Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana
Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana
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DOI：
10.1109/tnb.2016.2516950
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发表时间：
2016-03-01
影响因子：
3.9
通讯作者：
Heber, Steffen
中科院分区：
文献类型：
--
作者：
Hu, Qiwen;Merchante, Catharina;Heber, Steffen
上游开放阅读框（uORF）是出现在mRNA的5' UTR内的开放阅读框。在许多生物体中发现了uORF。它们在基因调控、细胞发育和各种代谢过程中发挥重要作用。据信，翻译的uORF降低主要编码区的翻译效率。然而，只有少数的uORF的实验特征。在本文中，我们使用核糖体足迹结合半监督方法的基础上堆叠分类模型，以确定在拟南芥中翻译的uORF。我们的方法在2051个基因中鉴定了5360个潜在翻译的uORF。在具有翻译的uORF的基因中富集的GO术语包括催化活性、结合、转移酶活性、磷酸转移酶活性、激酶活性和转录调节剂活性。已报道的uORFs在多亚型基因中出现的频率较高，并且一些uORFs受到可变转录起始位点或可变剪接事件的影响。关联规则挖掘揭示了与uORF的翻译状态相关的序列特征。我们推测uORF的翻译是一个受多种因素调控的复杂过程。鉴定的uORF可在以下网址在线获得：https://www.dropbox.com/sh/zdutupedx-afhly8/AABFsdNR5zDfiozB7B4igFcja? dl=0。本文是我们在ISBRA 2015上发表的研究的扩展版本。
Upstream open reading frames (uORFs) are open reading frames that occur within the 5' UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes. It is believed that translated uORFs reduce the translational efficiency of the main coding region. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana. Our approach identified 5360 potentially translated uORFs in 2051 genes. GO terms enriched in genes with translated uORFs include catalytic activity, binding, transferase activity, phosphotransferase activity, kinase activity, and transcription regulator activity. The reported uORFs occur with a higher frequency in multi-isoform genes, and some uORFs are affected by alternative transcript start sites or alternative splicing events. Association rule mining revealed sequence features associated with the translation status of the uORFs. We hypothesize that uORF translation is a complex process that might be regulated by multiple factors. The identified uORFs are available online at: https://www.dropbox.com/sh/zdutupedx-afhly8/AABFsdNR5zDfiozB7B4igFcja?dl=0. This paper is the extended version of our research presented at ISBRA 2015.