Main menu

Nano-DMS-MaP enables isoform-resolved RNA structure determination


HIV-1 is a retrovirus that packages an RNA genome, which upon cell entry is reverse transcribed and integrated into the host cell genome. Newly transcribed HIV RNA from this proviral DNA may then be spliced into multiple different transcripts to express viral proteins, or be packaged into the viral genome. Intriguingly, while all HIV RNAs share the majority of the 5' UTR, which contains a major packaging motif, only the unspliced genomic RNA is efficiently packaged into virions.
We therefore hypothesized that structural differences play a major role in regulating this packaging activity.

Current RNA structural probing methods, such as DMS-mutational profiling sequencing (DMS-MaP), use NGS technologies whose short reads cannot be reliably mapped to specific transcripts for shared regions of transcript isoforms. To circumvent this issue we developed and benchmarked Nanopore-based DMS mutational profiling (Nano-DMS-MaP) to simultaneously investigate RNA structures HIV-1 spliced and unspliced transcripts in cells. Our results demonstrate that HIV-1 splice variants have distinct structures that cluster with acceptor site usage. Importantly, our data suggest that in addition to increasing protein diversity, alternative splicing also resultsv in the generation of RNA transcripts with distinct functions through altered RNA structures.

Download the PDF

入门指南

购买 MinION 启动包 Nanopore 商城 测序服务提供商 全球代理商

纳米孔技术

订阅 Nanopore 更新 资源库及发表刊物 什么是 Nanopore 社区

关于 Oxford Nanopore

新闻 公司历程 可持续发展 领导团队 媒体资源和联系方式 投资者 合作者 在 Oxford Nanopore 工作 职位空缺 商业信息 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Chinese flag