The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Disentangling the Many Layers of Eukaryotic Transcriptional Regulation
Open accessAbstract
Regulation of gene expression in eukaryotes is an extremely complex process. In this review, we break down several critical steps, emphasizing new data and techniques that have expanded current gene regulatory models. We begin at the level of DNA sequence where cis-regulatory modules (CRMs) provide important regulatory information in the form of transcription factor (TF) binding sites. In this respect, CRMs function as instructional platforms for the assembly of gene regulatory complexes. We discuss multiple mechanisms controlling complex assembly, including cooperative DNA binding, combinatorial codes, and CRM architecture. The second section of this review places CRM assembly in the context of nucleosomes and condensed chromatin. We discuss how DNA accessibility and histone modifications contribute to TF function. Lastly, new advances in chromosomal mapping techniques have provided increased understanding of intra- and interchromosomal interactions. We discuss how these topological maps influence gene regulatory models.
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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
Regulation of chromatin by histone modifications
Bannister, A. J., & Kouzarides, T. (2011) · Cell Research · doi:10.1038/cr.2011.22 · Cited by 6,012
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
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×
“Monomethylated H3K4 is associated with enhancers, dimethylated H3K4 (H3K4me2) is associated with both enhancers and promoters or transcription start sites (TSSs) of actively transcribed genes, and trimethylated H3K4 (H3K4me3) is associated only with the promoters/TSSs of actively transcribed genes (11, 60, 140).”
The Polycomb complex PRC2 and its mark in life
Margueron, R., & Reinberg, D. (2011) · Nature · doi:10.1038/nature09784 · Cited by 3,347
Pioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
Charting histone modifications and the functional organization of mammalian genomes
Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147
The role of DNA shape in protein–DNA recognition
Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B. (2009) · Nature · doi:10.1038/nature08473 · Cited by 1,096
Self-citationDNA binding site sequence directs glucocorticoid receptor structure and activity
Meijsing, S. H., Pufall, M. A., So, A. Y., Bates, D. L., Chen, L., & Yamamoto, K. R. (2009) · Science · doi:10.1126/science.1164265 · Cited by 673
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., et al. (2008) · Cell · doi:10.1016/j.cell.2008.05.024 · Cited by 606
Cited by
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662
Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers
Lovén, J., Hoke, H. A., Lin, C. Y., Lau, A., Orlando, D. A., Vakoc, C. R., Bradner, J. E., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.036 · Cited by 2,961
Transcriptional Regulation and Its Misregulation in Disease
Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.014 · Cited by 1,620
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
O’Malley, R. C., Huang, S.-S. C., Song, L., Lewsey, M. G., Bartlett, A., Nery, J. R., Galli, M., Gallavotti, A., & Ecker, J. R. (2016) · Cell · doi:10.1016/j.cell.2016.04.038 · Cited by 1,608
Metadata
- Authors
- Lelli, K. M., Slattery, M., & Mann, R. S.
- Venue
- Annual Review of Genetics
- Publisher
- Annual Reviews
- Published
- 2012-12-15
- Volume
- 46
- Issue
- 1
- Pages
- 43-68
- ISSN
- 0066-4197 (ISSN-L)
- 1545-2948
- OpenAlex
- W2155538826
- Cited by
- 225
- References
- 28
- FWCI
- 1.15
- Type
- journal article
- Language
- en
- Open access
- green
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