Global transcription of CRISPR loci in the human oral cavity.
Global transcription of CRISPR loci in the human oral cavity.
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DOI：
10.1186/s12864-015-1615-0
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发表时间：
2015-05-21
期刊：
影响因子：
4.4
通讯作者：
Pride DT
中科院分区：
文献类型：
--
作者：
Lum AG;Ly M;Santiago-Rodriguez TM;Naidu M;Boehm TK;Pride DT
成簇规则间隔短回文重复序列 (CRISPR) 在许多环境中对噬菌体和质粒的获得性抗性中具有活性。在人类口腔中，CRISPR基因座进化以对抗口腔噬菌体，但这些CRISPR基因座的表达此前尚未被研究过。我们对多种不同口腔细菌中发现的 CRISPR 位点的 cDNA 进行了测序，并与口腔噬菌体群落进行比较，以确定 CRISPR 位点的转录是否专门针对口腔环境中存在的高度丰富的噬菌体。我们发现，在研究的 529,027 个 CRISPR 间隔基团中，88% 可以在转录本中被识别，这表明口腔中的绝大多数 CRISPR 位点都被转录了。 CRISPR 间隔区库与口腔健康状况或核酸类型之间没有很强的关联。我们还将 CRISPR 库与口腔噬菌体群落进行了比较，发现无论评估哪种 CRISPR 类型，CRISPR 转录本和口腔噬菌体之间都没有显着关联。我们对高表达的 CRISPR 间隔区进行了表征，发现它们并不比其他间隔区更可能匹配口腔噬菌体。通过将带有 CRISPR 的读数重新组装成更长的 CRISPR 基因座，我们发现大多数基因座没有与研究对象口腔中发现的病毒相匹配的间隔区。对于某些 CRISPR 类型，包含与口腔噬菌体匹配的间隔区的基因座明显更有可能具有多个间隔区，而不是与口腔噬菌体匹配的单个间隔区。这些数据表明，口腔 CRISPR 位点的转录相对普遍存在，并且高表达的 CRISPR 间隔区不一定针对最丰富的口腔噬菌体。本文的在线版本 (doi:10.1186/s12864-015-1615-0) 包含补充材料，可供授权用户使用。
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment. We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage. These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage. The online version of this article (doi:10.1186/s12864-015-1615-0) contains supplementary material, which is available to authorized users.
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DOI：
10.1038/nrg2749
发表时间：
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期刊：
Nature reviews. Genetics
影响因子：
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作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.1305923110
发表时间：
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影响因子：
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