Insights from genomic profiling of transcription factors (original) (raw)
Lee, T. I. & Young, R. A. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet.34, 77–137 (2000). A detailed review of transcriptional regulation, general factors and accessory proteins that control transcription initation and elongation. ArticleCASPubMed Google Scholar
Sandelin, A. et al. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Rev. Genet.8, 424–436 (2007). ArticleCASPubMed Google Scholar
ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature447, 799–816 (2007). This paper demonstrates how genome-wide studies of transcription factor binding, chromatin structure, DNA replication and sequence conservation can synergize.
Cooper, S. J., Trinklein, N. D., Anton, E. D., Nguyen, L. & Myers, R. M. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res.16, 1–10 (2006). ArticleCASPubMedPubMed Central Google Scholar
Kimura, K. et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res.16, 55–65 (2006). ArticleCASPubMedPubMed Central Google Scholar
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001). CASPubMed Google Scholar
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A. & Luscombe, N. M. A census of human transcription factors: function, expression and evolution. Nature Rev. Genet.10, 252–263 (2009). A summary of the expression, conservation and activity of the set of human sequence-specific transcription factors. ArticleCASPubMed Google Scholar
Wederell, E. D. et al. Global analysis of in vivo Foxa2-binding sites in mouse liver using massively parallel sequencing. Nucleic Acids Res.36, 4549–4564 (2008). ArticleCASPubMedPubMed Central Google Scholar
Reed, B. D., Charos, A. E., Szekely, A. M., Weissman, S. M. & Snyder, M. Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLOS Genet.4, e1000133 (2008). ArticlePubMedPubMed Central Google Scholar
Scacheri, P. C. et al. Genome-wide analysis of menin binding provides insights to MEN1 tumorigenesis. PLoS Genet.2, e51 (2006). ArticlePubMedPubMed Central Google Scholar
Hatzis, P. et al. Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol. Cell. Biol.28, 2732–2744 (2008). ArticleCASPubMedPubMed Central Google Scholar
Xu, X. et al. A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals iterchangeable roles of E2F family members. Genome Res.17, 1550–1561 (2007). ArticleCASPubMedPubMed Central Google Scholar
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods4, 1–7 (2007). An early demonstration that high-throughput sequencing of ChIP samples can be used to identify genome-wide binding sites of site-specific transcription factors. Article Google Scholar
Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science316, 1497–1502 (2007). ArticleCASPubMed Google Scholar
Rada-Iglesias, A. et al. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res.18, 380–392 (2008). ArticleCASPubMedPubMed Central Google Scholar
Vogel, M. J., Peric-Hupkes, D. & van Steensel, B. Detection of in vivo protein–DNA interactions using DamID in mammalian cells. Nature Protoc.2, 1467–1478 (2007). ArticleCAS Google Scholar
Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP–seq data. Nature Methods5, 829–834 (2008). ArticleCASPubMedPubMed Central Google Scholar
Johnson, D. S. et al. Systematic evaluation of variability in ChIP–chip experiments using predefined DNA targets. Genome Res.18, 393–403 (2008). ArticlePubMedPubMed Central Google Scholar
Bieda, M., Xu, X., Singer, M., Green, R. & Farnham, P. J. Unbiased location analysis of E2F1 binding sites suggests a widespread role for E2F1 in the human genome. Genome Res.16, 595–605 (2006). A demonstration that some factors bind exclusively to proximal promoters and do not have strict motif requirements for their binding sites. ArticleCASPubMedPubMed Central Google Scholar
Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature436, 876–880 (2005). An early demonstration that high-density oligonucleotide arrays can be used to identify genome-wide binding sites for human transcription factors. ArticleCASPubMedPubMed Central Google Scholar
Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell116, 499–509 (2004). ArticleCASPubMed Google Scholar
Nix, D. A., Courdy, S. J. & Boucher, K. M. Empirical methods for controlling false positives and estimating confidence in ChIP–seq peaks. BMC Bioinformatics9, 523 (2008). ArticlePubMedPubMed Central Google Scholar
Fejes, A. P. et al. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics24, 1729–1730 (2008). ArticleCASPubMedPubMed Central Google Scholar
Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP–seq experiments relative to controls. Nature Biotech.27, 66–75 (2009). ArticleCAS Google Scholar
Liu, Y., Michalopoulos, G. K. & Zarnegar, R. Structural and functional characterization of the mouse hepatocyte growth factor gene promoter. J. Biol. Chem.269, 4152–4160 (1994). CASPubMed Google Scholar
Fujishiro, K. et al. Analysis of tissue-specific and PPARα-dependent induction of FABP gene expression in the mouse liver by an in vivo DNA electroporation method. Mol. Cell. Biochem.239, 165–172 (2002). ArticleCASPubMed Google Scholar
Weinmann, A. S., Yan, P. S., Oberley, M. J., Huang, T. H.-M. & Farnham, P. J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev.16, 235–244 (2002). ArticleCASPubMedPubMed Central Google Scholar
Li, Z. et al. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl Acad. Sci. USA100, 8164–8169 (2003). ArticleCASPubMedPubMed Central Google Scholar
Ren, B. et al. E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints. Genes Dev.16, 245–256 (2002). ArticleCASPubMedPubMed Central Google Scholar
Consortium, T. E. P. The ENCODE (ENCyclopedia of DNA Elements) Project. Science306, 636–640 (2004). Article Google Scholar
Carroll, J. S. et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell122, 33–43 (2005). ArticleCASPubMed Google Scholar
Yang, A. et al. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell24, 593–602 (2006). ArticleCASPubMed Google Scholar
Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell133, 1106–1117 (2008). ArticleCASPubMed Google Scholar
Mann, R. S. & Carroll, S. B. Molecular mechanisms of selector gene function and evolution. Curr. Opin. Genet. Dev.12, 592–600 (2002). ArticleCASPubMed Google Scholar
Moorman, C. et al. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc. Natl Acad. Sci. USA103, 12027–12032 (2006). This demonstrates clustering of transcription factors throughout theD. melanogastergenome. ArticleCASPubMedPubMed Central Google Scholar
Elnitski, L., Jin, V. X., Farnham, P. J. & Jones, S. J. M. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res.16, 1455–1464 (2006). ArticleCASPubMed Google Scholar
Maniatis, T. et al. Structure and function of the interferon-β enhanceosome. Cold Spring Harb. Symp. Quant. Biol.63, 609–620 (1998). ArticleCASPubMed Google Scholar
Dean, A. On a chromosome far, far away: LCRs and gene expression. Trends Genet.22, 38–45 (2006). ArticleCASPubMed Google Scholar
Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature459, 108–112 (2009). This identifies specific histone modifications that are associated with cell-type-specific transcriptional regulation. ArticleCASPubMedPubMed Central Google Scholar
Heintzman, N. D. et al. Distinct predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet.39, 311–318 (2007). ArticleCASPubMed Google Scholar
Wright, W. E. & Funk, W. D. CASTing for multicomponent DNA-binding components. Trends Biochem. Sci.18, 77–80 (1993). ArticleCASPubMed Google Scholar
Morgan, X. C., Ni, S., Miranker, D. P. & Iyer, V. R. Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics8, 445 (2007). ArticlePubMedPubMed Central Google Scholar
Rabinovich, A., Jin, V. X., Rabinovich, R., Xu, X. & Farnham, P. J. E2F in vivo binding specificity: comparison of consensus versus non-consensus binding sites. Genome Res.18, 1763–1777 (2008). ArticleCASPubMedPubMed Central Google Scholar
Gineitis, D. & Treisman, R. Differential usage of signal transduction pathways defines two types of serum response factor target gene. J. Biol. Chem.276, 24531–24539 (2001). ArticleCASPubMed Google Scholar
Cooper, S. J., Trinklein, N. D., Nguyen, L. & Myers, R. M. Serum response factor binding sites differ in three human cell types. Genome Res.17, 136–144 (2009). Article Google Scholar
Jin, V. X., O'Geen, H., Iyengar, S., Green, R. & Farnham, P. J. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res.17, 807–817 (2007). ArticleCASPubMedPubMed Central Google Scholar
