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Article

The Forkhead Transcription Factor FOXK2 Promotes AP-1-Mediated Transcriptional Regulation

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Pages 385-398 | Received 15 Apr 2011, Accepted 01 Nov 2011, Published online: 20 Mar 2023

REFERENCES

  • Bolstad BM, Irizarry RA, Astrand M, Speed TP. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193.
  • Boros J, et al. 2009. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res. 19: 1963–1973.
  • Bottomly D, Kyler SL, McWeeney SK, Yochum GS. 2010. Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq. Nucleic Acids Res. 38: 5735–5745.
  • Carlsson P, Mahlapuu M. 2002. Forkhead transcription factors: key players in development and metabolism. Dev. Biol. 250: 1–23.
  • Carroll JS, et al. 2005. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122: 33–43.
  • Casas-Tinto S, Gomez-Velazquez M, Granadino B, Fernandez-Funez P. 2008. FoxK mediates TGF-beta signalling during midgut differentiation in flies. J. Cell Biol. 183: 1049–1060.
  • Eeckhoute J, et al. 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 19: 372–380.
  • ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816.
  • Freddie CT, Ji Z, Marais A, Sharrocks AD. 2007. Functional interactions between the Forkhead transcription factor FOXK1 and the MADS-box protein SRF. Nucleic Acids Res. 35: 5203–5212.
  • Fujii Y, Nakamura M. 2010. FOXK2 transcription factor is a novel G/T-mismatch DNA binding protein. J. Biochem. 147: 705–709.
  • Fujiwara T, et al. 2009. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol. Cell 36: 667–681.
  • Garry DJ, et al. 2000. Myogenic stem cell function is impaired in mice lacking the forkhead/winged helix protein MNF. Proc. Natl. Acad. Sci. U. S. A. 97: 5416–5421.
  • Gaulton KJ, et al. 2010. A map of open chromatin in human pancreatic islets. Nat. Genet. 42: 255–259.
  • Geisberg JV, Struhl K. 2004. Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo. Nucleic Acids Res. 32: e151.
  • Georges AB, Benayoun BA, Caburet S, Veitia RA. 2010. Generic binding sites, generic DNA-binding domains: where does specific promoter recognition come from? FASEB J. 24:346–356.
  • Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17: 877–885.
  • Goecks J, Nekrutenko A, Taylor J, Galaxy Team. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11: R86.
  • Hannenhalli S, Kaestner KH. 2009. The evolution of Fox genes and their role in development and disease. Nat. Rev. Genet. 10:233–240.
  • Hawke TJ, Jiang N, Garry DJ. 2003. Absence of p21CIP rescues myogenic progenitor cell proliferative and regenerative capacity in Foxk1 null mice. J. Biol. Chem. 278: 4015–4020.
  • Hess J, Angel P, Schorpp-Kistner M. 2004. AP-1 subunits: quarrel and harmony among siblings. J. Cell Sci. 117: 5965–5973.
  • Hoey T, Sun YL, Williamson K, Xu X. 1995. Isolation of two new members of the NF-AT gene family and functional characterization of the NF-AT proteins. Immunity 2: 461–472.
  • Hollenhorst PC, et al. 2009. DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet. 5: e1000778.
  • Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44–57.
  • Hurtado A, Holmes KA, Ross-Innes CS, Schmidt D, Carroll JS. 2011. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat. Genet. 43: 27–33.
  • Johnson WE, et al. 2006. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. U. S. A. 103: 12457–12462.
  • Kim SY, et al. 2009. Foxl2, a forkhead transcription factor, modulates nonclassical activity of the estrogen receptor-alpha. Endocrinology 150: 5085–5093.
  • Komorek J, et al. 2010. Adenovirus type 5 E1A and E6 proteins of low-risk cutaneous beta-human papillomaviruses suppress cell transformation through interaction with FOXK1/K2 transcription factors. J. Virol. 84: 2719–2731.
  • Li C, Lai CF, Sigman DS, Gaynor RB. 1991. Cloning of a cellular factor, interleukin binding factor, that binds to NFAT-like motifs in the human immunodeficiency virus long terminal repeat. Proc. Natl. Acad. Sci. U. S. A. 88: 7739–7743.
  • Li C, Wong WH. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U. S. A. 98: 31–36.
  • Lupien M, et al. 2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132: 958–970.
  • Maglott D, Ostell J, Pruitt KD, Tatusova T. 2011. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 39: D52–D57.
  • Mahony S, Benos PV. 2007. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35: W253–W258.
  • Marais A, et al. 2010. Cell cycle-dependent regulation of the Forkhead transcription factor FOXK2 by CDK-cyclin complexes. J. Biol. Chem. 285: 35728–35739.
  • Motallebipour M, et al. 2009. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Genome Biol. 10: R129.
  • Nirula A, Moore DJ, Gaynor RB. 1997. Constitutive binding of the transcription factor interleukin-2 (IL-2) enhancer binding factor to the IL-2 promoter. J. Biol. Chem. 272:7736–7745.
  • Norrmén C, et al. 2009. FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1. J. Cell Biol. 185: 439–457.
  • O'Donnell A, Yang SH, Sharrocks AD. 2008. MAP kinase-mediated c-fos regulation relies on a histone acetylation relay switch. Mol. Cell 29: 780–785.
  • Pavesi G, Mereghetti P, Mauri G, Pesole G. 2004. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res. 32: W199–W203.
  • Pierrou S, Hellqvist M, Samuelsson L, Enerbäck S, Carlsson P. 1994. Cloning and characterization of seven human forkhead proteins: binding site specificity and DNA bending. EMBO J. 13: 5002–5012.
  • Shin H, Liu T, Manrai AK, Liu XS. 2009. CEAS: cis-regulatory element annotation system. Bioinformatics 25: 2605–2606.
  • Smyth GK. 2004. Linear models and empirical Bayes for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3(1): Article3.
  • Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100:9440–9445.
  • Valouev A, et al. 2008. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5: 829–834.
  • Wallerman O, et al. 2009. Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res. 37: 7498–7508.
  • Yang Q, et al. 2000. The winged-helix/forkhead protein myocyte nuclear factor beta (MNF-beta) forms a co-repressor complex with mammalian sin3B. Biochem. J. 345: 335–343.
  • Zhang Y, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9: R137.