The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Histone modification levels are predictive for gene expression
Open accessAbstract
Histones are frequently decorated with covalent modifications. These histone modifications are thought to be involved in various chromatin-dependent processes including transcription. To elucidate the relationship between histone modifications and transcription, we derived quantitative models to predict the expression level of genes from histone modification levels. We found that histone modification levels and gene expression are very well correlated. Moreover, we show that only a small number of histone modifications are necessary to accurately predict gene expression. We show that different sets of histone modifications are necessary to predict gene expression driven by high CpG content promoters (HCPs) or low CpG content promoters (LCPs). Quantitative models involving H3K4me3 and H3K79me1 are the most predictive of the expression levels in LCPs, whereas HCPs require H3K27ac and H4K20me1. Finally, we show that the connections between histone modifications and gene expression seem to be general, as we were able to predict gene expression levels of one cell type using a model trained on another one.
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Cites
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High-Resolution Profiling of Histone Methylations in the Human Genome
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Combinatorial patterns of histone acetylations and methylations in the human genome
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Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
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Cited by
Deep learning for computational biology
Angermueller, C., Pärnamaa, T., Parts, L., & Stegle, O. (2016) · Molecular Systems Biology · doi:10.15252/msb.20156651 · Cited by 1,473
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111
Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502
Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure
Naftelberg, S., Schor, I. E., Ast, G., & Kornblihtt, A. R. (2015) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034242 · Cited by 448
Dorighi, K. M., Swigut, T., Henriques, T., Bhanu, N. V., Scruggs, B. S., Nady, N., Still, C. D., Garcia, B. A., Adelman, K., & Wysocka, J. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.018 · Cited by 403
Metadata
- Authors
- Karlić, R., Chung, H.-R., Lasserre, J., Vlahoviček, K., & Vingron, M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2010-02
- Volume
- 107
- Issue
- 7
- Pages
- 2926-2931
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2127081697
- Cited by
- 792
- References
- 8
- FWCI
- 18.90
- Type
- journal article
- Language
- en
- Open access
- green
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- Karlić, R., Chung, H.-R., Lasserre, J., Vlahoviček, K., & Vingron, M. (2010). Histone modification levels are predictive for gene expression. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0909344107
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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