Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions.
Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions.
复制标题
常氧和低氧条件下海分枝杆菌转录起始位点的基因组规模分析
DOI：
10.1186/s12864-021-07572-8
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发表时间：
2021-04-06
期刊：
影响因子：
4.4
通讯作者：
Chen S
中科院分区：
文献类型：
--
作者：
Huang S;Zhou W;Tang W;Zhang Y;Hu Y;Chen S
背景
低氧应激在结核分枝杆菌（Mtb）感染的持续性中起着关键作用，但这种适应性反应的机制仍不清楚。
材料和方法
在本研究中，使用M. marinum作为替代，我们通过Cappable-seq和常规RNA-seq分析在转录水平上分析了缺氧反应。
结果
在常氧和低氧条件下，共鉴定出6808个转录起始位点（TSS）。在这些TSS中，1112上调，1265下调，响应缺氧应激。使用SigE识别的共有序列，我们确定了59个SigE依赖性启动子，并且在低氧胁迫下均上调，表明SigE在此过程中发挥重要作用。我们还使用从常氧和缺氧条件下收集的相同RNA样品比较了Cappable-seq和常规RNA-seq的性能，并证实Cappable-seq是一种有价值的全局转录调控分析方法。
结论
我们的研究结果为进一步表征分枝杆菌对缺氧的反应提供了见解和信息，并证明Cappable-seq是分枝杆菌全球转录研究的一种有价值的方法。
Background
Hypoxic stress plays a critical role in the persistence of Mycobacterium tuberculosis (Mtb) infection, but the mechanisms underlying this adaptive response remain ill defined.
Material and methods
In this study, using M. marinum as a surrogate, we analyzed hypoxic responses at the transcriptional level by Cappable-seq and regular RNA-seq analyses.
Results
A total of 6808 transcriptional start sites (TSSs) were identified under normoxic and hypoxic conditions. Among these TSSs, 1112 were upregulated and 1265 were downregulated in response to hypoxic stress. Using SigE-recognized consensus sequence, we identified 59 SigE-dependent promoters and all were upregulated under hypoxic stress, suggesting an important role for SigE in this process. We also compared the performance of Cappable-seq and regular RNA-seq using the same RNA samples collected from normoxic and hypoxic conditions, and confirmed that Cappable-seq is a valuable approach for global transcriptional regulation analyses.
Conclusions
Our results provide insights and information for further characterization of responses to hypoxia in mycobacteria, and prove that Cappable-seq is a valuable approach for global transcriptional studies in mycobacteria.
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DOI：
10.1126/science.aad9822
发表时间：
2016-04-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dar D;Shamir M;Mellin JR;Koutero M;Stern-Ginossar N;Cossart P;Sorek R
通讯作者：
Sorek R
影响因子：
3.7
作者：
Manganelli, Riccardo
通讯作者：
Manganelli, Riccardo
影响因子：
11.3
作者：
Gengenbacher M;Kaufmann SH
通讯作者：
Kaufmann SH
影响因子：
8.8
作者：
Cortes T;Schubert OT;Rose G;Arnvig KB;Comas I;Aebersold R;Young DB
通讯作者：
Young DB
DOI：
10.1073/pnas.1710167114
发表时间：
2017-12-12
影响因子：
11.1
作者：
Bosserman, Rachel E.;Nguyen, Tiffany T.;Champion, Patricia A.
通讯作者：
Champion, Patricia A.