3'GAmES: Systematic refinement of gene termini by mRNA 3' end sequencing. 3'GAmES: Systematic refinement of gene termini by mRNA 3' end sequencing

Motivation: Alternative cleavage and polyadenylation generates mRNA 3´ isoforms in a cell type- and tissue-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes. Results: We developed 3'GAmES, a stand-alone analysis pipeline to identify and annotate novel (cell-type-specific) mRNA 3´ isoforms from 3' mRNA sequencing datasets. When applied to mouse embryonic stem cells or Zebrafish embryos, 3'GAmES expands currently available mRNA 3' annotations by 47% and 57%, respectively; and the resulting annotations significantly improve comprehensive gene-tag counting by cost-effective 3' mRNA sequencing to more accurately mirror whole-transcriptome RNAseq measurements. As a stand-alone analysis tool, 3'GAmES systematically augments cell type-specific transcript annotations and increases the robustness of quantitative gene expression profiling by 3' mRNA sequencing. Overall design: 3' end sequencing data from zebrafish 1dpf embryo

研究背景：可变切割与多聚腺苷酸化会以细胞类型和组织特异性的方式产生mRNA的3'端异构体。由于细胞类型极其多样的生物体可用RNA测序数据量有限，当前可用的基因注释资源并不完整，这给转录组的全面解析与定量分析带来了严峻挑战。研究结果：我们开发了3'GAmES这一独立分析流程，可从3'端mRNA测序数据集中识别并注释新型（细胞类型特异性）mRNA 3'端异构体。将其应用于小鼠胚胎干细胞或斑马鱼胚胎时，3'GAmES分别将现有mRNA 3'端注释库扩充了47%与57%；该工具生成的注释可显著优化低成本3'端mRNA测序的基因标签计数流程，使其能更精准地匹配全转录组RNA测序的检测结果。作为一款独立分析工具，3'GAmES可系统性增强细胞类型特异性转录本注释，并提升基于3'端mRNA测序的基因表达定量分析的稳健性。实验整体设计：取自斑马鱼1dpf胚胎的3'端测序数据