From microRNAs to targets: pathway discovery in cell fate transitions.

PubWeight™: 1.15‹?› | Rank: Top 10%

🔗 View Article (PMC 3210035)

Published in Curr Opin Genet Dev on June 01, 2011

Authors

Deepa Subramanyam1, Robert Blelloch

Author Affiliations

1: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Urology, University of California San Francisco, San Francisco, CA, USA.

Articles citing this

A molecular roadmap of reprogramming somatic cells into iPS cells. Cell (2012) 4.41

Regulation of epithelial-mesenchymal and mesenchymal-epithelial transitions by microRNAs. Curr Opin Cell Biol (2013) 1.39

The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res (2014) 1.02

Untangling the web: the diverse functions of the PIWI/piRNA pathway. Mol Reprod Dev (2013) 0.98

MicroRNA-based discovery of barriers to dedifferentiation of fibroblasts to pluripotent stem cells. Nat Struct Mol Biol (2013) 0.95

Novel insights into the molecular mechanisms of α-fetoprotein expression and malignant phenotypes of hepatocellular carcinoma. Cell Mol Immunol (2011) 0.88

Identification of micro-RNA networks in end-stage heart failure because of dilated cardiomyopathy. J Cell Mol Med (2013) 0.84

Learning the molecular mechanisms of the reprogramming factors: let's start from microRNAs. Mol Biosyst (2012) 0.84

Epithelial-mesenchymal transition transcription factors and miRNAs: "Plastic surgeons" of breast cancer. World J Clin Oncol (2014) 0.84

MicroRNA as a diagnostic tool in fine-needle aspiration biopsy of thyroid nodules. Oncologist (2012) 0.83

MicroRNA-383 regulates the apoptosis of tumor cells through targeting Gadd45g. PLoS One (2014) 0.83

RNA regulation of the immune system. Immunol Rev (2013) 0.82

A coregulatory network of NR2F1 and microRNA-140. PLoS One (2013) 0.81

The RNA binding protein SAM68 transiently localizes in the chromatoid body of male germ cells and influences expression of select microRNAs. PLoS One (2012) 0.81

Role of Sam68 in post-transcriptional gene regulation. Int J Mol Sci (2013) 0.78

MicroRNA-mediated myostatin silencing in caprine fetal fibroblasts. PLoS One (2014) 0.75

Articles cited by this

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell (2006) 120.51

MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (2005) 48.95

The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31

The impact of microRNAs on protein output. Nature (2008) 32.39

Widespread changes in protein synthesis induced by microRNAs. Nature (2008) 31.44

RAS is regulated by the let-7 microRNA family. Cell (2005) 30.24

The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol (2008) 24.27

Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04

Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38

Dicer is essential for mouse development. Nat Genet (2003) 15.87

Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet (2007) 15.46

The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2. Genes Dev (2008) 15.01

Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci U S A (2008) 13.09

Embryonic stem cell-specific MicroRNAs. Dev Cell (2003) 13.05

Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science (2007) 12.42

Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev (2005) 12.15

Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol (2009) 11.50

Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science (2008) 11.33

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol (2008) 10.97

Retracted A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell (2009) 10.51

Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell (2009) 10.50

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat Biotechnol (2008) 10.29

The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes Dev (2007) 10.15

The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2. J Biol Chem (2008) 10.08

Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet (2011) 9.79

DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet (2007) 9.25

Human embryonic stem cells express a unique set of microRNAs. Dev Biol (2004) 8.87

Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature (2009) 8.70

Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci U S A (2005) 8.35

Downregulation of miRNA-200c links breast cancer stem cells with normal stem cells. Cell (2009) 8.33

MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell (2009) 8.14

The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell (2007) 7.99

A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature (2009) 7.96

A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell (2010) 7.94

Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell (2008) 7.79

Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell (2010) 7.51

Role of the murine reprogramming factors in the induction of pluripotency. Cell (2009) 7.46

