Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India.
BMC Genomics. 2020 Feb 18;21(1):167. doi: 10.1186/s12864-020-6573-5.
Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcriptional regulation plays a significant role in microbial adaptation to different growth conditions. While the proteins associated with gene expression regulation have been extensively studied in the pathogenic strain M. tuberculosis H37Rv, post-transcriptional regulation involving small RNAs (sRNAs) remains poorly understood.
We developed a novel moving-window based approach to detect sRNA expression using RNA-Seq data. Overlaying ChIP-seq data of RNAP (RNA Polymerase) and NusA suggest that these putative sRNA coding regions are significantly bound by the transcription machinery. Besides capturing many experimentally validated sRNAs, we observe the context-dependent expression of novel sRNAs in the intergenic regions of M. tuberculosis genome. For example, ncRv11806 shows expression only in the stationary phase, suggesting its role in mycobacterial latency which is a key attribute to long term pathogenicity. Also, ncRv11875C showed expression in the iron-limited condition, which is prevalent inside the macrophages of the host cells.
The systems level analysis of sRNA highlights the condition-specific expression of sRNAs which might enable the pathogen survival by rewiring regulatory circuits.
结核病仍然是全球发病率和死亡率的主要原因之一。因此，了解结核分枝杆菌的病理生理学对于开发新药至关重要。转录后调控在微生物适应不同生长条件方面起着重要作用。虽然与基因表达调控相关的蛋白质在致病性结核分枝杆菌 H37Rv 菌株中已经得到了广泛研究，但涉及小 RNA（sRNA）的转录后调控仍知之甚少。
我们开发了一种新的基于移动窗口的方法，使用 RNA-Seq 数据来检测 sRNA 的表达。重叠 RNA 聚合酶（RNAP）和 NusA 的 ChIP-seq 数据表明，这些假定的 sRNA 编码区显著被转录机制结合。除了捕获许多经过实验验证的 sRNA 外，我们还观察到结核分枝杆菌基因组基因间区新型 sRNA 的上下文相关表达。例如，ncRv11806 仅在静止期表达，表明其在分枝杆菌潜伏期中的作用，这是长期致病性的关键属性。此外，ncRv11875C 在缺铁条件下表达，这在宿主细胞巨噬细胞中很常见。
sRNA 的系统水平分析强调了 sRNA 的条件特异性表达，这可能通过重新布线调控回路使病原体得以存活。
