Alternative ORFs and small ORFs: shedding light on the dark proteome
Alternative ORFs and small ORFs: shedding light on the dark proteome
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DOI：
10.1093/nar/gkz734
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发表时间：
2020-02-20
影响因子：
14.9
通讯作者：
Qian，Shu-Bing
中科院分区：
文献类型：
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作者：
Orr，Mona Wu;Mao，Yuanhui;Qian，Shu-Bing
蛋白质编码基因的传统注释依赖于假设，例如一个开放阅读框（ORF）编码一种蛋白质以及翻译蛋白质的最小长度。随着偶然发现翻译的 ORF 编码在带注释的 ORF 的上游和下游，来自嵌套在带注释的 ORF 内的替代起始位点以及来自以前被认为是非编码的 RNA，越来越清楚的是，这些最初的假设是不正确的。这些发现使人们认识到遗传信息的编码更加密集，蛋白质组比之前预期的更加复杂。因此，人们对先前被忽视的“暗蛋白质组”的识别和表征的兴趣正在增加，尽管我们注意到真核生物和细菌的研究在很大程度上是孤立取得的。为了弥合这一差距并说明暗蛋白质组研究中出现的令人兴奋的发现，我们重点介绍了真核细胞和细菌细胞的最新进展。我们讨论了替代 ORF 的检测以及功能理解及其表达调节方面的进展，并为未来的工作提出了问题。
Traditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored ‘dark proteome’ is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.