The Enrichment of miRNA-Targeted mRNAs in Translationally Less Active over More Active Polysomes.
The Enrichment of miRNA-Targeted mRNAs in Translationally Less Active over More Active Polysomes.
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MicroRNA (miRNA) 会抑制翻译并增强其靶标 mRNA 的降解，但效果有限。矛盾的是，miRNA 及其靶标 mRNA 是多核糖体相关的，这应该可以保护 mRNA 免遭降解。为了从机械上解决这个悖论，我们对人类细胞进行了翻译活性较低的轻多核糖体和活性较高的重多核糖体的比较分析。由于 DICER1 基因破坏而无法产生成熟 miRNA 的同基因突变细胞被用作背景模型。观察到轻多核糖体中 miRNA 靶向 mRNA 的富集程度高于重多核糖体。也就是说，尽管多核糖体相关，但 miRNA 靶向的 mRNA 在翻译活性较低的多核糖体复合物中富集。这种富集调和了看似矛盾的 miRNA 调控活性、它们的温和性和多核糖体关联。 miRNA 通过主要位于 3'-非翻译区 (UTR) 的同源结合位点适度抑制翻译并增强其靶 mRNA 的降解。矛盾的是，miRNA 靶标也与多核糖体相关。我们通过对野生型 (WT) 人类细胞系及其同基因突变体 (MT) 进行比较翻译活性较低的轻多聚核糖体和活性较高的重多聚核糖体分析来研究多核糖体关联，其中 DICER1 基因被破坏，从而产生成熟的 miRNA。正如预期的那样，开放阅读框 (ORF) 长度是轻链与重链多核糖体 mRNA 丰度比的主要决定因素，但由于 miRNA 调节活性，其在 WT 细胞中的作用不如 MT 细胞中的强大。我们还观察到，miRNA 倾向于靶向具有较长 ORF 的 mRNA，并且通过 ORF 长度调整 mRNA 丰度比可以改善其与 3'-UTR miRNA 结合位点计数的相关性。在 WT 细胞中，相对于重多核糖体，miRNA 靶向 mRNA 在光下表现出更高的丰度，即轻多核糖体富集。在MT细胞中，DICER1破坏不仅显着消除了轻多聚核糖体的富集，而且还缩小了mRNA丰度比值范围。此外，由于 DICER1 基因破坏而导致的富集取消，即从 WT 到 MT 细胞，ORF 长度调整的 mRNA 丰度比降低，与 3'-UTR 结合位点计数呈现近乎完美的线性相关。转录因子和蛋白激酶是最丰富的两个 mRNA 组。总而言之，这些结果为 miRNA 靶向 mRNA 的轻多聚核糖体富集提供了证据，以协调多核糖体关联和适度的翻译抑制，并且 ORF 长度是一个重要的转录组调节参数，尽管目前尚未得到充分重视。
MicroRNAs (miRNA) inhibit the translation and enhance the degradation of their target mRNAs, but only moderately. Paradoxically, miRNAs and their target mRNAs are polysome-associated, which should protect mRNAs from degradation. To mechanistically solve the paradox, we performed comparative translationally less-active light and more-active heavy polysome profiling of human cells. Isogenic mutant cells incapable of mature miRNA production due to a disrupted DICER1 gene were used as the background model. The enrichment of miRNA-targeted mRNAs in light- over heavy-polysome was observed. That is, though polysome-associated, miRNA-targeted mRNAs are enriched in the translationally less-active polysome complexes. This enrichment reconciles the seemingly contradictive miRNA regulatory activities, their moderateness and the polysome association. miRNAs moderately inhibit the translation and enhance the degradation of their target mRNAs via cognate binding sites located predominantly in the 3′-untranslated regions (UTR). Paradoxically, miRNA targets are also polysome-associated. We studied the polysome association by the comparative translationally less-active light- and more-active heavy-polysome profiling of a wild type (WT) human cell line and its isogenic mutant (MT) with a disrupted DICER1 gene and, thus, mature miRNA production. As expected, the open reading frame (ORF) length is a major determinant of light- to heavy-polysome mRNA abundance ratios, but is rendered less powerful in WT than in MT cells by miRNA-regulatory activities. We also observed that miRNAs tend to target mRNAs with longer ORFs, and that adjusting the mRNA abundance ratio with the ORF length improves its correlation with the 3′-UTR miRNA-binding-site count. In WT cells, miRNA-targeted mRNAs exhibit higher abundance in light relative to heavy polysomes, i.e., light-polysome enrichment. In MT cells, the DICER1 disruption not only significantly abrogated the light-polysome enrichment, but also narrowed the mRNA abundance ratio value range. Additionally, the abrogation of the enrichment due to the DICER1 gene disruption, i.e., the decreases of the ORF-length-adjusted mRNA abundance ratio from WT to MT cells, exhibits a nearly perfect linear correlation with the 3′-UTR binding-site count. Transcription factors and protein kinases are the top two most enriched mRNA groups. Taken together, the results provide evidence for the light-polysome enrichment of miRNA-targeted mRNAs to reconcile polysome association and moderate translation inhibition, and that ORF length is an important, though currently under-appreciated, transcriptome regulation parameter.
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DOI：
10.1038/s41379-021-00905-8
发表时间：
2022-01
期刊：
Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc
影响因子：
--
作者：
González IA;Stewart DR;Schultz KAP;Field AP;Hill DA;Dehner LP
通讯作者：
Dehner LP
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
64.8
作者：
Chendrimada, TP;Gregory, RI;Shiekhattar, R
通讯作者：
Shiekhattar, R
影响因子：
4.4
作者：
Bikas, Das Asim
通讯作者：
Bikas, Das Asim
MicroRNA结合位点中的单核苷酸多态性：大肠癌的影响。
影响因子：
--
作者：
Bhaumik P;Gopalakrishnan C;Kamaraj B;Purohit R
通讯作者：
Purohit R