Massively parallel analysis of human 3' UTRs reveals that AU-rich element length and registration predict mRNA destabilization.
Massively parallel analysis of human 3' UTRs reveals that AU-rich element length and registration predict mRNA destabilization.
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DOI：
10.1093/g3journal/jkab404
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发表时间：
2022-01-04
期刊：
影响因子：
--
通讯作者：
Erle DJ
中科院分区：
文献类型：
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作者：
Siegel DA;Le Tonqueze O;Biton A;Zaitlen N;Erle DJ
富au元件（AREs）是调节mrna稳定性的3′UTR顺式调控元件。已经确定了一致的ARE基序，但对于符合这些基序的3 ' UTR序列的差异如何影响其功能知之甚少。在这里，我们使用3 ' UTR序列的功能注释（fast-UTR），大规模平行报告基因试验（MPRA），研究了4653个转录本中的41,288个3 ' UTR序列片段对Jurkat和Beas2B细胞基因表达和mRNA稳定性的影响。我们的分析表明，一个ARE的长度和它的注册（第一个和最后一个核苷酸重复的ARE基序）对基因的表达和稳定性有显著的影响。基于这一发现，我们提出了改进的ARE分类和伴随方法来分类和预测AREs对基因表达和稳定性的影响。最后，为了研究我们的一般实验设计的优势，我们研究了其他基序，包括本构衰变元件（CDEs），我们发现CDE茎环的长度对稳态表达和mRNA稳定性有显著影响。我们的结论是，快速utr与我们的分析方法相结合，可以产生改进而简单的基于序列的规则来预测人类3 ' utr的活性。
AU-rich elements (AREs) are 3′ UTR cis-regulatory elements that regulate the stability of mRNAs. Consensus ARE motifs have been determined, but little is known about how differences in 3′ UTR sequences that conform to these motifs affect their function. Here, we use functional annotation of sequences from 3′ UTRs (fast-UTR), a massively parallel reporter assay (MPRA), to investigate the effects of 41,288 3′ UTR sequence fragments from 4653 transcripts on gene expression and mRNA stability in Jurkat and Beas2B cells. Our analyses demonstrate that the length of an ARE and its registration (the first and last nucleotides of the repeating ARE motif) have significant effects on gene expression and stability. Based on this finding, we propose improved ARE classification and concomitant methods to categorize and predict the effect of AREs on gene expression and stability. Finally, to investigate the advantages of our general experimental design we examine other motifs including constitutive decay elements (CDEs), where we show that the length of the CDE stem-loop has a significant impact on steady-state expression and mRNA stability. We conclude that fast-UTR, in conjunction with our analytical approach, can produce improved yet simple sequence-based rules for predicting the activity of human 3′ UTRs.