A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease.
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease.
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DOI：
10.1186/1471-2164-14-620
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发表时间：
2013-09-14
期刊：
影响因子：
4.4
通讯作者：
McDowall KJ
中科院分区：
文献类型：
--
作者：
Lin YF;A DR;Guan S;Mamanova L;McDowall KJ
痤疮丙酸杆菌的基因组测序产生了一个基因目录，其中许多基因使这种有机体能够在皮肤上定居并在暴露于自然环境中存活下来。尽管有了这个平台，但人们对产生对人类健康和福祉产生重大影响并导致皮肤以外感染的生物体的基因调控知之甚少。为了解决这一问题，我们进行了一项基因调控的全基因组研究，结合了改进的差异和全局rna测序以及考虑到数据中固有噪声的分析方法。我们已经制作了核苷酸分辨率转录组图，以识别和区分转录起始位点与稳定RNA加工和mRNA切割位点。此外，对这些图谱的分析为“普遍”转录提供了强有力的证据，并表明与最初的迹象相反，它并不偏向于产生反义rna。此外，这些图谱还揭示了大量的核开关、无领导mrna和小的非蛋白质编码rna，以及植物启动子和转录后事件，其中包括不寻常的tRNA加工。这些特征的识别将为复杂基因调控模型提供信息，如这里所示的核糖核苷酸还原酶和潜在的群体感应双组分系统。这里描述的方法，可转移到任何细菌物种，已经产生了一个步骤增加全细胞知识的基因调控痤疮假单胞杆菌。继续扩展我们的图谱，包括与不同生长条件和遗传背景相关的转录，将提供一个新的平台，从这个平台上计算决定痤疮假单胞杆菌生理及其在人类疾病中的作用的基因表达。
Sequencing of the genome of Propionibacterium acnes produced a catalogue of genes many of which enable this organism to colonise skin and survive exposure to the elements. Despite this platform, there was little understanding of the gene regulation that gives rise to an organism that has a major impact on human health and wellbeing and causes infections beyond the skin. To address this situation, we have undertaken a genome–wide study of gene regulation using a combination of improved differential and global RNA-sequencing and an analytical approach that takes into account the inherent noise within the data. We have produced nucleotide-resolution transcriptome maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for ‘pervasive’ transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events, which includes unusual tRNA processing. The identification of such features will inform models of complex gene regulation, as illustrated here for ribonucleotide reductases and a potential quorum-sensing, two-component system. The approach described here, which is transferable to any bacterial species, has produced a step increase in whole-cell knowledge of gene regulation in P. acnes. Continued expansion of our maps to include transcription associated with different growth conditions and genetic backgrounds will provide a new platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease.
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影响因子：
14.9
作者：
Benson DA;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
3.7
作者：
Beaume M;Hernandez D;Farinelli L;Deluen C;Linder P;Gaspin C;Romby P;Schrenzel J;Francois P
通讯作者：
Francois P
影响因子：
3.7
作者：
Brzuszkiewicz E;Weiner J;Wollherr A;Thürmer A;Hüpeden J;Lomholt HB;Kilian M;Gottschalk G;Daniel R;Mollenkopf HJ;Meyer TF;Brüggemann H
通讯作者：
Brüggemann H
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS
影响因子：
16
作者：
Bandyra, Katarzyna J.;Said, Nelly;Pfeiffer, Verena;Gorna, Maria W.;Vogel, Joerg;Luisi, Ben F.
通讯作者：
Luisi, Ben F.