轉位子Ds及Ds1經由顯子化提高玉米轉錄體及蛋白質組豐富度

The Extent of Ds and Ds1 Exonization to Enrich Transcriptomes and Proteome in Maize

張云甄(Yun-Chen Chang)

指導教授 ： 常玉強

國立臺灣大學/生物資源暨農學院/農藝學研究所/碩士(2022年)

https://doi.org/10.6342/NTU202203253

摘要

轉位子顯子化（exonization）指當轉位子插入基因隱子時，插入的轉位子序列能夠在轉錄時為插入基因提供取代其原顯子剪接位之新剪接位點，使後續轉錄產物除保有原顯子序列外，亦帶有部分轉位子及部分隱子之遺傳訊息。過去的研究顯示轉位子雖能提供新剪接位並發生顯子化，然而由於其序列本身所能夠提供的遺傳訊息很少，故此過程對基因多樣性之貢獻主要在於被導入的基因隱子序列。本次試驗模擬了轉位子Ds與Ds1在玉米基因體中的顯子化過程，分析轉位子於單一插入位點提供不同剪接組合對玉米基因組豐富度的影響。在所有Ds及Ds1顯子化轉錄產物分析中，有超過90%的產物其後續將衍生出功能受損之縮短蛋白。被預期能夠產生完整功能蛋白異構物的第4、5類非NMD顯子化產物在所有Ds1顯子化轉錄產物中的比例約為3.3%，而在Ds的結果中則顯示為1.8%。在顯子化蛋白質異構物方面，與參考蛋白相似度高於50%的C端異構物比例約為70%，此類蛋白產物有高機率能夠在盡可能不破壞原有蛋白功能的前提下，為植物體提供更多的篩選優勢。而內部異構物則大多為新增蛋白片段長度小於30的產物，這些新增的小片段蛋白可能會精細修飾參考基因，然而實際的蛋白功能仍需未來進一步分析。

關鍵字

Ds轉位子 ； Ds1轉位子 ； 顯子化 ； 無意義密碼子媒介式mRNA分解 ； 選擇性剪接

並列摘要

Exonization means that when a transposed element (TE) is inserted into intronic sequences, the TE sequence can provide new splice sites for the inserted gene to replace its original exon splice site during transcription, so that subsequent transcripts will contain both the original exon sequence and genetic informations from TEs and introns. Previous studies showed that although TEs can provide new splice sites and undergo exonization, since TE sequences can provide little genetic information, the contribution of exonization to gene diversity is mainly due to the exonized gene introns. We simulated the exonization of Ds and Ds1 in maize genome, and analyzed the effect of different splice sites provided by TEs at a single insertion site on the maize genome richness. Of all Ds and Ds1 exonization transcripts, more than 90% of the transcripts would subsequently produce functionally impaired shortened proteins. Type 4 and 5 non-NMD exonization transcripts, which is expected to produce fully functional protein isoforms, accounted for approximately 3.3% of all Ds1 exonization transcripts, compared with 1.8% in the Ds results. In terms of protein isomers, the proportion of C-terminal isomers that are more than 50% similar to the reference protein is about 70%. These protein products may be able to provide more screening advantages for plants without destroying the original protein function. Most of the interior isoforms are the products which number of additional amino acids less than 30. These newly additional small protein fragments may finely modify the reference gene, but the actual protein function still needs further analysis in the future.

並列關鍵字

Ds transposon ； Ds1 transposon ； exonization ； Nonsense-mediated mRNA decay ； alernative spilcing

參考文獻

Arkhipova, I.R. 2017. Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories. Mob DNA 6: 8-19.

Baek, J.-M., Han, P., Iandolino, A. and Cook, D. 2008. Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and maize. Plant Mol Biol 67: 499-510.

Bourque, G., Burns, K.H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin,H.L., Macfarlan,T.S., Mager,D.L., Feschotte, C. 2018. Ten things you should know about transposable elements. Genome Biol 19(1):199.

Campbell, M., Haas, B., Hamilton, J., Mount, S. and Buell, C.R. 2006. Comprehensive analysis of alternative splicing in maize and comparative analyses with Arabidopsis. BMC Genomics 7: 327.

Cartegni, L., Chew, S.L., Krainer, A.R. 2002. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet. 3(4):285–98.