The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals
Open accessAbstract
R-loops are three-stranded nucleic acid structures formed upon annealing of an RNA strand to one strand of duplex DNA. We profiled R-loops using a high-resolution, strand-specific methodology in human and mouse cell types. R-loops are prevalent, collectively occupying up to 5% of mammalian genomes. R-loop formation occurs over conserved genic hotspots such as promoter and terminator regions of poly(A)-dependent genes. In most cases, R-loops occur co-transcriptionally and undergo dynamic turnover. Detailed epigenomic profiling revealed that R-loops associate with specific chromatin signatures. At promoters, R-loops associate with a hyper-accessible state characteristic of unmethylated CpG island promoters. By contrast, terminal R-loops associate with an enhancer- and insulator-like state and define a broad class of transcription terminators. Altogether, this suggests that the retention of nascent RNA transcripts at their site of expression represents an abundant, dynamic, and programmed component of the mammalian chromatin that impacts chromatin patterning and the control of gene expression.
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Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 1×
“R-loop (+) terminator regions showed the strongest enrichment for the enhancer marks H3K4 mono-methylation (H3K4me1) and p300 (Heintzman et al., 2007; Figures 5A and 6A).”
BackgroundThe protein CTCF is required for the enhancer blocking activity of vertebrate insulators
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Getting up to speed with transcription elongation by RNA polymerase II
Jonkers, I., & Lis, J. T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3953 · Cited by 876
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. (2013) · Science · doi:10.1126/science.1229386 · Cited by 849
Jonkers, I., Kwak, H., & Lis, J. T. (2014) · eLife · doi:10.7554/elife.02407 · Cited by 581
PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression.
Liu, W., Tanasa, B., Tyurina, O. V., Zhou, T. Y., Gassmann, R., Liu, W. T., Ohgi, K. A., Benner, C., Garcia-Bassets, I., Aggarwal, A. K., et al. (2010) · Nature · doi:10.1038/nature09272 · Cited by 441 · cited 1×
“KDM4A andPHF8, two histone demethylases targeting H3K9/H3K36 and H3K9/H4K20, respectively (Klose et al., 2006; Liu et al., 2010) were also highly enriched, consistent with the observed reduction of H3K9me3 levels.”
BackgroundMayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., Sandstrom, R., Stamatoyannopoulos, J. A., & Churchman, L. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.010 · Cited by 367
Cited by
The regulation and functions of DNA and RNA G-quadruplexes
Varshney, D., Spiegel, J., Zyner, K., Tannahill, D., & Balasubramanian, S. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0236-x · Cited by 1,278
R-Loops as Cellular Regulators and Genomic Threats
Crossley, M. P., Bocek, M., & Cimprich, K. A. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.024 · Cited by 746
R Loops: From Physiological to Pathological Roles
García-Muse, T., & Aguilera, A. (2019) · Cell · doi:10.1016/j.cell.2019.08.055 · Cited by 697
Born to run: control of transcription elongation by RNA polymerase II
Chen, F. X., Smith, E. R., & Shilatifard, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0010-5 · Cited by 447
Chen, L., Chen, J.-Y., Zhang, X., Gu, Y., Xiao, R., Shao, C., Tang, P., Qian, H., Luo, D., Li, H., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.008 · Cited by 375
Metadata
- Authors
- Sanz, L. A., Hartono, S. R., Lim, Y. W., Steyaert, S., Rajpurkar, A., Ginno, P. A., Xu, X., & Chédin, F.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2016-07
- Volume
- 63
- Issue
- 1
- Pages
- 167-178
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2463453322
- Cited by
- 557
- References
- 8
- FWCI
- 20.62
- Type
- journal article
- Language
- en
- Open access
- bronze
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- The paper
- Sanz, L. A., Hartono, S. R., Lim, Y. W., Steyaert, S., Rajpurkar, A., Ginno, P. A., Xu, X., & Chédin, F. (2016). Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals. Molecular Cell. https://doi.org/10.1016/j.molcel.2016.05.032
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