密碼子使用偏移是指在編碼同一種氨基酸時，同義密碼子的使用頻率並不相等，而這種現象在原核生物及真核生物中視高度保守。然而在同一種生物中，當細胞面對不同的壓力環境（例如營養有限的環境和在生長發育）時，或是不同組織或狀態下的密碼子的使用頻率可能也會不同。在原核生物、較低等的真核生物以及模式生物中已經證明，密碼子使用偏移對於調節共翻譯蛋白折疊，新生信使RNA（mRNA）的轉錄和mRNA的穩定性中具有關鍵性的作用。在發芽酵母中的研究表明mRNA組成富含最佳密碼子（經常使用）時，它們通常具有更高的翻譯效率、穩定性和更高的蛋白質產量。相反地，如果mRNA組成含有大量非最佳密碼子（很少使用），可能會造成核醣體在轉譯時停滯以及較短的mRNA半衰期，最終導致蛋白質合成不完整以及使mRNA被降解。然而，大多數這些作用在哺乳動物中仍不清楚。為了量測密碼子對哺乳動物mRNA的影響，我們設計了具有不同密碼子使用組合的螢火蟲熒光素酶（FL）做為報導基因，再將這些帶有不同密碼子排列組成的質體，轉染到人類細胞株HEK293T或PANC-1中。首先，我們發現與先前的結果不同，無法偵測到非最佳密碼子所組成全長的FL mRNA。接著，藉由交換非最佳編碼序列的區域，我們得到結論，不論位置或長度都有密碼子使用偏移的影響。通過轉譯抑制劑和強力的結構阻止轉譯的發生，無法使以非最佳密碼子組成全長的mRNA 再現，如同最佳密碼子實驗結果。不可思議的是在細胞核中，非最佳密碼子pre-RNA的量如同最佳密碼子的組別。總的來說，我的結果指出密碼子使用偏移在細胞中存在著特異性，一個未確認且與轉譯無關的降解機制，感應密碼子使用偏移在人類細胞中調節mRNA的穩定性。

Codon usage bias (CUB) refers to the unequal usage of synonymous codons. This CUB phenomenon is highly conserved through prokaryotes to eukaryotes. Even in the same organism, there may be different CUB in different tissues or different status when cells face different stress environments, such as nutrient-limited environments and development. It has been shown, in prokaryotes, lower eukaryotes and model animals, that CUB plays a critical role in regulating co-translational protein folding, nascent messenger RNA (mRNA) transcription and mRNA stability. Previous studies in budding yeast showed that when transcripts enrich with optimal codons (frequently used), they usually have higher translation efficiency, more stable mRNA, and higher protein production. Otherwise, transcripts with abundant non-optimal codons (rarely used) may result in stalling of ribosomes and shorter mRNA half-life, which ultimately leads to incomplete protein synthesis and mRNA degradation. However, most of these effects are still unclear in mammals. To monitor the codon effect on mRNA levels in mammals, we designed firefly luciferase (FL) reporter genes with distinct codon usage patterns followed by the transfection of these constructs into target cell lines, HEK293T or Panc-1. We observed that the full-length of non-optimal FL mRNA is undetectable, unlike to previous results. Next, by swapping the non-optimal coding sequences, we concluded that the position and the length are coordinated the CUB effect on mRNA level. Blocking the translation by translation inhibitor and/or a strong structure cannot rescue the poor codon mRNA. Intriguingly, the pre-mRNA level of non-optimal FL is similar to the optimal ones. In sum, my data suggested that there existed a cell type-specific unidentified translation-independent degradation that senses CUB to regulate transcript stability in human cells.

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