Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors
Abstract
Very little is known regarding regulation of microRNA (miRNA) biogenesis in normal tissues, tumors, and cell lines. Here, we profiled the expression of 225 precursor and mature miRNAs using real-time PCR and compared the expression levels to determine the processing patterns. RNA from 22 different human tissues, 37 human cancer cell lines, and 16 pancreas and liver tissues/tumors was profiled. The relationship between precursor and mature miRNA expression fell into the following four categories: (1) a direct correlation exists between the precursor and mature miRNA expression in all cells/tissues studied; (2) direct correlation of the precursor and mature miRNA exists, yet the expression is restricted to specific cell lines or tissues; (3) there is detectable expression of mature miRNA in certain cells and tissues while the precursor is expressed in all or most cells/tissues; or (4) both precursor and mature miRNA are not expressed. Pearson correlation between the precursor and mature miRNA expression was closer to one for the tissues but was closer to zero for the cell lines, suggesting that processing of precursor miRNAs is reduced in cancer cell lines. By using Northern blotting, we show that many of these miRNAs (e.g., miR-31, miR-105 and miR-128a) are processed to the precursor, but in situ hybridization analysis demonstrates that these miRNA precursors are retained in the nucleus. We provide a database of the levels of precursor and mature miRNA in a variety of cell types. Our data demonstrate that a large number of miRNAs are transcribed but are not processed to the mature miRNA.
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Discordant correlations of miRNA and precursor were also reported for other miRNAs.
“The discordant correlations of miRNA and the precursor were also reported for other miRNAs [39].”
From Expression of miR-15/107 Family MicroRNAs in Human Tissues and Cultured Rat Brain Cells (2014) · cites this paper as [39]
The brain-specific expression of miR-124a has been demonstrated previously.
“the brain-specific expression of miR-124a [40] has been demonstrated previously [39,40].”
From Expression of miR-15/107 Family MicroRNAs in Human Tissues and Cultured Rat Brain Cells (2014) · cites this paper as [39]
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Cites
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Self-citationThe multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a
Guil, S., & Cáceres, J. F. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1250 · Cited by 567 · see citing works
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Research works printed but not linked: 5
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Wang, W.-X., Danaher, R. J., Miller, C. S., Berger, J. R., Nubia, V. G., Wilfred, B. S., Neltner, J. H., Norris, C. M., & Nelson, P. T. (2014) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2013.10.003 · Cited by 67 · see citing works
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Brain cell-specific origin of circulating microRNA biomarkers in experimental temporal lobe epilepsy
Brindley, E., Heiland, M., Mooney, C., Diviney, M., Mamad, O., Hill, T. D. M., Yan, Y., Venø, M. T., Reschke, C. R., Batool, A., et al. (2023) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2023.1230942 · Cited by 21 · see citing works
- Authors
- Lee, E. J., Baek, M., Gusev, Y., Brackett, D. J., Nuovo, G. J., & Schmittgen, T. D.
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-11-19
- Volume
- 14
- Issue
- 1
- Pages
- 35-42
- ISSN
- 1355-8382
- 1469-9001
- Cited by
- 333
- References
- 2
- Language
- en
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