HeLa和SH-SY5Y细胞系mRNA衰减率的量化揭示了膜蛋白编码转录物的新特性

IF 4.7 2区 医学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Melanie B Martinez, Colton J Williamson, Tareian Cazares, Chunlao Tang, Marjoke F Debets, Pooja Gangras
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引用次数: 0

摘要

转录后调控对siRNA设计至关重要,因为细胞系中的衰减率影响siRNA的效力。这项研究描述了HeLa和SH-SY5Y细胞中具有“快速”和“慢”半衰期的转录本,通常用于药物发现。我们计算了1815个HeLa和5376个SH-SY5Y转录本的半衰期,发现细胞系之间的半衰期相当,尽管HeLa细胞的半衰期通常更长。比较mRNA和蛋白质的半衰期,“快速”衰变转录本编码半衰期较短的蛋白质,而“缓慢”衰变转录本编码稳定的蛋白质。我们通过将HeLa数据与之前的siRNA筛选相比较,将mRNA的衰减率与siRNA活性联系起来,发现更快的衰减转录本具有更低的敲除。令人惊讶的是,稳定的转录本,更容易被敲除,被膜蛋白编码转录本过度代表。尽管它们很稳定,但这些转录本在不受miRNA调控的情况下具有低至中等水平的表达。我们探索了影响mRNA稳定性和表达的顺式和反式特征,表明低RNA结合蛋白(RBP)结合,结合特异性稳定RBP调控,有助于这些膜蛋白编码转录物的稳定性。这项研究强调了了解转录物特征、mRNA衰变及其对siRNA功效的潜在影响的重要性,特别是对编码膜蛋白的转录物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Quantification of mRNA Decay Rates in HeLa and SH-SY5Y Cell Lines Reveals Novel Properties of Membrane Protein Coding Transcripts.

Posttranscriptional regulation is crucial for siRNA design, as decay rates in cell lines influence perceived siRNA potency. This study profiles transcripts with 'fast' and 'slow' half-lives in HeLa and SH-SY5Y cells, commonly used in drug discovery. We calculated half-lives for 1,815 HeLa and 5,376 SH-SY5Y transcripts, finding comparable half-lives between cell lines, though HeLa cells generally had longer half-lives. Comparing mRNA and protein half-lives, 'fast' decay transcripts encoded proteins with shorter half-lives, while 'slow' decay transcripts encoded stable proteins. We linked mRNA decay rates to siRNA activity by comparing HeLa data to a previous siRNA screen, discovering that faster decay transcripts had lower knockdown. Surprisingly, stable transcripts, more amenable to knockdown, were over-represented by membrane protein-coding transcripts. Despite their stability, these transcripts had low-to-moderate expression, regardless of miRNA regulation. We explored cis- and trans- features affecting mRNA stability and expression, suggesting that low RNA binding protein (RBP) binding, combined with specific stabilizing RBP regulation, contributes to the stability of these membrane protein-coding transcripts. This study highlights the importance of understanding transcript features, mRNA decay and its potential impact on siRNA efficacy, particularly for transcripts encoding membrane proteins.

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来源期刊
Nucleic acid therapeutics
Nucleic acid therapeutics BIOCHEMISTRY & MOLECULAR BIOLOGY-CHEMISTRY, MEDICINAL
CiteScore
7.60
自引率
7.50%
发文量
47
审稿时长
>12 weeks
期刊介绍: Nucleic Acid Therapeutics is the leading journal in its field focusing on cutting-edge basic research, therapeutic applications, and drug development using nucleic acids or related compounds to alter gene expression. The Journal examines many new approaches for using nucleic acids as therapeutic agents or in modifying nucleic acids for therapeutic purposes including: oligonucleotides, gene modification, aptamers, RNA nanoparticles, and ribozymes.
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