Nanopore-Based Detection of Viral RNA Modifications.
Nanopore-Based Detection of Viral RNA Modifications.
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作者：
核糖核苷酸的化学修饰在各种病毒及其真核宿主细胞的生物学中起着不可或缺的作用。绘制修饰核糖核苷酸的准确身份、位置和丰度图仍然是许多研究的关键目标，目的是表征特定修饰的功能和重要性。虽然通过短读测序方法绘制特定RNA修饰的图谱在过去十年中促进了大量新发现，但这种方法受到固有偏见和缺乏连锁信息的限制。此外，在病毒环境中，由于病毒基因组的紧凑性质导致许多重叠的转录异构体，使用短读测序方法不能充分解决这些问题，这增加了挑战。最近出现的纳米孔测序，特别是直接对感染病毒的宿主细胞的天然RNA进行测序的能力，不仅为绘制修饰的核苷酸图谱提供了一种新的方法，而且为从所产生的测序数据中得出什么提供了新的概念框架。在这篇简短的综述中，我们提供了纳米孔直接RNA测序如何工作的详细概述，应用于识别修饰的核糖核苷酸的计算方法，以及两者背后的核心概念。我们进一步强调了最近将这种方法应用于询问病毒生物学的研究，最后讨论了关键的实验考虑因素以及我们如何预测这些方法将继续发展。
The chemical modification of ribonucleotides plays an integral role in the biology of diverse viruses and their eukaryotic host cells. Mapping the precise identity, location, and abundance of modified ribonucleotides remains a key goal of many studies aimed at characterizing the function and importance of a given modification. While mapping of specific RNA modifications through short-read sequencing approaches has powered a wealth of new discoveries in the past decade, this approach is limited by inherent biases and an absence of linkage information. Moreover, in viral contexts, the challenge is increased due to the compact nature of viral genomes giving rise to many overlapping transcript isoforms that cannot be adequately resolved using short-read sequencing approaches. The recent emergence of nanopore sequencing, specifically the ability to directly sequence native RNAs from virus-infected host cells, provides not just a new methodology for mapping modified ribonucleotides but also a new conceptual framework for what can be derived from the resulting sequencing data. In this minireview, we provide a detailed overview of how nanopore direct RNA sequencing works, the computational approaches applied to identify modified ribonucleotides, and the core concepts underlying both. We further highlight recent studies that have applied this approach to interrogating viral biology and finish by discussing key experimental considerations and how we predict that these methodologies will continue to evolve.
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DOI：
10.3390/v13112108
发表时间：
2021-10-20
期刊：
Viruses
影响因子：
--
作者：
Campos JHC;Maricato JT;Braconi CT;Antoneli F;Janini LMR;Briones MRS
通讯作者：
Briones MRS
Simian Vericella病毒转录组的结构。
影响因子：
6.7
作者：
Braspenning SE;Verjans GMGM;Mehraban T;Messaoudi I;Depledge DP;Ouwendijk WJD
通讯作者：
Ouwendijk WJD
DOI：
10.1093/bioinformatics/btz586
发表时间：
2019-12-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
通讯作者：
--
影响因子：
3.7
作者：
Delahaye C;Nicolas J
通讯作者：
Nicolas J
影响因子：
14.9
作者：
Boccaletto P;Stefaniak F;Ray A;Cappannini A;Mukherjee S;Purta E;Kurkowska M;Shirvanizadeh N;Destefanis E;Groza P;Avşar G;Romitelli A;Pir P;Dassi E;Conticello SG;Aguilo F;Bujnicki JM
通讯作者：
Bujnicki JM