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      Embryonic Stem Cell Specific MicroRNAs Regulate the G1/S Transition and Promote Rapid Proliferation

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          Abstract

          Dgcr8 knockout embryonic stem (ES) cells lack microprocessor activity and hence all canonical microRNAs (miRNAs). These cells proliferate slowly and accumulate in G1 phase of the cell cycle 1. Here, by screening a comprehensive library of individual miRNAs in the background of the Dgcr8 knockout ES cells, we report that multiple ES cell-specific miRNAs, members of the miR-290 family, rescue the ES cell proliferation defect. Furthermore, rescued cells no longer accumulate in the G1 phase of the cell cycle. These miRNAs function by suppressing several key regulators of the G1/S transition. These results show that post-transcriptional regulation by miRNAs promotes the G1/S transition of the ES cell cycle enabling their rapid proliferation. Furthermore, our screening strategy provides an alternative and powerful approach for uncovering the role of individual miRNAs in biological processes as it overcomes the common problem of redundancy and saturation in the miRNA system.

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          Most cited references19

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          Prediction of mammalian microRNA targets.

          MicroRNAs (miRNAs) can play important gene regulatory roles in nematodes, insects, and plants by basepairing to mRNAs to specify posttranscriptional repression of these messages. However, the mRNAs regulated by vertebrate miRNAs are all unknown. Here we predict more than 400 regulatory target genes for the conserved vertebrate miRNAs by identifying mRNAs with conserved pairing to the 5' region of the miRNA and evaluating the number and quality of these complementary sites. Rigorous tests using shuffled miRNA controls supported a majority of these predictions, with the fraction of false positives estimated at 31% for targets identified in human, mouse, and rat and 22% for targets identified in pufferfish as well as mammals. Eleven predicted targets (out of 15 tested) were supported experimentally using a HeLa cell reporter system. The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions.
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            DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal.

            The molecular controls that govern the differentiation of embryonic stem (ES) cells remain poorly understood. DGCR8 is an RNA-binding protein that assists the RNase III enzyme Drosha in the processing of microRNAs (miRNAs), a subclass of small RNAs. Here we study the role of miRNAs in ES cell differentiation by generating a Dgcr8 knockout model. Analysis of mouse knockout ES cells shows that DGCR8 is essential for biogenesis of miRNAs. On the induction of differentiation, DGCR8-deficient ES cells do not fully downregulate pluripotency markers and retain the ability to produce ES cell colonies; however, they do express some markers of differentiation. This phenotype differs from that reported for Dicer1 knockout cells, suggesting that Dicer has miRNA-independent roles in ES cell function. Our findings indicate that miRNAs function in the silencing of ES cell self-renewal that normally occurs with the induction of differentiation.
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              Embryonic stem cell-specific MicroRNAs.

              We have identified microRNAs (miRNAs) in undifferentiated and differentiated mouse embryonic stem (ES) cells. Some of these appear to be ES cell specific, have related sequences, and are encoded by genomic loci clustered within 2.2 kb of each other. Their expression is repressed as ES cells differentiate into embryoid bodies and is undetectable in adult mouse organs. In contrast, the levels of many previously described miRNAs remain constant or increase upon differentiation. Our results suggest that miRNAs may have a role in the maintenance of the pluripotent cell state and in the regulation of early mammalian development.
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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nature genetics
                1061-4036
                1546-1718
                12 September 2008
                2 November 2008
                December 2008
                1 June 2009
                : 40
                : 12
                : 1478-1483
                Affiliations
                [1 ] Institute for Regeneration Medicine, Center for Reproductive Sciences and Department of Urology, University of California – San Francisco
                [2 ] Dharmacon Technologies, Thermo Fisher Scientific, Lafayette, CO
                Author notes

                Author Contributions YW performed all experiments except Fig. 3a (JEB). SB developed and provided miRNA mimic library. AS built mutant reporters for Fig. 4. LB provided technical support. YW and RB designed all experiments, analyzed data and wrote the manuscript.

                [3 ] Correspondence to RB: BlellochR@ 123456stemcell.ucsf.edu
                Article
                nihpa69456
                10.1038/ng.250
                2630798
                18978791
                d29b972a-ea7c-4b08-9764-5e3dc0db4ea3
                History
                Funding
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: R01 NS057221-02 ||NS
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: R01 NS057221-01A1 ||NS
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: K08 NS048118-04 ||NS
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: K08 NS048118-03 ||NS
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: K08 NS048118-02 ||NS
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: K08 NS048118-01A1 ||NS
                Categories
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                Genetics
                Genetics

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