Kobayashi H, Tomari Y. RISC assembly: Coordination between small RNAs and Argonaute proteins. Biochimica et biophysica acta. 2016;1859:71–81.

Article  CAS  PubMed  Google Scholar 

Nakanishi K. Anatomy of four human Argonaute proteins. Nucleic Acids Res. 2022;50:6618–38.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bartel DP. Metazoan MicroRNAs. Cell. 2018;173:20–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet. 2016;17:719–32.

Article  CAS  PubMed  Google Scholar 

Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet. 2024;25:211–32.

Article  CAS  PubMed  Google Scholar 

Bracken CP, Goodall GJ, Gregory PA. RNA regulatory mechanisms controlling TGF-beta signaling and EMT in cancer. Semin Cancer Biol. 2024;102-103:4–16.

Article  CAS  PubMed  Google Scholar 

Cursons J, Pillman KA, Scheer KG, Gregory PA, Foroutan M, Hediyeh-Zadeh S, et al. Combinatorial targeting by MicroRNAs co-ordinates post-transcriptional control of EMT. Cell Syst. 2018;7:77–91.e77.

Article  CAS  PubMed  Google Scholar 

Yang J, Antin P, Berx G, Blanpain C, Brabletz T, Bronner M, et al. Guidelines and definitions for research on epithelial-mesenchymal transition. Nat Rev Mol Cell Biol. 2020;21:341–52.

Article  PubMed  PubMed Central  Google Scholar 

Alles J, Fehlmann T, Fischer U, Backes C, Galata V, Minet M, et al. An estimate of the total number of true human miRNAs. Nucleic Acids Res. 2019;47:3353–64.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fromm B, Zhong X, Tarbier M, Friedlander MR, Hackenberg M. The limits of human microRNA annotation have been met. RNA. 2022;28:781–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hansen TB, Kjems J, Bramsen JB. Enhancing miRNA annotation confidence in miRBase by continuous cross dataset analysis. RNA Biol. 2011;8:378–83.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langenberger DBS, Hertel J, Hoffmann S, Tafer H, Stadler PF. MicroRNA or Not MicroRNA? Adv Bioinf Comput Biol. 2011;6832:1–9.

Schopman NC, Heynen S, Haasnoot J, Berkhout B. A miRNA-tRNA mix-up: tRNA origin of proposed miRNA. RNA Biol. 2010;7:573–6.

Article  CAS  PubMed  Google Scholar 

Thomson DW, Pillman KA, Anderson ML, Lawrence DM, Toubia J, Goodall GJ, et al. Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin. Nucleic Acids Res. 2015;43:470–81.

Article  CAS  PubMed  Google Scholar 

Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic acids Res. 2019;47:D155–d162.

Article  CAS  PubMed  Google Scholar 

Fromm B, Domanska D, Hoye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, et al. MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Res. 2020;48:D1172.

Article  PubMed  Google Scholar 

Mani SA, Guo W, Liao MJ, Eaton EN, Ayyanan A, Zhou AY, et al. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell. 2008;133:704–15.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gagnon KT, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protoc. 2014;9:2045–60.

Article  CAS  Google Scholar 

Ikeda K, Satoh M, Pauley KM, Fritzler MJ, Reeves WH, Chan EK. Detection of the argonaute protein Ago2 and microRNAs in the RNA induced silencing complex (RISC) using a monoclonal antibody. Journal immunol Methods. 2006;317:38–44.

Article  CAS  Google Scholar 

Jensen KB, Darnell RB. CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol Biol (Clifton, NJ). 2008;488:85–98.

Article  CAS  Google Scholar 

Andrews S FastQC: A quality control tool for high throughput sequence data. https://www.bioinformaticsbabrahamacuk/projects/fastqc/ 2010.

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17:10–12.

Google Scholar 

Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 2017;27:491–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.

Article  PubMed  PubMed Central  Google Scholar 

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nature Biotechnol. 2011;29:24–26.

Article  CAS  Google Scholar 

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, et al. Ensembl 2021. Nucleic Acids Res. 2021;49:D884–D891.

Article  CAS  PubMed  Google Scholar 

Griffiths-Jones S. The microRNA registry. Nucleic Acids Res. 2004;32:D109–111.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saunders K, Bert AG, Dredge BK, Toubia J, Gregory PA, Pillman KA, et al. Insufficiently complex unique-molecular identifiers (UMIs) distort small RNA sequencing. Sci Rep. 2020;10:14593.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.

Article  PubMed  PubMed Central  Google Scholar 

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

Article  CAS  PubMed  Google Scholar 

Migault M, Sapkota S, Bracken CP. Transcriptional and post-transcriptional control of epithelial-mesenchymal plasticity: why so many regulators?. Cell Mol Life Sci. 2022;79:182.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Petri R, Brattas PL, Sharma Y, Jonsson ME, Pircs K, Bengzon J, et al. LINE-2 transposable elements are a source of functional human microRNAs and target sites. PLoS Genet. 2019;15:e1008036.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, et al. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 2010;24:992–1009.

Article  CAS  PubMed  PubMed Central