Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
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蛋白质组学通过转录组学告知，以表征伊蚊中的主动转座元件和基因组注释。
DOI：
10.1186/s12864-016-3432-5
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发表时间：
2017-01-19
期刊：
影响因子：
4.4
通讯作者：
Davidson AD
中科院分区：
文献类型：
--
作者：
Maringer K;Yousuf A;Heesom KJ;Fan J;Lee D;Fernandez-Sesma A;Bessant C;Matthews DA;Davidson AD
埃及伊蚊是（重新）出现的人类病原体登革热、基孔肯雅热、黄热病和寨卡病毒的媒介。几乎一半的Ae。埃及伊蚊基因组由转座因子（TE）组成。转座子与多种细胞过程有关，包括在昆虫中建立病毒持久性，这是媒介传播病毒的一个重要步骤。然而，到目前为止，还没有可能研究来自生物体的移动的遗传元件的整体蛋白质组，部分原因是TE的高度分化性质。此外，与许多非模式生物一样，不完整的基因组注释阻碍了Ae蛋白质组学研究。埃及人。我们分析了Ae。埃及蛋白质组使用我们的新的蛋白质组学的转录组学（PIT）技术，绕过需要通过识别蛋白质匹配的转录组（而不是基因组）数据的基因组注释。我们的数据大大增加了实验证实的Ae的数量。埃及蛋白。PIT分析还确定了不完整基因组注释的热点，并表明差的序列和组装质量不能解释所有的注释缺口。最后，在一项原理验证研究中，我们制定了蛋白质组学活性TE的表征标准。在不同的分类水平，蛋白质表达与TE的基因组丰度无关。最值得注意的是，与其他元件相比，长末端重复序列（LTR）反转录转座子明显富集。在转座子和基因组注释分析中，PIT上级“常规”蛋白质组学方法。我们提出了第一个蛋白质组表征的生物体的剧目的移动的遗传因素，这将开辟新的途径研究转座子蛋白质的功能在健康和疾病。此外，我们的研究提供了一个概念验证，即PIT可用于评估基因组的注释，以指导注释工作，这有可能提高非模式生物中注释项目的效率。因此，PIT代表了一个有价值的新工具，研究重要的载体物种Ae的生物学。埃及，包括其在传播引起全球公共卫生关切的新病毒方面的作用。本文的在线版本（doi：10.1186/s12864-016-3432-5）包含补充材料，可供授权用户使用。
Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism’s mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti. We analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE’s genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to ‘conventional’ proteomic approaches in both our transposon and genome annotation analyses. We present the first proteomic characterisation of an organism’s repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome’s annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern. The online version of this article (doi:10.1186/s12864-016-3432-5) contains supplementary material, which is available to authorized users.