Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq).
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq).
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DOI：
10.1186/s12864-016-2920-y
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发表时间：
2016-08-12
期刊：
影响因子：
4.4
通讯作者：
Soppa J
中科院分区：
文献类型：
--
作者：
Babski J;Haas KA;Näther-Schindler D;Pfeiffer F;Förstner KU;Hammelmann M;Hilker R;Becker A;Sharma CM;Marchfelder A;Soppa J
差异RNA-Seq (dRNA-Seq) 是最近开发的一种进行初级转录组分析的方法，可以对转录起始位点(TSS) 进行全基因组定位并识别新转录本。尽管不同细菌物种的转录组已通过 dRNA-Seq 进行了表征，但古细菌物种的转录组分析仍然相当有限。因此，我们使用 dRNA-Seq 来表征模型古菌 Haloferax volcanii 的初级转录组。 Hfx 的三种独立文化。在最佳条件下生长至指数生长期中期的火山菌用于确定初级转录组并绘制转录本的 5' 末端图谱。总共检测到 4749 个潜在的 TSS。为启动子预测导出了位置权重矩阵 (PWM)，结果表明 64% 的 TSS 之前有严格或宽松的基础启动子。在已识别的 TSS 中，1851 个属于蛋白质编码基因。因此，4040 个蛋白质编码基因中只有不到一半 (46%) 在最佳生长条件下得到表达。所有蛋白质编码转录本中有 72% 是无前导序列，这强调了该途径是盐古菌翻译起始的主要途径。总共 2898 个 TSS 属于潜在的非编码 RNA，占所有转录本的比例出乎意料地高 (61%)。大多数非编码 TSS 以前没有被描述过 (2792)，并且代表新颖的序列（占所有 TSS 的 59%）。很大一部分潜在的新型非编码转录本是顺式反义 RNA (1244 aTSS)。研究发现反义转录本和同源有义 mRNA 水平之间存在很强的负相关性，这表明通过反义 RNA 对基因表达的负调控可能在盐古菌中发挥重要作用。其他类型的新型非编码转录本对应于与 mRNA（1153 个 iTSS）和基因间小 RNA（sRNA）候选物（395 个 TSS）重叠的内部转录本。这项研究提供了 Hfx 初级转录组的综合图谱。在最佳条件下生长的火山。不到一半的蛋白质编码基因在这些条件下被转录。出乎意料的是，检测到的 TSS 中有一半以上属于几类非编码 RNA。因此，基于 RNA 的调控似乎在盐古菌中发挥着比之前预期更重要的作用。本文的在线版本 (doi:10.1186/s12864-016-2920-y) 包含补充材料，可供授权用户使用。
Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii. Three independent cultures of Hfx. volcanii grown under optimal conditions to the mid-exponential growth phase were used to determine the primary transcriptome and map the 5′-ends of the transcripts. In total, 4749 potential TSSs were detected. A position weight matrix (PWM) was derived for the promoter predictions, and the results showed that 64 % of the TSSs were preceded by stringent or relaxed basal promoters. Of the identified TSSs, 1851 belonged to protein-coding genes. Thus, fewer than half (46 %) of the 4040 protein-coding genes were expressed under optimal growth conditions. Seventy-two percent of all protein-coding transcripts were leaderless, which emphasized that this pathway is the major pathway for translation initiation in haloarchaea. A total of 2898 of the TSSs belonged to potential non-coding RNAs, which accounted for an unexpectedly high fraction (61 %) of all transcripts. Most of the non-coding TSSs had not been previously described (2792) and represented novel sequences (59 % of all TSSs). A large fraction of the potential novel non-coding transcripts were cis-antisense RNAs (1244 aTSSs). A strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs was found, which suggested that the negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts corresponded to internal transcripts overlapping with mRNAs (1153 iTSSs) and intergenic small RNA (sRNA) candidates (395 TSSs). This study provides a comprehensive map of the primary transcriptome of Hfx. volcanii grown under optimal conditions. Fewer than half of all protein-coding genes have been transcribed under these conditions. Unexpectedly, more than half of the detected TSSs belonged to several classes of non-coding RNAs. Thus, RNA-based regulation appears to play a more important role in haloarchaea than previously anticipated. The online version of this article (doi:10.1186/s12864-016-2920-y) contains supplementary material, which is available to authorized users.