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Is H3K4me3 instructive for transcription activation?
Abstract
Tri‐methylation of lysine 4 on histone H3 (H3K4me3) is a near‐universal chromatin modification at the transcription start site of active genes in eukaryotes from yeast to man and its levels reflect the amount of transcription. Because of this association, H3K4me3 is often described as an ‘activating’ histone modification and assumed to have an instructive role in the transcription of genes, but the field is lacking a conserved mechanism to support this view. The overwhelming finding from genome‐wide studies is that actually very little transcription changes upon removal of most H3K4me3 under steady‐state or dynamically changing conditions, including at mammalian CpG island promoters. Instead, rather than a major role in instructing transcription, time‐resolved experiments provide more evidence supporting the deposition of H3K4me3 into chromatin as a result of transcription, influencing processes such as memory of previous states, transcriptional consistency between cells in a population and transcription termination.
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Cites
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
Active Genes Are Tri-Methylated at K4 of Histone H3
Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C. T., Schreiber, S. L., Mellor, J., & Kouzarides, T. (2002) · Nature · doi:10.1038/nature01080 · Cited by 2,138
Self-citationSingle-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006) · Nature · doi:10.1038/nature04785 · Cited by 1,483
Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark
Ruthenburg, A. J., Allis, C. D., & Wysocka, J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2006.12.014 · Cited by 1,147
Shilatifard, A. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051710-134100 · Cited by 1,091
Nascent transcript sequencing visualizes transcription at nucleotide resolution
Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823
CpG islands influence chromatin structure via the CpG-binding protein Cfp1
Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., et al. (2010) · Nature · doi:10.1038/nature08924 · Cited by 625
Greer, E. L., Maures, T. J., Hauswirth, A. G., Green, E. M., Leeman, D. S., Maro, G. S., Han, S., Banko, M. R., Gozani, O., & Brunet, A. (2010) · Nature · doi:10.1038/nature09195 · Cited by 543
H3K4me3 breadth is linked to cell identity and transcriptional consistency
Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., Devarajan, K., Daugherty, A. C., Kundaje, A. B., Mancini, E., et al. (2014) · Cell · doi:10.1016/j.cell.2014.06.027 · Cited by 536
H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation
Lauberth, S. M., Nakayama, T., Wu, X., Ferris, A. L., Tang, Z., Hughes, S. H., & Roeder, R. G. (2013) · Cell · doi:10.1016/j.cell.2013.01.052 · Cited by 473
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Metadata
- Authors
- Howe, F. S., Fischl, H., Murray, S. C., & Mellor, J.
- Venue
- BioEssays
- Publisher
- Wiley
- Published
- 2016-11-07
- Volume
- 39
- Issue
- 1
- Pages
- 1-12
- ISSN
- 0265-9247 (ISSN-L)
- 1521-1878
- OpenAlex
- W2551929191
- Cited by
- 513
- References
- 13
- FWCI
- 2.82
- Type
- journal article
- Language
- en
- Open access
- closed
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