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

Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X, Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney AJ, Gunaratne PH - PLoS ONE (2008)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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Northern Analyses of ES-specific mmu-miR 290–295 and adult-specific let-7c.The right panel shows the expression profile of the mmu-miR-290-295 cluster in ES cells during RA-induction. The left panel shows the expression profile of the mmu-miR-290-295 cluster in ES (GCNF−/−) mutant during RA-induction. Here we see that the mmu-miR-290-295 cluster is enriched in ES cells and go down during RA-induced differentiation. This is by contrast, to let-7c which is not present in ES cells and goes up during RA-induction only in the ES (GCNF−/−) mutant. The expression pattern of the mmu-miR-290-295 cluster is perturbed in the ES (GCNF−/−) mutant and characterized by a failure to down-regulate in the mutant as compared to wild type ES.
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pone-0002548-g003: Northern Analyses of ES-specific mmu-miR 290–295 and adult-specific let-7c.The right panel shows the expression profile of the mmu-miR-290-295 cluster in ES cells during RA-induction. The left panel shows the expression profile of the mmu-miR-290-295 cluster in ES (GCNF−/−) mutant during RA-induction. Here we see that the mmu-miR-290-295 cluster is enriched in ES cells and go down during RA-induced differentiation. This is by contrast, to let-7c which is not present in ES cells and goes up during RA-induction only in the ES (GCNF−/−) mutant. The expression pattern of the mmu-miR-290-295 cluster is perturbed in the ES (GCNF−/−) mutant and characterized by a failure to down-regulate in the mutant as compared to wild type ES.

Mentions: The mmu-mir-290-295 cluster and mmu-mir-302-cluster were the first sets of ES cell enriched miRNAs to be discovered [35]. Northern analysis of a subset including mmu-miR-290-295 is shown in Figure 3. This group of miRNAs is highly-expressed in ES cells and down-regulated during RA-induced differentiation – but their down-regulation fails in the ES (GCNF−/−) mutant. In order to identify distinct classes of ES-related miRNAs that may be involved in pluripotence vs. differentiation, we carried out statistical analysis of the expression trends of these groups in the differentiation-impaired ES (GCNF−/−) cells as compared to wild-type ES cells. RNA was isolated from ES and ES (GCNF−/−) cells before (RA-D0) and after retinoic acid treatment on Day-1, 3 and 6. We linearly interpolated between the mean expression values at each of the 4 time points to obtain a 7-value time profile including Day-0, 1, 2, 3, 4, 5 and 6. As shown in Supplemental Table S5A and S5B, our analysis revealed three significant classes of temporal variation: Class 1 (Figure 4A) representing miRNAs that are enriched in ES cells and down-regulated (105 miRNAs and candidates); Class 2 (Figure 4B): Transiently induced miRNAs (46 novel miRNA candidates); and Class 3 (Figure 4C): miRNAs that are absent or present only in low abundance in ES cells and up-regulated upon RA-induced differentiation (78 miRNAs and candidates). All miRNAs and candidates that exhibited minimal changes in expression during the RA treatment were classified by default in Class 4 (881 miRNAs and candidates). The majority of Class 1 (61%) and Class 2 (85%) miRNAs and candidates were enriched in undifferentiated ES cells (RA-D0) over the Adult Pool. Conversely, the majority of Class 3 miRNAs and candidates (74%) were enriched in the Adult Pool over undifferentiated ES cells (RA-D0).


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

Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X, Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney AJ, Gunaratne PH - PLoS ONE (2008)

Northern Analyses of ES-specific mmu-miR 290–295 and adult-specific let-7c.The right panel shows the expression profile of the mmu-miR-290-295 cluster in ES cells during RA-induction. The left panel shows the expression profile of the mmu-miR-290-295 cluster in ES (GCNF−/−) mutant during RA-induction. Here we see that the mmu-miR-290-295 cluster is enriched in ES cells and go down during RA-induced differentiation. This is by contrast, to let-7c which is not present in ES cells and goes up during RA-induction only in the ES (GCNF−/−) mutant. The expression pattern of the mmu-miR-290-295 cluster is perturbed in the ES (GCNF−/−) mutant and characterized by a failure to down-regulate in the mutant as compared to wild type ES.
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Related In: Results  -  Collection

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pone-0002548-g003: Northern Analyses of ES-specific mmu-miR 290–295 and adult-specific let-7c.The right panel shows the expression profile of the mmu-miR-290-295 cluster in ES cells during RA-induction. The left panel shows the expression profile of the mmu-miR-290-295 cluster in ES (GCNF−/−) mutant during RA-induction. Here we see that the mmu-miR-290-295 cluster is enriched in ES cells and go down during RA-induced differentiation. This is by contrast, to let-7c which is not present in ES cells and goes up during RA-induction only in the ES (GCNF−/−) mutant. The expression pattern of the mmu-miR-290-295 cluster is perturbed in the ES (GCNF−/−) mutant and characterized by a failure to down-regulate in the mutant as compared to wild type ES.
Mentions: The mmu-mir-290-295 cluster and mmu-mir-302-cluster were the first sets of ES cell enriched miRNAs to be discovered [35]. Northern analysis of a subset including mmu-miR-290-295 is shown in Figure 3. This group of miRNAs is highly-expressed in ES cells and down-regulated during RA-induced differentiation – but their down-regulation fails in the ES (GCNF−/−) mutant. In order to identify distinct classes of ES-related miRNAs that may be involved in pluripotence vs. differentiation, we carried out statistical analysis of the expression trends of these groups in the differentiation-impaired ES (GCNF−/−) cells as compared to wild-type ES cells. RNA was isolated from ES and ES (GCNF−/−) cells before (RA-D0) and after retinoic acid treatment on Day-1, 3 and 6. We linearly interpolated between the mean expression values at each of the 4 time points to obtain a 7-value time profile including Day-0, 1, 2, 3, 4, 5 and 6. As shown in Supplemental Table S5A and S5B, our analysis revealed three significant classes of temporal variation: Class 1 (Figure 4A) representing miRNAs that are enriched in ES cells and down-regulated (105 miRNAs and candidates); Class 2 (Figure 4B): Transiently induced miRNAs (46 novel miRNA candidates); and Class 3 (Figure 4C): miRNAs that are absent or present only in low abundance in ES cells and up-regulated upon RA-induced differentiation (78 miRNAs and candidates). All miRNAs and candidates that exhibited minimal changes in expression during the RA treatment were classified by default in Class 4 (881 miRNAs and candidates). The majority of Class 1 (61%) and Class 2 (85%) miRNAs and candidates were enriched in undifferentiated ES cells (RA-D0) over the Adult Pool. Conversely, the majority of Class 3 miRNAs and candidates (74%) were enriched in the Adult Pool over undifferentiated ES cells (RA-D0).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH