- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Data Supplement
-
All Versions of this Article:
genetics.107.072553v1
176/2/1323 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Piriyapongsa, J.
- Articles by Jordan, I. K.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Piriyapongsa, J.
- Articles by Jordan, I. K.
Originally published as Genetics Published Articles Ahead of Print on April 15, 2007.
Genetics, Vol. 176, 1323-1337, June 2007, Copyright © 2007
doi:10.1534/genetics.107.072553
Origin and Evolution of Human microRNAs From Transposable Elements
Jittima Piriyapongsa*,
Leonardo Mariño-Ramírez
and
I. King Jordan*,1
* School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
1 Corresponding author: School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332-0230.
E-mail: king.jordan{at}biology.gatech.edu
We sought to evaluate the extent of the contribution of transposable elements (TEs) to human microRNA (miRNA) genes along with the evolutionary dynamics of TE-derived human miRNAs. We found 55 experimentally characterized human miRNA genes that are derived from TEs, and these TE-derived miRNAs have the potential to regulate thousands of human genes. Sequence comparisons revealed that TE-derived human miRNAs are less conserved, on average, than non-TE-derived miRNAs. However, there are 18 TE-derived miRNAs that are relatively conserved, and 14 of these are related to the ancient L2 and MIR families. Comparison of miRNA vs. mRNA expression patterns for TE-derived miRNAs and their putative target genes showed numerous cases of anti-correlated expression that are consistent with regulation via mRNA degradation. In addition to the known human miRNAs that we show to be derived from TE sequences, we predict an additional 85 novel TE-derived miRNA genes. TE sequences are typically disregarded in genomic surveys for miRNA genes and target sites; this is a mistake. Our results indicate that TEs provide a natural mechanism for the origination miRNAs that can contribute to regulatory divergence between species as well as a rich source for the discovery of as yet unknown miRNA genes.
This article has been cited by other articles:
 |
|
 |
|
  T. Mourier and E. Willerslev Retrotransposons and non-protein coding RNAs Briefings in Functional Genomics, November 1, 2009; 8(6): 493 - 501. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. M. Drake, E. C. Ruteshouser, R. Natrajan, P. Harbor, J. Wegert, M. Gessler, K. Pritchard-Jones, P. Grundy, J. Dome, V. Huff, et al. Loss of Heterozygosity at 2q37 in Sporadic Wilms' Tumor: Putative Role for miR-562 Clin. Cancer Res., October 1, 2009; 15(19): 5985 - 5992. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Das Evolutionary Origin and Genomic Organization of Micro-RNA Genes in Immunoglobulin Lambda Variable Region Gene Family Mol. Biol. Evol., May 1, 2009; 26(5): 1179 - 1189. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Kuang, C. Padmanabhan, F. Li, A. Kamei, P. B. Bhaskar, S. Ouyang, J. Jiang, C. R. Buell, and B. Baker Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs Genome Res., January 1, 2009; 19(1): 42 - 56. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Moxon, R. Jing, G. Szittya, F. Schwach, R. L. Rusholme Pilcher, V. Moulton, and T. Dalmay Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening Genome Res., October 1, 2008; 18(10): 1602 - 1609. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Zhang, Y.-Q. Wang, and B. Su Molecular Evolution of a Primate-Specific microRNA Family Mol. Biol. Evol., July 1, 2008; 25(7): 1493 - 1502. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Takabatake, H. Ishihara, Y. Ohmachi, I. Tanaka, M. M. Nakamura, K. Fujikawa, T. Hirouchi, S. Kakinuma, Y. Shimada, Y. Oghiso, et al. Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome Nucleic Acids Res., June 1, 2008; 36(10): e59 - e59. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Piriyapongsa and I. K. Jordan Dual coding of siRNAs and miRNAs by plant transposable elements RNA, May 1, 2008; 14(5): 814 - 821. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Calabrese, A. C. Seila, G. W. Yeo, and P. A. Sharp RNA sequence analysis defines Dicer's role in mouse embryonic stem cells PNAS, November 13, 2007; 104(46): 18097 - 18102. [Abstract] [Full Text] [PDF]
|
|
|