Discovery of novel MicroRNAs in female reproductive tract using next generation sequencing

Chad J. Creighton, Ashley L. Benham, Huifeng Zhu, Mahjabeen F. Khan, Jeffrey G. Reid, Ankur K. Nagaraja, Michael D. Fountain, Olivia Dziadek, Derek Han, Lang Ma, Jong Kim, Shannon Hawkins, Matthew L. Anderson, Martin M. Matzuk, Preethi H. Gunaratne

Research output: Contribution to journalArticle

73 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional gene silencing. Over 700 human miRNAs have currently been identified, many of which are mutated or de-regulated in diseases. Here we report the identification of novel miRNAs through deep sequencing the small RNAome (<30 nt) of over 100 tissues or cell lines derived from human female reproductive organs in both normal and disease states. These specimens include ovarian epithelium and ovarian cancer, endometrium and endometriomas, and uterine myometrium and uterine smooth muscle tumors. Sequence reads not aligning with known miRNAs were each mapped to the genome to extract flanking sequences. These extended sequence regions were folded in silico to identify RNA hairpins. Sequences demonstrating the ability to form a stem loop structure with low minimum free energy (<-225 kcal) and predicted Drosha and Dicer cut sites yielding a mature miRNA sequence matching the actual sequence were considered putative novel miRNAs. Additional confidence was achieved when putative novel hairpins assembled a collection of sequences highly similar to the putative mature miRNA but with heterogeneous 3′-ends. A confirmed novel miRNA fulfilled these criteria and had its "star" sequence in our collection. We found 7 distinct confirmed novel miRNAs, and 51 additional novel miRNAs that represented highly confident predictions but without detectable star sequences. Our novel miRNAs were detectable in multiple samples, but expressed at low levels and not specific to any one tissue or cell type. To date, this study represents the largest set of samples analyzed together to identify novel miRNAs.

Original languageEnglish (US)
Article numbere9637
JournalPLoS One
Volume5
Issue number3
DOIs
StatePublished - Mar 10 2010
Externally publishedYes

Fingerprint

MicroRNAs
microRNA
Myometrium
Stars
Genes
Smooth Muscle Tumor
Tissue
myometrium
stem form
High-Throughput Nucleotide Sequencing
Small Untranslated RNA
ovarian neoplasms
endometrium
Endometriosis
Endometrial Neoplasms
RNA Interference
RNA interference
Computer Simulation
smooth muscle
Ovarian Neoplasms

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Creighton, C. J., Benham, A. L., Zhu, H., Khan, M. F., Reid, J. G., Nagaraja, A. K., ... Gunaratne, P. H. (2010). Discovery of novel MicroRNAs in female reproductive tract using next generation sequencing. PLoS One, 5(3), [e9637]. https://doi.org/10.1371/journal.pone.0009637

Discovery of novel MicroRNAs in female reproductive tract using next generation sequencing. / Creighton, Chad J.; Benham, Ashley L.; Zhu, Huifeng; Khan, Mahjabeen F.; Reid, Jeffrey G.; Nagaraja, Ankur K.; Fountain, Michael D.; Dziadek, Olivia; Han, Derek; Ma, Lang; Kim, Jong; Hawkins, Shannon; Anderson, Matthew L.; Matzuk, Martin M.; Gunaratne, Preethi H.

In: PLoS One, Vol. 5, No. 3, e9637, 10.03.2010.

Research output: Contribution to journalArticle

Creighton, CJ, Benham, AL, Zhu, H, Khan, MF, Reid, JG, Nagaraja, AK, Fountain, MD, Dziadek, O, Han, D, Ma, L, Kim, J, Hawkins, S, Anderson, ML, Matzuk, MM & Gunaratne, PH 2010, 'Discovery of novel MicroRNAs in female reproductive tract using next generation sequencing', PLoS One, vol. 5, no. 3, e9637. https://doi.org/10.1371/journal.pone.0009637
Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK et al. Discovery of novel MicroRNAs in female reproductive tract using next generation sequencing. PLoS One. 2010 Mar 10;5(3). e9637. https://doi.org/10.1371/journal.pone.0009637
Creighton, Chad J. ; Benham, Ashley L. ; Zhu, Huifeng ; Khan, Mahjabeen F. ; Reid, Jeffrey G. ; Nagaraja, Ankur K. ; Fountain, Michael D. ; Dziadek, Olivia ; Han, Derek ; Ma, Lang ; Kim, Jong ; Hawkins, Shannon ; Anderson, Matthew L. ; Matzuk, Martin M. ; Gunaratne, Preethi H. / Discovery of novel MicroRNAs in female reproductive tract using next generation sequencing. In: PLoS One. 2010 ; Vol. 5, No. 3.
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