Limits...
Identification and characterization of FGF2-dependent mRNA: microRNA networks during lens fiber cell differentiation.

Wolf L, Gao CS, Gueta K, Xie Q, Chevallier T, Podduturi NR, Sun J, Conte I, Zelenka PS, Ashery-Padan R, Zavadil J, Cvekl A - G3 (Bethesda) (2013)

Bottom Line: Specific miRNA:mRNA interaction networks were predicted for c-Maf, N-Myc, and Nfib (DNA-binding transcription factors); Cnot6, Cpsf6, Dicer1, and Tnrc6b (RNA to miRNA processing); and Ash1l, Med1/PBP, and Kdm5b/Jarid1b/Plu1 (chromatin remodeling).Three miRNAs, including miR-143, miR-155, and miR-301a, down-regulated expression of c-Maf in the 3'-UTR luciferase reporter assays.These present studies demonstrate for the first time global impact of activated FGF signaling in lens cell culture system and predicted novel gene regulatory networks connected by multiple miRNAs that regulate lens differentiation.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461.

ABSTRACT
MicroRNAs (miRNAs) and fibroblast growth factor (FGF) signaling regulate a wide range of cellular functions, including cell specification, proliferation, migration, differentiation, and survival. In lens, both these systems control lens fiber cell differentiation; however, a possible link between these processes remains to be examined. Herein, the functional requirement for miRNAs in differentiating lens fiber cells was demonstrated via conditional inactivation of Dicer1 in mouse (Mus musculus) lens. To dissect the miRNA-dependent pathways during lens differentiation, we used a rat (Rattus norvegicus) lens epithelial explant system, induced by FGF2 to differentiate, followed by mRNA and miRNA expression profiling. Transcriptome and miRNome analysis identified extensive FGF2-regulated cellular responses that were both independent and dependent on miRNAs. We identified 131 FGF2-regulated miRNAs. Seventy-six of these miRNAs had at least two in silico predicted and inversely regulated target mRNAs. Genes modulated by the greatest number of FGF-regulated miRNAs include DNA-binding transcription factors Nfib, Nfat5/OREBP, c-Maf, Ets1, and N-Myc. Activated FGF signaling influenced bone morphogenetic factor/transforming growth factor-β, Notch, and Wnt signaling cascades implicated earlier in lens differentiation. Specific miRNA:mRNA interaction networks were predicted for c-Maf, N-Myc, and Nfib (DNA-binding transcription factors); Cnot6, Cpsf6, Dicer1, and Tnrc6b (RNA to miRNA processing); and Ash1l, Med1/PBP, and Kdm5b/Jarid1b/Plu1 (chromatin remodeling). Three miRNAs, including miR-143, miR-155, and miR-301a, down-regulated expression of c-Maf in the 3'-UTR luciferase reporter assays. These present studies demonstrate for the first time global impact of activated FGF signaling in lens cell culture system and predicted novel gene regulatory networks connected by multiple miRNAs that regulate lens differentiation.

Show MeSH

Related in: MedlinePlus

A summary of major GO categories of miRNA targets. Four individual groups of RNA targets (665, 376, 458, and 380; see Table 1) were analyzed by the use of DAVID GO databases and four groups, including Cell homeostasis, Motility, Signaling, and Gene Regulation, related to lens fiber cell biology are shown. Relative levels of down- and up-regulated genes are shown with negative and no sign, respectively. A total number of genes from each of four columns was calculated and used to rank the “GO term” from the greatest to lowest numbers of regulated genes. The individual genes are shown in File S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3852386&req=5

fig4: A summary of major GO categories of miRNA targets. Four individual groups of RNA targets (665, 376, 458, and 380; see Table 1) were analyzed by the use of DAVID GO databases and four groups, including Cell homeostasis, Motility, Signaling, and Gene Regulation, related to lens fiber cell biology are shown. Relative levels of down- and up-regulated genes are shown with negative and no sign, respectively. A total number of genes from each of four columns was calculated and used to rank the “GO term” from the greatest to lowest numbers of regulated genes. The individual genes are shown in File S2.

Mentions: The individual genes from the 1041 and 838 gene lists (Table 1) were imported into the GO (Biological Process, Molecular Function, and Cellular Compartment) and KEGG Pathway functional annotations to link the FGF2-regulated/miRNA-dependent genes with the function and subcellular localization. The miRNA-dependent mRNAs distributed primarily among the groups of nuclear proteins, cell-surface receptors, and intracellular signaling proteins (data not shown), suggesting a role for FGF-induced miRNAs as main effectors of rapid remodeling of gene expression programs in response to external stimulus. The GO and KEGG Pathway functional classification identified four “high” GO levels, including Cell Homeostasis, Motility, “Signaling,” and Gene Regulation, and their numerous subcategories (see Figure 4). They include “Regulation of cell death,” “Regulation of cell proliferation,” and “Regulation of cell cycle”; all these categories were shown to be regulated by FGF2 in rat lens cell explants using cell biology studies (Lovicu and McAvoy 2005; Griep 2006; West-Mays et al. 2010). The “Cell homeostasis” group contains more than a 3-times greater number of genes in the “early” compared with the “late” response phase. This category includes “Regulation of cell death” and “Regulation of cell proliferation.” These data suggest that FGF2 controls the cell-cycle machinery/survival pathways as soon as the level of FGF2 is increased to induce cellular differentiation (see section below: FGF2-induced miRNAs are key major regulators of cell-cycle arrest). In contrast, the “Motility group” is represented in both “early” and “late” stages, the number of regulated genes is ~1.4 greater in the “late” group.


