title: Discovery of novel human breast cancer microRNAs from deep sequencing data by analysis of pri-microRNA secondary structures.
abstract: MicroRNAs (miRNAs) are key regulators of gene expression and contribute to a variety of biological processes. Abnormal miRNA expression has been reported in various diseases including pathophysiology of breast cancer, where they regulate protumorigenic processes including vascular invasiveness, estrogen receptor status, chemotherapy resistance, invasion and metastasis. The miRBase sequence database, a public repository for newly discovered miRNAs, has grown rapidly with approximately >10,000 entries to date. Despite this rapid growth, many miRNAs have not yet been validated, and several others are yet to be identified. A lack of a full complement of miRNAs has imposed limitations on recognizing their important roles in cancer, including breast cancer. Using deep sequencing technology, we have identified 189 candidate novel microRNAs in human breast cancer cell lines with diverse tumorigenic potential. We further show that analysis of 500-nucleotide pri-microRNA secondary structure constitutes a reliable method to predict bona fide miRNAs as judged by experimental validation. Candidate novel breast cancer miRNAs with stem lengths of greater than 30 bp resulted in the generation of precursor and mature sequences in vivo. On the other hand, candidates with stem length less than 30 bp were less efficient in producing mature miRNA. This approach may be used to predict which candidate novel miRNA would qualify as bona fide miRNAs from deep sequencing data with approximately 90% accuracy.
authors.affiliation: Department of Cardiothoracic Surgery, Weill Cornell Medical College of Cornell University, New York, New York, United States of America.
authors.forename: Seongho
authors.initials: S
authors.lastname: Ryu
authors.forename: Natasha
authors.initials: N
authors.lastname: Joshi
authors.forename: Kevin
authors.initials: K
authors.lastname: McDonnell
authors.forename: Jongchan
authors.initials: J
authors.lastname: Woo
authors.forename: Hyejin
authors.initials: H
authors.lastname: Choi
authors.forename: Dingcheng
authors.initials: D
authors.lastname: Gao
authors.forename: William R
authors.initials: WR
authors.lastname: McCombie
authors.forename: Vivek
authors.initials: V
authors.lastname: Mittal
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D045744:Cell Line, Tumor; D019295:Computational Biology; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics*; D009690:Nucleic Acid Conformation; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs