多种内在特性决定了烟曲霉中转录本的稳定性和稳定性。

IF 4 Q1 GENETICS & HEREDITY NAR Genomics and Bioinformatics Pub Date : 2024-11-04 eCollection Date: 2024-09-01 DOI:10.1093/nargab/lqae147
Huaming Sun, Diego A Vargas-Blanco, Ying Zhou, Catherine S Masiello, Jessica M Kelly, Justin K Moy, Dmitry Korkin, Scarlet S Shell
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引用次数: 0

摘要

分枝杆菌通过调节转录本降解来促进对环境压力的适应。然而,这种调控的机制尚不清楚。在此,我们试图通过研究与转录本稳定性差异和应激诱导的转录本稳定相关的转录本特性,来了解控制 mRNA 稳定的机制。我们测量了烟曲霉菌在对数生长期和缺氧诱导生长停滞期整个转录组的 mRNA 半衰期。在低氧诱导下,转录组在整体上趋于稳定,但必需基因的转录物通常比非必需基因的转录物更稳定。然后,我们开发了机器学习模型,使我们能够识别一系列转录本特性对转录本稳定性和稳定化的非线性集体影响。我们确定了在对数相中对半衰期更有预测性的特性,以及在缺氧条件下更有预测性的特性,其中许多特性在有领导和无领导转录本之间存在差异。总之,我们发现转录本特性与转录本稳定性的关系因转录本类型和生长条件而异。我们的研究结果揭示了转录本特征与微环境之间复杂的相互作用,这种相互作用影响了分枝杆菌中转录本的稳定性。
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Diverse intrinsic properties shape transcript stability and stabilization in Mycolicibacterium smegmatis.

Mycobacteria regulate transcript degradation to facilitate adaptation to environmental stress. However, the mechanisms underlying this regulation are unknown. Here we sought to gain understanding of the mechanisms controlling mRNA stability by investigating the transcript properties associated with variance in transcript stability and stress-induced transcript stabilization. We measured mRNA half-lives transcriptome-wide in Mycolicibacterium smegmatis in log phase growth and hypoxia-induced growth arrest. The transcriptome was globally stabilized in response to hypoxia, but transcripts of essential genes were generally stabilized more than those of non-essential genes. We then developed machine learning models that enabled us to identify the non-linear collective effect of a compendium of transcript properties on transcript stability and stabilization. We identified properties that were more predictive of half-life in log phase as well as properties that were more predictive in hypoxia, and many of these varied between leadered and leaderless transcripts. In summary, we found that transcript properties are differentially associated with transcript stability depending on both the transcript type and the growth condition. Our results reveal the complex interplay between transcript features and microenvironment that shapes transcript stability in mycobacteria.

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来源期刊
CiteScore
8.00
自引率
2.20%
发文量
95
审稿时长
15 weeks
期刊最新文献
Diverse intrinsic properties shape transcript stability and stabilization in Mycolicibacterium smegmatis. Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR v4. Tumor purity estimated from bulk DNA methylation can be used for adjusting beta values of individual samples to better reflect tumor biology. Intronic RNA secondary structural information captured for the human MYC pre-mRNA. The next-generation sequencing-chess problem.
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