Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.
Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.
PLoS Comput Biol. 2022 Mar 31;18(3):e1010022. doi: 10.1371/journal.pcbi.1010022. eCollection 2022 Mar.
microRNAs (miRNAs) are (18-22nt long) noncoding short (s)RNAs that suppress gene expression by targeting the 3' untranslated region of target mRNAs. This occurs through the seed sequence located in position 2-7/8 of the miRNA guide strand, once it is loaded into the RNA induced silencing complex (RISC). G-rich 6mer seed sequences can kill cells by targeting C-rich 6mer seed matches located in genes that are critical for cell survival. This results in induction of Death Induced by Survival gene Elimination (DISE), through a mechanism we have called 6mer seed toxicity. miRNAs are often quantified in cells by aligning the reads from small (sm)RNA sequencing to the genome. However, the analysis of any smRNA Seq data set for predicted 6mer seed toxicity requires an alternative workflow, solely based on the exact position 2-7 of any short (s)RNA that can enter the RISC. Therefore, we developed SPOROS, a semi-automated pipeline that produces multiple useful outputs to predict and compare 6mer seed toxicity of cellular sRNAs, regardless of their nature, between different samples. We provide two examples to illustrate the capabilities of SPOROS: Example one involves the analysis of RISC-bound sRNAs in a cancer cell line (either wild-type or two mutant lines unable to produce most miRNAs). Example two is based on a publicly available smRNA Seq data set from postmortem brains (either from normal or Alzheimer's patients). Our methods (found at https://github.com/ebartom/SPOROS and at Code Ocean: https://doi.org/10.24433/CO.1732496.v1) are designed to be used to analyze a variety of smRNA Seq data in various normal and disease settings.
微小 RNA（miRNA）是 18-22nt 长的非编码短 RNA（sRNA），通过靶向靶 mRNA 的 3'非翻译区来抑制基因表达。这是通过位于 miRNA 引导链第 2-7/8 位的种子序列发生的，一旦 miRNA 被加载到 RNA 诱导沉默复合物（RISC）中。富含 G 的 6mer 种子序列可以通过靶向位于对细胞生存至关重要的基因中富含 C 的 6mer 种子匹配物来杀死细胞。这导致通过我们称之为 6mer 种子毒性的机制诱导生存基因消除诱导的死亡（DISE）。miRNA 通常通过将小 RNA 测序的读数与基因组对齐来在细胞中进行定量。然而，任何 smRNA Seq 数据集中预测 6mer 种子毒性的分析都需要一种替代工作流程，该流程仅基于可以进入 RISC 的任何短（s）RNA 的精确位置 2-7。因此，我们开发了 SPOROS，这是一个半自动的管道，它可以产生多个有用的输出，以预测和比较不同样本中细胞 sRNA 的 6mer 种子毒性，无论其性质如何。我们提供了两个示例来说明 SPOROS 的功能：示例一涉及分析癌细胞系（野生型或两种无法产生大多数 miRNA 的突变系）中结合 RISC 的 sRNA。示例二基于来自死后大脑的公开可用的 smRNA Seq 数据集（来自正常或阿尔茨海默病患者）。我们的方法（可在 https://github.com/ebartom/SPOROS 和 Code Ocean 上找到：https://doi.org/10.24433/CO.1732496.v1）旨在用于分析各种正常和疾病环境中的各种 smRNA Seq 数据。
