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Elizabeth T. Bartom Masha Kocherginsky Bidur Paudel Aparajitha Vaidyanathan Ashley Haluck-Kangas Monal Patel Kaitlyn L. OShea Andrea E. Murmann Marcus E. Peter 《PLoS computational biology》2022,18(3)
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. 相似文献
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Srinivasan Aparajitha Sundaram Vijayakumar Vidya Muthulakshmi M. Srivastava Smita 《Journal of plant biochemistry and biotechnology.》2022,31(1):154-167
Journal of Plant Biochemistry and Biotechnology - Alpha-tocopherol, a highly active form of the antioxidant vitamin E in humans, effectively scavenges free radicals and protects the cell membranes.... 相似文献
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