Large-scale investigation of short read archives for disruption of transcription termination and circular splicing

对短读档案进行大规模研究以破坏转录终止和循环剪接

• 批准号: 417339504
• 负责人: Professorin Dr. Caroline Friedel
• 金额: --
• 依托单位: Lehr- und Forschungseinheit Bioinformatik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2021-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/417339504?language=en
• 关键词: Large; scale; investigation; short; read

We and others recently reported that both lytic herpes simplex virus 1 (HSV-1) infection and salt and heat stress lead to a disruption of transcription termination (DoTT) of the majority of human genes. This results in massive transcription downstream of genes (DoG transcription). Considering that stress-induced transcription changes have already been studied intensively, it is surprising that DoTT/DoG transcription has been discovered only so recently. The most likely reason for this is that standard RNA-seq analysis focuses only on known transcripts, thus ignoring transcription outside of annotated genes. However, most journals now require that before publication of manuscripts raw sequencing data is submitted to short read archives such as the NCBI SRA. Thus, even if the original studies did not investigate DoTT/DoG transcription, the raw data is available for reanalysis. While the sheer size of RNA-seq data in short read archives previously made it prohibitive to perform a large-scale reanalysis of all available published data, recent developments now make this feasible. On the on hand, these developments include novel alignment-free methods for both short read indexing and searching as well as fast transcript quantification. On the other hand, genome-wide read coverage and splice junction data is now provided by the recount2 database for the majority of human RNA-seq experiments in the SRA. In this project, we propose to leverage these new tools to address specific questions arising from our previous analysis of HSV-1 infection and heat and salt stress. First, we plan to characterize the prevalence and similarity of DoTT/DoG transcription in different conditions and its conservation between species. Second, we will study de novo production of circular RNAs as well as investigate their induction relative to linear RNAs in different conditions. For this purpose, we will pursue both a re-analysis of the recount2 data to quickly characterize DoTT/DoG transcription in a wide range of conditions in human as well as combine this with alignment-free approaches to extend this analysis to the remaining SRA and circular splicing. In summary, this project not only aims to address important biological questions on DoTT/DoG transcription and circular splicing in an SRA-wide manner, but it will also serve as a proof-of-concept that the large-scale investigation of SRAs for specific transcription events is both feasible and useful.

我们和其他人最近报道，溶解性单纯疱疹病毒1型（HSV-1）感染和盐和热应激导致大多数人类基因的转录终止（DoTT）中断。这导致基因下游的大量转录（DoG转录）。考虑到胁迫诱导的转录变化已经被深入研究，令人惊讶的是，DoTT/DoG转录只是最近才被发现。最可能的原因是标准的RNA-seq分析只关注已知的转录本，从而忽略了注释基因之外的转录。然而，大多数期刊现在要求在出版手稿之前，将原始测序数据提交给短读档案，如NCBI SRA。因此，即使原始研究没有研究DoTT/DoG转录，原始数据也可用于再分析。虽然短读档案中RNA-seq数据的庞大规模以前使其无法对所有可用的已发表数据进行大规模重新分析，但最近的发展现在使其成为可能。另一方面，这些发展包括用于短读段索引和搜索以及快速转录本定量的新的无干扰方法。另一方面，全基因组读段覆盖率和剪接点数据现在由recount 2数据库提供，用于SRA中的大多数人类RNA-seq实验。在这个项目中，我们建议利用这些新工具来解决我们以前对HSV-1感染和热盐应激的分析中出现的具体问题。首先，我们计划描述DoTT/DoG转录在不同条件下的流行性和相似性及其在物种之间的保守性。其次，我们将研究从头生产的环状RNA，以及调查他们的诱导相对于线性RNA在不同的条件下。为此，我们将对重新计数2数据进行重新分析，以快速表征人类各种条件下的DoTT/DoG转录，并将其与无干扰方法联合收割机结合，以将该分析扩展到剩余的SRA和环状剪接。总而言之，该项目不仅旨在以整个SLA的方式解决有关DoTT/DoG转录和环状剪接的重要生物学问题，而且还将作为概念验证，证明针对特定转录事件的大规模研究是可行的和有用的。