sRNA-Effector: A tool to expedite discovery of small RNA regulators
Year: 2024
Type: article
Abstract: microRNAs (miRNAs) are small regulatory RNAs that repress target mRNA transcripts through base pairing. Although the mechanisms of miRNA production and function are clearly established, new insights into miRNA regulation or miRNA-mediated gene silencing are still emerging. In order to facilitate the discovery of miRNA regulators or effectors, we have developed sRNA-Effector, a machine learning algorithm trained on enhanced crosslinking and immunoprecipitation sequencing and RNA sequencing data following knockdown of specific genes. sRNA-Effector can accurately identify known miRNA biogenesis and effector proteins and identifies 9 putative regulators of miRNA function, including serine/threonine kinase STK33, splicing factor SFPQ, and proto-oncogene BMI1. We validated the role of STK33, SFPQ, and BMI1 in miRNA regulation, showing that sRNA-Effector is useful for identifying new players in small RNA biology. sRNA-Effector will be a web tool available for all researchers to identify potential miRNA regulators in any cell line of interest.
Source: iScience
Authors: Briana Wilson, Fatemeh Esmaeili, Matthew Parsons, Wafa Salah, Zhangli Su, Anindya Dutta
Institutions: University of Virginia, University of Alabama at Birmingham
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,150
Awards: Studies on ORC and double strand DNA break repair, Stability of a novel family of short noncoding RNAs, tRFs: Effect on oncogenesis, Involvement of Noncanonical Short RNAs in gene repression through the RNA-induced-silencing complex, The role of small RNA modifications in glioma, University of Virginia Cancer Center Support Grant
OpenAlex ID: W4391966641