Li, X.-Y. et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol.6, e27 (2008). ArticlePubMedPubMed Central Google Scholar
Shi, X. et al. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J. Biol. Chem.282, 2450–2455 (2007). ArticleCASPubMed Google Scholar
Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell131, 58–69 (2007). ArticleCASPubMed Google Scholar
Albert, T. et al. The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements. J. Biol. Chem.276, 20482–20490 (2001). ArticleCASPubMed Google Scholar
Jin, V. X., Rabinovich, A., Squazzo, S. L., Green, R. & Farnham, P. J. A computational genomics approach to identify _cis_-regulatory modules from chromatin immunoprecipitation microarray data — a case study using E2F1. Genome Res.16, 1585–1595 (2006). ArticleCASPubMedPubMed Central Google Scholar
Krig, S. R. et al. Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)–chip assays. J. Biol. Chem.282, 9703–9712 (2007). ArticleCASPubMed Google Scholar
Krum, S. A. et al. Unique ERα cistromes control cell type-specific gene regulation. Mol. Endocrinol.22, 2393–2406 (2008). ArticleCASPubMed Google Scholar
Voss, T. C. & Hager, G. L. Visualizing chromatin dynamics in intact cells. Biochem. Biophys. Acta1783, 2044–2051 (2008). ArticleCASPubMed Google Scholar
Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet.36, 1065–1071 (2004). ArticleCASPubMed Google Scholar
Bartlett, J. et al. Specialized transcription factories. Biochem. Soc. Symp.73, 67–75 (2006). ArticleCAS Google Scholar
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science295, 1306–1311 (2002). ArticleCASPubMed Google Scholar
Visel, A. et al. ChIP–seq accurately predicts tissue-specific activity of enhancers. Nature457, 854–858 (2009). This study demonstrates that using ChIP–seq to identify binding sites for p300 is a highly accurate method for identifying enhancers that can be shown, using follow-up assays in transgenic mice, to function in a tissue-specific manner. ArticleCASPubMedPubMed Central Google Scholar
Camenisch, T. D., Brilliant, M. H. & Segal, D. J. Critical parameters for genome editing using zinc finger nucleases. Mini Rev. Med. Chem.8, 669–676 (2008). ArticleCASPubMed Google Scholar
Bletran, A., Liu, Y., Parikh, S., Temple, B. & Blancafort, P. Interrogating genomes with combinatorial artificial transcription factor libraries: asking zinc finger questions. Assay Drug Dev. Technol.4, 317–331 (2006). Article Google Scholar
Faruqi, A. F., Egholm, M. & Glazer, P. M. Peptide nucleic acid-targeted mutagenesis of a chromosomal gene in mouse cells. Proc. Natl Acad. Sci. USA95, 1398–1403 (1998). ArticleCASPubMedPubMed Central Google Scholar
Burnett, R. et al. DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA-TCC repeats in Friedreich's ataxia. Proc. Natl Acad. Sci. USA103, 11497–11502 (2006). ArticleCASPubMedPubMed Central Google Scholar
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell130, 77–88 (2007). ArticleCASPubMedPubMed Central Google Scholar
Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet.39, 1507–1511 (2007). ArticleCASPubMed Google Scholar
Komashko, V. M. et al. Using ChIP–chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res.18, 521–532 (2008). ArticleCASPubMedPubMed Central Google Scholar
O'Neill, L. P., VerMilyea, M. D. & Turner, B. M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nature Genet.38, 835–841 (2006). ArticleCASPubMed Google Scholar
Dahl, J. A. & Collas, P. Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells25, 1037–1046 (2007). ArticleCASPubMed Google Scholar
Attema, J. L. et al. Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl Acad. Sci. USA104, 12371–12376 (2007). ArticleCASPubMedPubMed Central Google Scholar
Xu, H., Wei, C.-L., Lin, F. & Sung, W.-K. An HMM approach to genome-wide identification of differential histone modification sites from ChIP–seq data. Bioinformatics24, 2344–2349 (2008). ArticleCASPubMed Google Scholar
Jothi, R., Cuddapah, S., Barski, A., Cui, K. & Zhao, K. Genome-wide identification of in vivo protein–DNA binding sites from ChIP–seq data. Nucleic Acids Res.36, 5221–5231 (2008). ArticleCASPubMedPubMed Central Google Scholar
Hoffman, B. G. & Jones, S. J. Genome-wide identification of DNA–protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J. Endocrinol.201, 1–13 (2009). ArticleCASPubMed Google Scholar