The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
Open accessAbstract
SUMMARY MicroRNAs (miRNAs) are crucial for normal embryonic stem (ES) cell self-renewal and cellular differentiation, but how miRNA gene expression is controlled by the key transcriptional regulators of ES cells has not been established. We describe here a new map of the transcriptional regulatory circuitry of ES cells that incorporates both protein-coding and miRNA genes, and which is based on high-resolution ChIP-seq data, systematic identification of miRNA promoters, and quantitative sequencing of short transcripts in multiple cell types. We find that the key ES cell transcription factors are associated with promoters for most miRNAs that are preferentially expressed in ES cells and with promoters for a set of silent miRNA genes. This silent set of miRNA genes is co-occupied by Polycomb Group proteins in ES cells and expressed in a tissue-specific fashion in differentiated cells. These data reveal how key ES cell transcription factors promote the miRNA expression program that contributes to normal self-renewal and cellular differentiation, and integrate miRNAs and their targets into an expanded model of the regulatory circuitry controlling ES cell identity.
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Citations
Cites
Bartel (2004) · doi:10.1016/s0092-8674(04)00045-5 · Cited by 34,714
Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
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High-Resolution Profiling of Histone Methylations in the Human Genome
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A bivalent chromatin structure marks key developmental genes in embryonic stem cells
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Self-citationCombinatorial microRNA target predictions
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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Self-citationA Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing
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“Third, most miRNA promoters showed evidence of H3K4me3 enrichment in multiple tissues, as observed at the promoters of most protein-coding genes (Barski et al., 2007; Guenther et al., 2007; Heintzman et al., 2007) (Figure 2D).”
BackgroundNetwork motifs: theory and experimental approaches
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The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution
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Self-citation
Cited by
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Bartel, D. P. (2018) · Cell · doi:10.1016/j.cell.2018.03.006 · Cited by 3,751
Self-citationRNA sequencing: advances, challenges and opportunities
Ozsolak, F., & Milos, P. M. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2934 · Cited by 2,135
“These limitations may be partly alleviated when combined with other methods such as chromatin-based TSS prediction, which relies on detecting histone modifications that are indicative of active transcriptio”
MethodMediator and cohesin connect gene expression and chromatin architecture
Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939
Self-citationFunctional genomics reveal that the serine synthesis pathway is essential in breast cancer
Possemato, R., Marks, K. M., Shaul, Y. D., Pacold, M. E., Kim, D., Birsoy, K., Sethumadhavan, S., Woo, H.-K., Jang, H. G., Jha, A. K., et al. (2011) · Nature · doi:10.1038/nature10350 · Cited by 1,683
Metadata
- Authors
- Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J., Calabrese, J. M., Dennis, L. M., Volkert, T. L., Gupta, S., Love, J., Hannett, N., Sharp, P. A., Bartel, D. P., Jaenisch, R., & Young, R. A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2008-08
- Volume
- 134
- Issue
- 3
- Pages
- 521-533
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W4232123484
- Cited by
- 1,370
- References
- 12
- FWCI
- 39.52
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J., Calabrese, J. M., Dennis, L. M., Volkert, T. L., Gupta, S., Love, J., Hannett, N., Sharp, P. A., Bartel, D. P., Jaenisch, R., & Young, R. A. (2008). Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells. Cell. https://doi.org/10.1016/j.cell.2008.07.020
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