Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures

Research output: Contribution to journalArticle

Seongho Ryu, Natasha Joshi, Kevin McDonnell, Jongchan Woo, Hyejin Choi, Dingcheng Gao, William R. McCombie, Vivek Mittal

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.

Original languageEnglish
Article numbere16403
JournalPLoS ONE
Volume6
Issue number2
DOIs
StatePublished - Feb 18 2011

PMID: 21346806

PMCID: PMC3035615

Altmetrics

Cite this

Standard

Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures. / Ryu, Seongho; Joshi, Natasha; McDonnell, Kevin; Woo, Jongchan; Choi, Hyejin; Gao, Dingcheng; McCombie, William R.; Mittal, Vivek.

In: PLoS ONE, Vol. 6, No. 2, e16403, 18.02.2011.

Research output: Contribution to journalArticle

Harvard

Ryu, S, Joshi, N, McDonnell, K, Woo, J, Choi, H, Gao, D, McCombie, WR & Mittal, V 2011, 'Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures' PLoS ONE, vol. 6, no. 2, e16403. https://doi.org/10.1371/journal.pone.0016403

APA

Ryu, S., Joshi, N., McDonnell, K., Woo, J., Choi, H., Gao, D., ... Mittal, V. (2011). Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures. PLoS ONE, 6(2), [e16403]. https://doi.org/10.1371/journal.pone.0016403

Vancouver

Ryu S, Joshi N, McDonnell K, Woo J, Choi H, Gao D et al. Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures. PLoS ONE. 2011 Feb 18;6(2). e16403. https://doi.org/10.1371/journal.pone.0016403

Author

Ryu, Seongho ; Joshi, Natasha ; McDonnell, Kevin ; Woo, Jongchan ; Choi, Hyejin ; Gao, Dingcheng ; McCombie, William R. ; Mittal, Vivek. / Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures. In: PLoS ONE. 2011 ; Vol. 6, No. 2.

BibTeX

@article{21555b55a46a4d04bc08ccf88535c2d5,
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.",
author = "Seongho Ryu and Natasha Joshi and Kevin McDonnell and Jongchan Woo and Hyejin Choi and Dingcheng Gao and McCombie, {William R.} and Vivek Mittal",
year = "2011",
month = "2",
day = "18",
doi = "10.1371/journal.pone.0016403",
language = "English",
volume = "6",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "2",

}

RIS

TY - JOUR

T1 - Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures

AU - Ryu, Seongho

AU - Joshi, Natasha

AU - McDonnell, Kevin

AU - Woo, Jongchan

AU - Choi, Hyejin

AU - Gao, Dingcheng

AU - McCombie, William R.

AU - Mittal, Vivek

PY - 2011/2/18

Y1 - 2011/2/18

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=79951568817&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79951568817&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0016403

DO - 10.1371/journal.pone.0016403

M3 - Article

VL - 6

JO - PLoS ONE

T2 - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 2

M1 - e16403

ER -

ID: 2720292