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PLoS One. 2008 Jul 2;3(7):e2548. doi: 10.1371/journal.pone.0002548.

Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells.

Author information

1
Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America.

Abstract

BACKGROUND:

MicroRNAS (miRNAS: a class of short non-coding RNAs) are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence).

METHODOLOGY/PRINCIPAL FINDINGS:

In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES) cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer(-/-)) ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues) during retinoic acid (RA)-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF(-/-)) cells, which display loss of repression of pluripotence genes upon differentiation.

CONCLUSION/SIGNIFICANCE:

Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF(-/-)) mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.

PMID:
18648548
PMCID:
PMC2481296
DOI:
10.1371/journal.pone.0002548
[Indexed for MEDLINE]
Free PMC Article
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