Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.
Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.
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DOI：
10.1080/15476286.2021.1917891
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发表时间：
2021-12
期刊：
影响因子：
4.1
通讯作者：
Breaker RR
中科院分区：
文献类型：
--
作者：
Brewer KI;Greenlee EB;Higgs G;Yu D;Mirihana Arachchilage G;Chen X;King N;White N;Breaker RR
比较序列分析方法对于从细菌基因组DNA序列数据集中发现新型结构化非编码RNA（ncRNA）是非常有效的。以前，我们开发了一个计算管道，以更全面地识别来自单个细菌基因组的结构化ncRNA代表。这个搜索过程利用了这样一个事实，即作为结构化RNA转录模板的基因组区域往往存在于比平均非编码“基因间区域”（IGR）更长的区域中，与基因组的其余部分相比，IGR富含G和C核苷酸。在本研究中，我们应用这种计算管道来识别来自26种不同细菌物种的结构化ncRNA候选物。许多新的结构的ncRNA基序被发现，包括几个核糖开关候选人，其配体已被确定和其他尚未实验验证。我们的研究结果支持了最近的预测，即在基因组已被完全测序的有限数量的细菌物种中，仍有数百种新型核糖开关类和其他ncRNA未被发现。
Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding ‘intergenic regions’ (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.
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DOI：
10.1126/science.aad9822
发表时间：
2016-04-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dar D;Shamir M;Mellin JR;Koutero M;Stern-Ginossar N;Cossart P;Sorek R
通讯作者：
Sorek R
DOI：
10.1073/pnas.86.18.7054
发表时间：
1989-09-01
影响因子：
11.1
作者：
BENNER, SA;ELLINGTON, AD;TAUER, A
通讯作者：
TAUER, A
DOI：
10.1261/rna.067975.118
发表时间：
2019-01
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Atilho RM;Perkins KR;Breaker RR
通讯作者：
Breaker RR
影响因子：
4.1
作者：
Greenlee, Etienne B.;Stav, Shira;Breaker, Ronald R.
通讯作者：
Breaker, Ronald R.
影响因子：
7.2
作者：
Breaker, Ronald R.
通讯作者：
Breaker, Ronald R.