The Ink4/Arf locus is a barrier for iPS cell reprogramming. Nature (2009) 7.39

A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat Cell Biol (2008) 7.35

A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res (2005) 7.24

RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell (2007) 7.06

Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature (2009) 6.85

Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell (2011) 6.11

Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet (2007) 5.33

miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat Neurosci (2009) 5.27

Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet (2008) 5.26

The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev (2007) 5.16

Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat Biotechnol (2009) 5.14

Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature (2010) 5.10

Two supporting factors greatly improve the efficiency of human iPSC generation. Cell Stem Cell (2008) 5.04

Senescence impairs successful reprogramming to pluripotent stem cells. Genes Dev (2009) 4.69

Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell (2010) 4.20

Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells. Mol Cell Biol (2008) 4.07

Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat Biotechnol (2011) 4.06

MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol (2008) 3.98

A parsimonious model for gene regulation by miRNAs. Science (2011) 3.79

MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature (2009) 3.66

The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors. Cell (2009) 3.60

Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells. Mol Cell (2010) 3.53

The RNAseIII enzyme Drosha is critical in T cells for preventing lethal inflammatory disease. J Exp Med (2008) 3.45

Small RNA-mediated regulation of iPS cell generation. EMBO J (2011) 2.95

Many families of C. elegans microRNAs are not essential for development or viability. Curr Biol (2010) 2.90

nhl-2 Modulates microRNA activity in Caenorhabditis elegans. Cell (2009) 2.87

Progress in understanding reprogramming to the induced pluripotent state. Nat Rev Genet (2011) 2.81

A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol (2010) 2.53

A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol (2008) 2.43

MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1. Stem Cells (2007) 2.40

Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat Cell Biol (2010) 2.40

Regulation of somatic cell reprogramming through inducible mir-302 expression. Nucleic Acids Res (2010) 2.40

Conserved MicroRNA miR-8/miR-200 and its target USH/FOG2 control growth by regulating PI3K. Cell (2009) 2.39

MicroRNA let-7b regulates neural stem cell proliferation and differentiation by targeting nuclear receptor TLX signaling. Proc Natl Acad Sci U S A (2010) 2.36

Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell (2010) 2.12

MicroRNA cluster 302-367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition. J Biol Chem (2011) 2.08

miR-21 and miR-31 converge on TIAM1 to regulate migration and invasion of colon carcinoma cells. J Biol Chem (2010) 2.05

Retracted Concomitant suppression of three target genes can explain the impact of a microRNA on metastasis. Genes Dev (2009) 1.74

microRNAs regulate human embryonic stem cell division. Cell Cycle (2009) 1.58

miR-200b targets Ets-1 and is down-regulated by hypoxia to induce angiogenic response of endothelial cells. J Biol Chem (2010) 1.53

MicroRNA-21 targets tumor suppressor genes ANP32A and SMARCA4. Oncogene (2011) 1.31

DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish. PLoS One (2009) 1.29

Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol (2007) 1.20

Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy. PLoS One (2009) 1.17

MiR-124 regulates early neurogenesis in the optic vesicle and forebrain, targeting NeuroD1. Nucleic Acids Res (2010) 1.07

MicroRNA Regulation of Embryonic Stem Cell Self-Renewal and Differentiation. Adv Exp Med Biol (2010) 1.05

miR-21 downregulates the tumor suppressor P12 CDK2AP1 and stimulates cell proliferation and invasion. J Cell Biochem (2011) 0.93

Articles by these authors

DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet (2007) 9.25

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev (2010) 7.14

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev (2008) 7.07

Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet (2008) 5.26

Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat Biotechnol (2009) 5.14

Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature (2010) 5.10

Generation of induced pluripotent stem cells in the absence of drug selection. Cell Stem Cell (2007) 4.94

Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat Biotechnol (2011) 4.06

Posttranscriptional crossregulation between Drosha and DGCR8. Cell (2009) 3.54

Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev (2004) 2.75

MicroRNA-29 regulates T-box transcription factors and interferon-γ production in helper T cells. Immunity (2011) 2.71

