McClure Ryan S, Rericha Yvonne, Waters Katrina M, Tanguay Robyn L
Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States.
Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States.
Front Bioinform. 2023 Jul 27;3:1234218. doi: 10.3389/fbinf.2023.1234218. eCollection 2023.
The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.
RNA测序技术的应用在研究复杂生物系统中的基因表达水平方面带来了众多突破。其中包括了解诸如脊椎动物模式生物斑马鱼等生物体如何对毒物暴露做出反应。最近，3' RNA测序的发展使得与标准RNA测序相比，只需一小部分所需读数就能确定基因表达水平。虽然3' RNA测序有许多优点，但尚未在全生物体毒性和稀疏数据的背景下与标准RNA测序进行比较。在这里，我们用3' RNA测序或标准RNA测序检测了暴露于全氟丁烷磺酰胺（FBSA）的斑马鱼样本，以确定每种方法在识别功能富集途径方面的优势。我们发现，当关注基因组的注释或未注释区域时，3' RNA测序和标准RNA测序显示出特定的优势。我们还发现，标准RNA测序识别出更多差异表达基因（DEG），但在稀疏数据条件下这种优势消失了。我们还发现，通过对DEG列表的分析，标准RNA测序在识别功能富集途径方面具有显著优势，但在通过对所有基因进行基因集富集分析来识别途径时，这种优势最小。这些结果表明，每种方法都有其可能具有优势的实验条件。我们的观察结果可以帮助指导其他人在选择3' RNA测序与标准RNA测序时，以查询一系列生物系统中的基因表达水平。
