Mapping the Clostridium acetobutylicum transcriptome under butanol and butyrate stresses using strand-specific RNA-seq data. Clostridium acetobutylicum ATCC 824

The C. acetobutylicum genome annotation cab me markedly improved by integrating bioinformatic predictions with Illumina-based strand-specific deep RNA sequencing (RNA-seq) data. Samples were acquired under low, medium and high butanol or butyrate stress, with unstressed conditions as control, across exponential and transition-phase time points to assess the cell’s transcriptome as it responds to metabolite stress in various physiological states represented by the aforementioned culture conditions. Reference assembly and curation were used to identify transcript boundaries, operon organization, and regulatory regions. This combined approach minimized false positive errors from the highly sensitive sequencing technique. Transcript boundaries from several canonical transcripts were determined to the exact base pair. This dataset was used to generate the first strand-specific transcriptome assembly in a Clostridium organism. The data were also used for comparative analysis against corresponding proteome data in order to assess more complex regulation of genes and programs involving post-transcriptional regulation.

丙酮丁醇梭菌（Clostridium acetobutylicum）的基因组注释可通过将生物信息学预测与基于Illumina平台的链特异性深度RNA测序（RNA-seq）数据相结合，得到显著优化。我们在低、中、高浓度丁醇或丁酸盐胁迫条件下，以及无胁迫的对照条件下，采集了处于指数生长期与过渡生长期不同时间点的样本，以此评估细胞在上述培养条件所代表的不同生理状态下，应对代谢物胁迫时的转录组特征。通过参考基因组组装与注释梳理流程，我们得以鉴定转录本边界、操纵子（operon）结构与调控区域。这种整合策略有效降低了高灵敏度测序技术易引入的假阳性误差。多个经典转录本的边界被精准定位至单个碱基对水平。本数据集被用于构建梭菌属（Clostridium）生物体首个链特异性转录组组装集。该数据集还被用于与对应蛋白质组（proteome）数据开展比较分析，以评估涉及转录后调控的基因与调控程序的更为复杂的调控机制。