MicroRNA function is globally suppressed in mouse oocytes and early embryos. Curr Biol (2010) 2.57

Loss of cardiac microRNA-mediated regulation leads to dilated cardiomyopathy and heart failure. Circ Res (2009) 2.44

Microfluidic-based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in the sera of prostate cancer patients. Cancer Res (2010) 1.89

Cell cycle regulation by MicroRNAs in embryonic stem cells. Cancer Res (2009) 1.69

A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. RNA (2011) 1.52

Distinct requirements of microRNAs in NK cell activation, survival, and function. J Immunol (2010) 1.48

Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition. Genes Dev (2011) 1.47

Regulation of epithelial-mesenchymal and mesenchymal-epithelial transitions by microRNAs. Curr Opin Cell Biol (2013) 1.39

miR-380-5p represses p53 to control cellular survival and is associated with poor outcome in MYCN-amplified neuroblastoma. Nat Med (2010) 1.35

Small RNAs in early mammalian development: from gametes to gastrulation. Development (2011) 1.33

Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8. PLoS One (2009) 1.18

Monoallelic deletion of the microRNA biogenesis gene Dgcr8 produces deficits in the development of excitatory synaptic transmission in the prefrontal cortex. Neural Dev (2011) 1.16

MicroRNA Regulation of Embryonic Stem Cell Self-Renewal and Differentiation. Adv Exp Med Biol (2010) 1.05

miR-294/miR-302 promotes proliferation, suppresses G1-S restriction point, and inhibits ESC differentiation through separable mechanisms. Cell Rep (2013) 0.99

Loss of microRNAs in pyramidal neurons leads to specific changes in inhibitory synaptic transmission in the prefrontal cortex. Mol Cell Neurosci (2012) 0.98

TRA-1/GLI controls development of somatic gonadal precursors in C. elegans. Development (2004) 0.97

MicroRNA-based discovery of barriers to dedifferentiation of fibroblasts to pluripotent stem cells. Nat Struct Mol Biol (2013) 0.95

Nuclear transplantation, embryonic stem cells and the potential for cell therapy. Hematol J (2004) 0.95

Small RNAs in germline development. Curr Top Dev Biol (2013) 0.91

PML-RAR{alpha} and Dnmt3a1 cooperate in vivo to promote acute promyelocytic leukemia. Cancer Res (2010) 0.90

Cell cycle regulation by microRNAs in stem cells. Results Probl Cell Differ (2011) 0.89

Sox1 marks an activated neural stem/progenitor cell in the hippocampus. Development (2012) 0.88

High throughput microRNA profiling: optimized multiplex qRT-PCR at nanoliter scale on the fluidigm dynamic arrayTM IFCs. J Vis Exp (2011) 0.87

An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immunol (2012) 0.87

Watching reprogramming in real time. Nat Biotechnol (2009) 0.87

microRNA induced transdifferentiation. F1000 Biol Rep (2012) 0.86

Dgcr8 controls neural crest cells survival in cardiovascular development. Dev Biol (2011) 0.85

Efficiency and specificity in microRNA biogenesis. Nat Struct Mol Biol (2012) 0.85

DGCR8-mediated production of canonical microRNAs is critical for regulatory T cell function and stability. PLoS One (2013) 0.81

Generation of induced pluripotent stem cells from the prairie vole. PLoS One (2012) 0.80

CompMoby: comparative MobyDick for detection of cis-regulatory motifs. BMC Bioinformatics (2008) 0.80

Epigenetics, noncoding RNAs, and cell signaling--crossroads in the regulation of cell fate decisions. Curr Opin Cell Biol (2013) 0.79

Regenerative medicine: short cut to cell replacement. Nature (2008) 0.77

On the streets of San Francisco: highlights from the ISSCR Annual Meeting 2010. Cell Stem Cell (2010) 0.75