The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Comparative Epigenomic Annotation of Regulatory DNA
Open accessAbstract
Despite the explosive growth of genomic data, functional annotation of regulatory sequences remains difficult. Here, we introduce "comparative epigenomics"-interspecies comparison of DNA and histone modifications-as an approach for annotation of the regulatory genome. We measured in human, mouse, and pig pluripotent stem cells the genomic distributions of cytosine methylation, H2A.Z, H3K4me1/2/3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, transcribed RNAs, and P300, TAF1, OCT4, and NANOG binding. We observed that epigenomic conservation was strong in both rapidly evolving and slowly evolving DNA sequences, but not in neutrally evolving sequences. In contrast, evolutionary changes of the epigenome and the transcriptome exhibited a linear correlation. We suggest that the conserved colocalization of different epigenomic marks can be used to discover regulatory sequences. Indeed, seven pairs of epigenomic marks identified exhibited regulatory functions during differentiation of embryonic stem cells into mesendoderm cells. Thus, comparative epigenomics reveals regulatory features of the genome that cannot be discerned from sequence comparisons alone.
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Cites
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
Human DNA methylomes at base resolution show widespread epigenomic differences
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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“Our data show that the degree of epigenomic conservation is not always correlated with the degree of genomic conservation but that epigenomic conservation can yield additional information to genomic conservation.”
BackgroundMethodInfluentialA unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233
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The NIH Roadmap Epigenomics Mapping Consortium
Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1045 · Cited by 1,892
Conserved role of intragenic DNA methylation in regulating alternative promoters
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Self-citationHistones: annotating chromatin
Campos, E. I., & Reinberg, D. (2009) · Annual Review of Genetics · doi:10.1146/annurev.genet.032608.103928 · Cited by 852
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008) · Nature · doi:10.1038/nature07324 · Cited by 593
Cited by
Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer
Yang, X., Han, H., De Carvalho, D. D., Lay, F. D., Jones, P. A., & Liang, G. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.028 · Cited by 1,199
Enhancer Evolution across 20 Mammalian Species
Villar, D., Berthelot, C., Aldridge, S., Rayner, T. F., Lukk, M., Pignatelli, M., Park, T. J., Deaville, R., Erichsen, J. T., Jasinska, A. J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.006 · Cited by 825
Psat1-Dependent Fluctuations in α-Ketoglutarate Affect the Timing of ESC Differentiation
Hwang, I.-Y., Kwak, S., Lee, S., Kim, H., Lee, S. E., Kim, J.-H., Kim, Y. A., Jeon, Y. K., Chung, D. H., Jin, X., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.06.014 · Cited by 180
DNA methylation: Insights into human evolution
Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J., & Marques-Bonet, T. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005661 · Cited by 128
DNA methylation networks underlying mammalian traits
Haghani, A., Li, C. Z., Robeck, T. R., Zhang, J., Lu, A. T., Ablaeva, J., Acosta-Rodríguez, V. A., Adams, D. M., Alagaili, A. N., Almunia, J., et al. (2023) · Science · doi:10.1126/science.abq5693 · Cited by 128
Metadata
- Authors
- Xiao, S., Xie, D., Cao, X., Yu, P., Xing, X., Chen, C.-C., Musselman, M., Xie, M., West, F. D., Lewin, H. A., Wang, T., & Zhong, S.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-06
- Volume
- 149
- Issue
- 6
- Pages
- 1381-1392
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W1980197759
- Cited by
- 202
- References
- 13
- FWCI
- 9.06
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Xiao, S., Xie, D., Cao, X., Yu, P., Xing, X., Chen, C.-C., Musselman, M., Xie, M., West, F. D., Lewin, H. A., Wang, T., & Zhong, S. (2012). Comparative Epigenomic Annotation of Regulatory DNA. Cell. https://doi.org/10.1016/j.cell.2012.04.029
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