The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
Characterization and Identification of MicroRNA Core Promoters in Four Model Species
Open accessAbstract
MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote), which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.
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Bartel (2004) · doi:10.1016/s0092-8674(04)00045-5 · Cited by 34,714
(1992) · Cited by 23,431
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993) · Cell · doi:10.1016/0092-8674(93)90529-y · Cited by 12,948
Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond
Schölkopf, B., & Smola, A. J. (2001) · The MIT Press eBooks · doi:10.7551/mitpress/4175.001.0001 · Cited by 11,703
Data mining: practical machine learning tools and techniques with Java implementations
Witten, I. H., & Frank, E. (2002) · ACM SIGMOD Record · doi:10.1145/507338.507355 · Cited by 5,137
The nuclear RNase III Drosha initiates microRNA processing
Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Rådmark, O., Kim, S., et al. (2003) · Nature · doi:10.1038/nature01957 · Cited by 5,114
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R., & Ruvkun, G. (2000) · Nature · doi:10.1038/35002607 · Cited by 4,981
Identification of Novel Genes Coding for Small Expressed RNAs
Lagos-Quintana, M., Rauhut, R., Lendeckel, W., & Tuschl, T. (2001) · Science · doi:10.1126/science.1064921 · Cited by 4,956
MicroRNA genes are transcribed by RNA polymerase II
Lee, Y., Kim, M., Han, J., Yeom, K., Lee, S., Baek, S. H., & Kim, V. N. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600385 · Cited by 4,373
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Tumour invasion and metastasis initiated by microRNA-10b in breast cancer
Ma, L., Teruya-Feldstein, J., & Weinberg, R. A. (2007) · Nature · doi:10.1038/nature06174 · Cited by 2,605
Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.07.020 · Cited by 1,370
A microRNA DNA methylation signature for human cancer metastasis
Lujambio, A., Calin, G. A., Villanueva, A., Ropero, S., Sánchez-Céspedes, M., Blanco, D., Montuenga, L. M., Rossi, S., Nicoloso, M. S., Faller, W. J., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803055105 · Cited by 1,078
MicroRNAs in Development and Disease
Sayed, D., & Abdellatif, M. (2011) · Physiological Reviews · doi:10.1152/physrev.00006.2010 · Cited by 1,078
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Saini, H. K., Griffiths-Jones, S., & Enright, A. J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703890104 · Cited by 554
Metadata
- Authors
- Zhou, X., Ruan, J., Wang, G., & Zhang, W.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-03-09
- Volume
- 3
- Issue
- 3
- Pages
- e37
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2038303173
- Cited by
- 306
- References
- 47
- FWCI
- 38.12
- Type
- journal article
- Language
- en
- Open access
- gold
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