Antisense transcription is pervasive but rarely conserved in enteric bacteria.
Antisense transcription is pervasive but rarely conserved in enteric bacteria.
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作者：
Raghavan R;Sloan DB;Ochman H
非编码RNA，包括源自蛋白质编码基因互补链的反义RNA（asRNA），参与调节生命所有领域的基因表达。最近深度测序技术的应用揭示了asRNA的转录在细菌中发生在全基因组范围内。虽然绝大多数asRNA的作用仍然未知，但通常认为它们的存在意味着重要的调控功能，类似于其他非编码RNA。或者，许多反义转录物可以通过启动子样序列的偶然转录事件产生，所述启动子样序列由细菌转录因子结合位点的简并性质产生。为了研究反义转录物的生物学相关性，我们通过进行链特异性转录组测序，比较了密切相关的肠道细菌、大肠杆菌和沙门氏菌血清型鼠伤寒沙门氏菌中asRNA表达的全基因组模式。尽管反义转录物在这两个物种中都很丰富，但在这两个物种中只有不到3%的asRNA以高水平表达，并且只有约14%的asRNA在物种之间是保守的。与蛋白质编码基因的启动子不同，asRNA启动子在物种之间甚至物种内部都没有序列保守性的证据。我们的研究结果表明，许多甚至大多数细菌asRNA是细胞转录机制的非适应性副产品。高通量方法的应用已经揭示了在与蛋白质编码基因互补的链上编码的转录物在整个细菌基因组中的表达。由于转录是昂贵的，通常认为这些转录本，称为反义RNA（asRNA），提供一些功能;然而，大多数asRNA的作用是不清楚的，提出了关于它们在细胞过程中的相关性的问题。由于自然选择保存功能元件，相关物种之间的比较提供了一种评估全基因组功能的方法。应用这种方法，我们分析了两种密切相关的细菌，大肠杆菌和沙门氏菌血清型鼠伤寒沙门氏菌的所有成绩单，并证明，虽然全基因组反义转录的水平在两种细菌中同样高，只有一小部分的asRNA跨物种共享。此外，与asRNA相关的启动子没有证据表明物种之间或甚至物种内的序列保守性。这些发现表明，尽管asRNA的全基因组转录，但这些转录物中的许多可能是无功能的。
Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To investigate the biological relevance of antisense transcripts, we compared genome-wide patterns of asRNA expression in closely related enteric bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, by performing strand-specific transcriptome sequencing. Although antisense transcripts are abundant in both species, less than 3% of asRNAs are expressed at high levels in both species, and only about 14% appear to be conserved among species. And unlike the promoters of protein-coding genes, asRNA promoters show no evidence of sequence conservation between, or even within, species. Our findings suggest that many or even most bacterial asRNAs are nonadaptive by-products of the cell’s transcription machinery. Application of high-throughput methods has revealed the expression throughout bacterial genomes of transcripts encoded on the strand complementary to protein-coding genes. Because transcription is costly, it is usually assumed that these transcripts, termed antisense RNAs (asRNAs), serve some function; however, the role of most asRNAs is unclear, raising questions about their relevance in cellular processes. Because natural selection conserves functional elements, comparisons between related species provide a method for assessing functionality genome-wide. Applying such an approach, we assayed all transcripts in two closely related bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, and demonstrate that, although the levels of genome-wide antisense transcription are similarly high in both bacteria, only a small fraction of asRNAs are shared across species. Moreover, the promoters associated with asRNAs show no evidence of sequence conservation between, or even within, species. These findings indicate that despite the genome-wide transcription of asRNAs, many of these transcripts are likely nonfunctional.