Differences in vertebrate microRNA expression
Abstract
MicroRNAs (miRNAs) attenuate gene expression by means of translational inhibition and mRNA degradation. They are abundant, highly conserved, and predicted to regulate a large number of transcripts. Several hundred miRNA classes are known, and many are associated with cell proliferation and differentiation. Many exhibit tissue-specific expression, which aids in evaluating their functions, and it has been assumed that their high level of sequence conservation implies a high level of expression conservation. A limited amount of data supports this, although discrepancies do exist. By comparing the expression of ≈100 miRNAs in medaka and chicken with existing data for zebrafish and mouse, we conclude that the timing and location of miRNA expression is not strictly conserved. In some instances, differences in expression are associated with changes in miRNA copy number, genomic context, or both between species. Variation in miRNA expression is more pronounced the greater the differences in physiology, and it is enticing to speculate that changes in miRNA expression may play a role in shaping the physiological differences produced during animal development.
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In a study of embryos from different species using miRNA in situ hybridization, miR-107 is essentially brain-specific in Japanese killifish, highly expressed in almost all tissues in chicken, but neither pattern is observed in mouse.
“The complexity of this situation is illustrated in a study of embryos from different species using miRNA in situ hybridization, finding that miR-107 is essentially brain-specific in the Japanese killifish, highly expressed in almost all tissues in chicken, but neither pattern is observed in mouse [38].”
From Expression of miR-15/107 Family MicroRNAs in Human Tissues and Cultured Rat Brain Cells (2014) · cites this paper as [38]
A cluster on chromosome 8 contains both miR-181a and miR-181b, but there is an additional copy of miR-181a on chromosome 22 and of miR-181b on chromosome 20.
“A cluster on chromosome 8 contains both miR-181a and miR-181b but there is an additional copy of miR-181a on chromosome 22 and of miR-181b on chromosome 20 [19,44].”
From MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system (2007) · cites this paper as [19]
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Cites
Initial sequence of the chimpanzee genome and comparison with the human genome
The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459 · see citing works
The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution
Farh, K. K.-H., Grimson, A., Jan, C., Lewis, B. P., Johnston, W. K., Lim, L. P., Burge, C. B., & Bartel, D. P. (2005) · Science · doi:10.1126/science.1121158 · Cited by 1,484 · see citing works
Morphogenesis in skin is governed by discrete sets of differentially expressed microRNAs
Yi, R., O'Carroll, D., Pasolli, H. A., Zhang, Z., Dietrich, F. S., Tarakhovsky, A., & Fuchs, E. (2006) · Nature Genetics · doi:10.1038/ng1744 · Cited by 555 · see citing works
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Research works printed but not linked: 4
- [22]Sapede D, Gompel N, Dambly-Chaudiere C, Ghysen A (2002) Development (Cambridge, UK) 129:605-615.
- [32]Westerfield M (1993) The Zebrafish Book (Univ Oregon Press, Eugene).
- [35]Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, et al . (2006) Genome Res , in press.
- [36]Darnell DK, Stanislaw SK, Konieczka JK, Yatskievych TA, Antin PB (2006) Dev Dyn , in press.
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The evolution of gene regulation by transcription factors and microRNAs
Chen, K., & Rajewsky, N. (2007) · Nature Reviews Genetics · doi:10.1038/nrg1990 · Cited by 1,547 · see citing works
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
Tessmar-Raible, K., Raible, F., Christodoulou, F., Guy, K., Rembold, M., Hausen, H., & Arendt, D. (2007) · Cell · doi:10.1016/j.cell.2007.04.041 · Cited by 384 · see citing works
Kapsimali, M., Kloosterman, W. P., de Bruijn, E., Rosa, F., Plasterk, R. H., & Wilson, S. W. (2007) · Genome Biology · doi:10.1186/gb-2007-8-8-r173 · Cited by 376 · see citing works
Self-citationExpression of miR-15/107 Family MicroRNAs in Human Tissues and Cultured Rat Brain Cells
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
- Authors
- Ason, B., Darnell, D. K., Wittbrodt, B., Berezikov, E., Kloosterman, W. P., Wittbrodt, J., Antin, P. B., & Plasterk, R. H. A.
- Affiliations
- Hubrecht Laboratory, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands;
- Department of Cell Biology and Anatomy, University of Arizona, Tucson, AZ 85724-5044; and
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69012 Heidelberg, Germany
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2006-09-26
- Volume
- 103
- Issue
- 39
- Pages
- 14385-14389
- ISSN
- 0027-8424
- 1091-6490
- Cited by
- 223
- References
- 3
- Language
- en
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