MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues
Abstract
MicroRNAs (MIRs) are a novel group of conserved short ∼22 nucleotide-long RNAs with important roles in regulating gene expression. We have established a MIR-specific oligonucleotide microarray system that enables efficient analysis of the expression of the human MIRs identified so far. We show that the 60-mer oligonucleotide probes on the microarrays hybridize with labeled cRNA of MIRs, but not with their precursor hairpin RNAs, derived from amplified, size-fractionated, total RNA of human origin. Signal intensity is related to the location of the MIR sequences within the 60-mer probes, with location at the 5′ region giving the highest signals, and at the 3′ end, giving the lowest signals. Accordingly, 60-mer probes harboring one MIR copy at the 5′ end gave signals of similar intensity to probes containing two or three MIR copies. Mismatch analysis shows that mutations within the MIR sequence significantly reduce or eliminate the signal, suggesting that the observed signals faithfully reflect the abundance of matching MIRs in the labeled cRNA. Expression profiling of 150 MIRs in five human tissues and in HeLa cells revealed a good overall concordance with previously published results, but also with some differences. We present novel data on MIR expression in thymus, testes, and placenta, and have identified MIRs highly enriched in these tissues. Taken together, these results highlight the increased sensitivity of the DNA microarray over other methods for the detection and study of MIRs, and the immense potential in applying such microarrays for the study of MIRs in health and disease.
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Several miRNAs, including miR-9, miR-124a, miR-125b, miR-127, miR-128, and members of the let-7 family, were highly enriched in the mouse brain, giving strong hybridization signals on miRNA arrays.
“In agreement with previous reports, several miRNAs, including miR-9, miR-124a, miR-125b, miR-127, miR-128, and members of the let-7 family, were highly enriched in the mouse brain, giving strong hybridization signals on the miRNA arrays (Fig. 1A; Babak et al. 2004;Barad et al. 2004;Miska et al. 2004;Sempere et al. 2004;Shingara et al. 2005;Thomson et al. 2004).”
From MicroRNA expression in the adult mouse central nervous system (2008) · cites this paper as Barad et al. 2004
Expression profiling in adult tissues has identified miRNAs enriched in the CNS, suggesting that these miRNAs could play important regulatory roles in mature neurons.
“On the other hand, expression profiling in adult tissues has identified miRNAs enriched in the CNS, suggesting that these miRNAs could play important regulatory roles in mature neurons (Babak et al. 2004;Barad et al. 2004;Miska et al. 2004;Sempere et al. 2004;Thomson et al. 2004).”
From MicroRNA expression in the adult mouse central nervous system (2008) · cites this paper as Barad et al. 2004
The human brain has been examined for miR expression and miR-219-5p, miR-338-5p, miR-338-3p, and members of the miR-17-92 cluster have been reported to be expressed.
“The human brain has also been examined for miR expression and miR-219-5p, miR-338-5p, miR-338-3p, and members of the miR-17-92 cluster have been reported to be expressed (Barad et al., 2004; Sempere et al., 2004).”
From Regulation of miRNA 219 and miRNA Clusters 338 and 17-92 in Oligodendrocytes (2012) · cites this paper as Barad et al., 2004
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Cites
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MicroRNA expression in the adult mouse central nervous system
Bak, M., Silahtaroglu, A., Møller, M., Christensen, M., Rath, M. F., Skryabin, B., Tommerup, N., & Kauppinen, S. (2008) · RNA · doi:10.1261/rna.783108 · Cited by 463 · see citing works
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Hébert, S. S., Horré, K., Nicolaï, L., Bergmans, B., Papadopoulou, A. S., Delacourte, A., & De Strooper, B. (2009) · Neurobiology of Disease · doi:10.1016/j.nbd.2008.11.009 · Cited by 436 · see citing works
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McCall, M. N., Kim, M.-S., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., et al. (2017) · Genome Research · doi:10.1101/gr.222067.117 · Cited by 151 · see citing works
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Hodyl, N. A., Aboustate, N., Bianco-Miotto, T., Roberts, C. T., Clifton, V. L., & Stark, M. J. (2017) · Placenta · doi:10.1016/j.placenta.2017.06.009 · Cited by 76 · see citing works
Regulation of miRNA 219 and miRNA Clusters 338 and 17-92 in Oligodendrocytes
de Faria Jr., O., Cui, Q.-L., Bin, J. M., Bull, S.-J., Kennedy, T. E., Bar-Or, A., Antel, J. P., Colman, D. R., & Dhaunchak, A. S. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00046 · Cited by 54 · see citing works
The Unique Expression and Function of miR-424 in Human Placental Trophoblasts1
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Potential Roles of microRNAs in the Regulation of Monoamine Oxidase A in the Brain
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- Authors
- Barad, O., Meiri, E., Avniel, A., Aharonov, R., Barzilai, A., Bentwich, I., Einav, U., Gilad, S., Hurban, P., Karov, Y., Lobenhofer, E. K., Sharon, E., Shiboleth, Y. M., Shtutman, M., Bentwich, Z., & Einat, P.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-12
- Volume
- 14
- Issue
- 12
- Pages
- 2486-2494
- ISSN
- 1088-9051
- Cited by
- 445
- References
- 3
- Language
- en
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