSND1-A2和PtrVND6-C1 是首次發現會經由內含子保留,產生具相互調節對方轉錄因子家族成員的mRNA剪接異構體。PtrSND1-A2 和PtrVND6-C1的mRNA,最後一個內含子都會被保留下來,並轉譯成N端不帶有完整NAC家族保守蛋白質序列,且失去C端活化區域的蛋白質結構。前人發現這兩種相似的剪接異構體,其蛋白質產物會抑制對方家族成員正常轉譯的蛋白質,以及下游生合成細胞壁相關基因。為了研究這種相似結構的剪接異構體是否為廣泛存在植物界的負調節者。我們設計了Python編譯的程式碼,MoBIReF,偵測帶有相似基因結構的內含子保留剪接異構體。利用MoBIReF,13個維管束植物的VNS家族都偵測到保守的內含子剪接異構體。且這些VNS剪接異構體,其基因結構皆相似PtrSND1-A2和PtrVND6-C1的內含子剪接異構體。但這種保守的剪接異構體在非維管束植物中並無觀測到。帶有相似內含子保留VNS剪接異構體的物種,與維管束植物在演化上的同步出現,暗示著這種保守的內含子保留VNS剪接異構體可能參與了維管束發育的演進。96個NAC基因於14種陸生植物都帶有這種保守的內含子保留剪接異構體,包括早期的蘚苔陸生植物,小立碗蘚。我們發現相似的內含子保留現象可廣泛的存在於植物的演進,且內含子保留剪接異構體可能藉由維持VNS成員,甚至NAC家族成員的基因表現,以調控維管束發育和其他生物功能。 The reciprocal regulation across different transcription factors (TFs) families by intron-retained splice variants were first reported in vascular development associated VNS family members, one of the subfamily in plant-specific NAC family. Two of the VNS members, PtrSND1-A2 and PtrVND6-C1, in Populus trichocarpa undergo last intron retention (IR) and the transcripts yielded C-terminal truncated proteins with incomplete NAC domains and no activation domain. Such truncated proteins were found as dominant-negatives, suppressing the full-size proteins translated from the normally spliced transcript. To understand whether the intron retentions are conservative events throughout the VNS family in plant kingdom, we developed a Python package, MoBIReF (Motif based intron retention finder), for the transcriptomic analysis of Illumina RNA-seq to detects the conserved IR events. Total 15 species from bryophyte, pterophyte, and angiosperm were used for MoBIReF. The conserved IR events were discovered in 13 vascular species from pterophyte and angiosperm, but were not observed in the non-vascular species, the bryophyte. The synchronization between the emergence of VNSIR and vascular plants suggested that the conserved IR events may participate in the development of the vascular tissue. We further investigate such conserved IR events throughout the whole NAC family. A total of 96 NAC genes were found to possess the conserved IR events across 14 species, including the early land plant, Physcomitrella patens (moss). In this study, we demonstrated the conserved IR events are widespread in VNS and even NAC families and preserved in land plant evolution. The IR events may be general mechanism to maintain the homeostasis of VNS and NAC families for vascular development and other plant-growth related mechanisms. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/21684 |
DOI: | 10.6342/NTU201900874 |
全文授權: | 未授權 |
顯示於系所單位: | 植物科學研究所 |
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