The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
Open accessAbstract
Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome's primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally engaged RNA polymerases in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ∼40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol II's entry into elongation. Furthermore, “bivalent” ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb group complexes PRC1 (Polycomb-repressive complex 1) and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5′ proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation.
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Cites
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
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Stem cell transcriptome profiling via massive-scale mRNA sequencing
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“3A), bolstering the view that pausing is associated more with transcribed, rather than strictly nontranscribed, genes (Core et al. 2008).”
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Defining mechanisms that regulate RNA polymerase II transcription in vivo
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Self-citationNechaev, S., Fargo, D. C., dos Santos, G., Liu, L., Gao, Y., & Adelman, K. (2010) · Science · doi:10.1126/science.1181421 · Cited by 424
Myeloid or Lymphoid Promiscuity as a Critical Step in Hematopoietic Lineage Commitment
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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
Multiscale 3D Genome Rewiring during Mouse Neural Development
Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.043 · Cited by 1,338
Quintin, J., Saeed, S., Martens, J. H. A., Giamarellos-Bourboulis, E. J., Ifrim, D. C., Logie, C., Jacobs, L., Jansen, T., Kullberg, B.-J., Wijmenga, C., et al. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.06.006 · Cited by 1,289
Cancer Epigenetics: Tumor Heterogeneity, Plasticity of Stem-like States, and Drug Resistance
Easwaran, H., Tsai, H.-C., & Baylin, S. B. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.015 · Cited by 915
Getting up to speed with transcription elongation by RNA polymerase II
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Metadata
- Authors
- Min, I. M., Waterfall, J. J., Core, L. J., Munroe, R. J., Schimenti, J., & Lis, J. T.
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-04
- Volume
- 25
- Issue
- 7
- Pages
- 742-754
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- OpenAlex
- W2097009498
- Cited by
- 302
- References
- 7
- Type
- posted content
- Language
- en
- Open access
- diamond
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- Min, I. M., Waterfall, J. J., Core, L. J., Munroe, R. J., Schimenti, J., & Lis, J. T. (2011). Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes & Development. https://doi.org/10.1101/gad.2005511
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