Identification and characterization of FGF2-dependent mRNA: microRNA networks during lens fiber cell differentiation.

Wolf L, Gao CS, Gueta K, Xie Q, Chevallier T, Podduturi NR, Sun J, Conte I, Zelenka PS, Ashery-Padan R, Zavadil J, Cvekl A - G3 (Bethesda) (2013)

A summary of major GO categories of miRNA targets. Four individual groups of RNA targets (665, 376, 458, and 380; see Table 1) were analyzed by the use of DAVID GO databases and four groups, including Cell homeostasis, Motility, Signaling, and Gene Regulation, related to lens fiber cell biology are shown. Relative levels of down- and up-regulated genes are shown with negative and no sign, respectively. A total number of genes from each of four columns was calculated and used to rank the “GO term” from the greatest to lowest numbers of regulated genes. The individual genes are shown in File S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852386&req=5

fig4: A summary of major GO categories of miRNA targets. Four individual groups of RNA targets (665, 376, 458, and 380; see Table 1) were analyzed by the use of DAVID GO databases and four groups, including Cell homeostasis, Motility, Signaling, and Gene Regulation, related to lens fiber cell biology are shown. Relative levels of down- and up-regulated genes are shown with negative and no sign, respectively. A total number of genes from each of four columns was calculated and used to rank the “GO term” from the greatest to lowest numbers of regulated genes. The individual genes are shown in File S2.
Mentions: The individual genes from the 1041 and 838 gene lists (Table 1) were imported into the GO (Biological Process, Molecular Function, and Cellular Compartment) and KEGG Pathway functional annotations to link the FGF2-regulated/miRNA-dependent genes with the function and subcellular localization. The miRNA-dependent mRNAs distributed primarily among the groups of nuclear proteins, cell-surface receptors, and intracellular signaling proteins (data not shown), suggesting a role for FGF-induced miRNAs as main effectors of rapid remodeling of gene expression programs in response to external stimulus. The GO and KEGG Pathway functional classification identified four “high” GO levels, including Cell Homeostasis, Motility, “Signaling,” and Gene Regulation, and their numerous subcategories (see Figure 4). They include “Regulation of cell death,” “Regulation of cell proliferation,” and “Regulation of cell cycle”; all these categories were shown to be regulated by FGF2 in rat lens cell explants using cell biology studies (Lovicu and McAvoy 2005; Griep 2006; West-Mays et al. 2010). The “Cell homeostasis” group contains more than a 3-times greater number of genes in the “early” compared with the “late” response phase. This category includes “Regulation of cell death” and “Regulation of cell proliferation.” These data suggest that FGF2 controls the cell-cycle machinery/survival pathways as soon as the level of FGF2 is increased to induce cellular differentiation (see section below: FGF2-induced miRNAs are key major regulators of cell-cycle arrest). In contrast, the “Motility group” is represented in both “early” and “late” stages, the number of regulated genes is ~1.4 greater in the “late” group.

Bottom Line: Specific miRNA:mRNA interaction networks were predicted for c-Maf, N-Myc, and Nfib (DNA-binding transcription factors); Cnot6, Cpsf6, Dicer1, and Tnrc6b (RNA to miRNA processing); and Ash1l, Med1/PBP, and Kdm5b/Jarid1b/Plu1 (chromatin remodeling).Three miRNAs, including miR-143, miR-155, and miR-301a, down-regulated expression of c-Maf in the 3'-UTR luciferase reporter assays.These present studies demonstrate for the first time global impact of activated FGF signaling in lens cell culture system and predicted novel gene regulatory networks connected by multiple miRNAs that regulate lens differentiation.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461.

ABSTRACT
MicroRNAs (miRNAs) and fibroblast growth factor (FGF) signaling regulate a wide range of cellular functions, including cell specification, proliferation, migration, differentiation, and survival. In lens, both these systems control lens fiber cell differentiation; however, a possible link between these processes remains to be examined. Herein, the functional requirement for miRNAs in differentiating lens fiber cells was demonstrated via conditional inactivation of Dicer1 in mouse (Mus musculus) lens. To dissect the miRNA-dependent pathways during lens differentiation, we used a rat (Rattus norvegicus) lens epithelial explant system, induced by FGF2 to differentiate, followed by mRNA and miRNA expression profiling. Transcriptome and miRNome analysis identified extensive FGF2-regulated cellular responses that were both independent and dependent on miRNAs. We identified 131 FGF2-regulated miRNAs. Seventy-six of these miRNAs had at least two in silico predicted and inversely regulated target mRNAs. Genes modulated by the greatest number of FGF-regulated miRNAs include DNA-binding transcription factors Nfib, Nfat5/OREBP, c-Maf, Ets1, and N-Myc. Activated FGF signaling influenced bone morphogenetic factor/transforming growth factor-β, Notch, and Wnt signaling cascades implicated earlier in lens differentiation. Specific miRNA:mRNA interaction networks were predicted for c-Maf, N-Myc, and Nfib (DNA-binding transcription factors); Cnot6, Cpsf6, Dicer1, and Tnrc6b (RNA to miRNA processing); and Ash1l, Med1/PBP, and Kdm5b/Jarid1b/Plu1 (chromatin remodeling). Three miRNAs, including miR-143, miR-155, and miR-301a, down-regulated expression of c-Maf in the 3'-UTR luciferase reporter assays. These present studies demonstrate for the first time global impact of activated FGF signaling in lens cell culture system and predicted novel gene regulatory networks connected by multiple miRNAs that regulate lens differentiation.

Show MeSH
Related in: MedlinePlus