Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium.
Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium.
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DOI：
10.1186/gb-2012-13-4-r30
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发表时间：
2012-04-26
期刊：
影响因子：
12.3
通讯作者：
Økstad OA
中科院分区：
文献类型：
--
作者：
Kristoffersen SM;Haase C;Weil MR;Passalacqua KD;Niazi F;Hutchison SK;Desany B;Kolstø AB;Tourasse NJ;Read TD;Økstad OA
近年来，用于基因表达定量的下一代测序技术（RNA 测序、RNA-Seq）的使用显着增加。基因的表达水平是其转录速率和 RNA 衰减的函数，并且在革兰氏阳性细菌的全基因组研究中，mRNA 衰减速率对基因表达的影响尚未得到充分研究。在这项工作中，我们采用 RNA-Seq 来测定革兰氏阳性细菌蜡样芽孢杆菌中 mRNA 的半衰期。通过利用新开发的标准化方案，RNA-Seq 成功用于确定单核苷酸水平的全局 mRNA 衰减率。分析揭示了位置降解模式，mRNA 从分子的两端降解，表明蜡样芽胞杆菌中存在 5' 至 3' 和 3' 至 5' 方向的 RNA 降解。其他操纵子表现出分段降解模式，其中多顺反子内的特定 ORF 以不同的速率降解，强调了 RNA 加工在基因调控中的重要性。我们测定了蜡状芽胞杆菌 ATCC 10987 中 2,700 多个 ORF 的半衰期，范围从不到一分钟到超过 15 分钟，并表明 mRNA 衰减率与 mRNA 表达水平、GC 含量和 ORF 的功能类别总体相关。据我们所知，这项研究首次以单核苷酸分辨率对细菌中的 mRNA 衰减进行了全局分析。我们提供了在细菌 mRNA 衰减分析中使用 RNA-Seq 的原理证明，揭示了单核苷酸水平的 RNA 加工模式。
Recent years have shown a marked increase in the use of next-generation sequencing technologies for quantification of gene expression (RNA sequencing, RNA-Seq). The expression level of a gene is a function of both its rate of transcription and RNA decay, and the influence of mRNA decay rates on gene expression in genome-wide studies of Gram-positive bacteria is under-investigated. In this work, we employed RNA-Seq in a genome-wide determination of mRNA half-lives in the Gram-positive bacterium Bacillus cereus. By utilizing a newly developed normalization protocol, RNA-Seq was used successfully to determine global mRNA decay rates at the single nucleotide level. The analysis revealed positional degradation patterns, with mRNAs being degraded from both ends of the molecule, indicating that both 5' to 3' and 3' to 5' directions of RNA decay are present in B. cereus. Other operons showed segmental degradation patterns where specific ORFs within polycistrons were degraded at variable rates, underlining the importance of RNA processing in gene regulation. We determined the half-lives for more than 2,700 ORFs in B. cereus ATCC 10987, ranging from less than one minute to more than fifteen minutes, and showed that mRNA decay rate correlates globally with mRNA expression level, GC content, and functional class of the ORF. To our knowledge, this study presents the first global analysis of mRNA decay in a bacterium at single nucleotide resolution. We provide a proof of principle for using RNA-Seq in bacterial mRNA decay analysis, revealing RNA processing patterns at the single nucleotide level.
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影响因子：
12.3
作者：
Andersson, Anders F.;Lundgren, Magnus;Nilsson, Peter
通讯作者：
Nilsson, Peter
DOI：
10.1073/pnas.84.2.498
发表时间：
1987-01-01
影响因子：
11.1
作者：
BECHHOFER, DH;DUBNAU, D
通讯作者：
DUBNAU, D
DOI：
10.1073/pnas.0402414101
发表时间：
2004-06-01
影响因子：
11.1
作者：
Hoffmaster, AR;Ravel, J;Fraser, CM
通讯作者：
Fraser, CM
影响因子：
14.9
作者：
Even S;Pellegrini O;Zig L;Labas V;Vinh J;Bréchemmier-Baey D;Putzer H
通讯作者：
Putzer H
DOI：
10.1073/pnas.112318199
发表时间：
2002-07-23
影响因子：
11.1
作者：
Bernstein, JA;Khodursky, AB;Cohen, SN
通讯作者：
Cohen, SN