Advanced search
Publication Cover
Epigenomics Volume 3, 2011 - Issue 4
Submit an article Journal homepage
227
Views
0
CrossRef citations to date
0
Altmetric
Review

Transcription Factor Interactions in Genomic Nuclear Receptor Function

Charlotte L George1 Henry Wellcome Laboratories for Integrative Neuroscience & Endocrinology, Faculty of Medicine & Dentistry, University of Bristol, Bristol, BS1 3NY, UKView further author information
,
Stafford L Lightman1 Henry Wellcome Laboratories for Integrative Neuroscience & Endocrinology, Faculty of Medicine & Dentistry, University of Bristol, Bristol, BS1 3NY, UKView further author information
&
Simon C Biddie1 Henry Wellcome Laboratories for Integrative Neuroscience & Endocrinology, Faculty of Medicine & Dentistry, University of Bristol, Bristol, BS1 3NY, UK;2 Dorothy Hodgkin Building, Whitson Street, University of Bristol, Bristol, BS1 3NY, UK. [email protected]View further author information
Pages 471-485 | Published online: 18 Aug 2011

Bibliography

  • Lee W , HaslingerA, KarinM, TjianR. Activation of transcription by two factors that bind promoter and enhancer sequences of the human metallothionein gene and SV40. Nature325(6102) , 368–372 (1987).
  • Renkawitz R , SchützG, von der Ahe D, Beato M. Sequences in the promoter region of the chicken lysozyme gene required for steroid regulation and receptor binding. Cell37(2) , 503–510 (1984).
  • Schüle R , MullerM, KaltschmidtC, RenkawitzR. Many transcription factors interact synergistically with steroid-receptors. Science242(4884) , 1418–1420 (1988).
  • Carroll JS , MeyerCA, SongJet al. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 38(11) , 1289–1297 (2006).
  • Krum SA , Miranda-CarboniGA, LupienM, EeckhouteJ, CarrollJS, BrownM. Unique ERα cistromes control cell type-specific gene regulation. Mol. Endocrinol.22(11) , 2393–2406 (2008).
  • Lefterova MI , StegerDJ, ZhuoDet al. Cell-specific determinants of peroxisome proliferator-activated receptor γ function in adipocytes and macrophages. Mol. Cell. Biol. 30(9) , 2078–2089 (2010).
  • Ravasi T , SuzukiH, CannistraciCVet al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140(5) , 744–752 (2010).
  • Archer TK , CordingleyMG, WolfordRG, HagerGL. Transcription factor access is mediated by accurately positioned nucleosomes on the mouse mammary tumor virus promoter. Mol. Cell. Biol.11(2) , 688–698 (1991).
  • John S , SaboPJ, JohnsonTAet al. Interaction of the glucocorticoid receptor with the chromatin landscape. Mol. Cell 29(5) , 611–624 (2008).
  • Fletcher T , XiaoN, MautinoGet al. ATP-dependent mobilization of the glucocorticoid receptor during chromatin remodeling. Mol. Cell. Biol. 22(10) , 3255–3263 (2002).
  • Richard-Foy H , HagerGL. Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J.6(8) , 2321–2328 (1987).
  • Green CD , HanJJ. Epigenetic regulation by nuclear receptors. Epigenomics3(1) , 59–72 (2011).
  • Klokk TI , KurysP, ElbiCet al. Ligand-specific dynamics of the androgen receptor at its response element in living cells. Mol. Cell. Biol. 27(5) , 1823–1843 (2007).
  • Nagaich AK , WalkerD, WolfordR, HagerGL. Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol. Cell14(2) , 163–174 (2004).
  • Zaret K , YamamotoKR. Reversible and persistent changes in chromatin structure accompany activation of a gluocorticoid-dependent enhancer element. Cell38(1) , 29–38 (1984).
  • McNally JG , MüllerWG, WalkerD, WolfordR, HagerGL. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science287(5456) , 1262–1265 (2000).
  • Fletcher T , RyuB, BaumannCet al. Structure and dynamic properties of a glucocorticoid receptor-induced chromatin transition. Mol. Cell. Biol. 20(17) , 6466–6475 (2000).
  • Östlund Farrants AK , BlomquistP, KwonH, WrangeO. Glucocorticoid receptor-glucocorticoid response element binding stimulates nucleosome disruption by the SWI/SNF complex. Mol. Cell. Biol.17(2) , 895–905 (1997).
  • Brüggemeier U , RoggeL, WinnackerEL, BeatoM. Nuclear factor I acts as a transcription factor on the MMTV promoter but competes with steroid hormone receptors for DNA binding. EMBO J.9(7) , 2233–2239 (1990).
  • Cordingley MG , RiegelAT, HagerGL. Steroid-dependent interaction of transcription factors with the inducible promoter of mouse mammary tumor virus in vivo. Cell48(2) , 261–270 (1987).
  • Stenoien DL , PatelK, ManciniMet al. FRAP reveals that mobility of oestrogen receptor-α is ligand- and proteasome-dependent. Nat. Cell Biol. 3(1) , 15–23 (2001).
  • Métivier R , PenotG, HübnerMRet al. Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115(6) , 751–763 (2003).
  • Conway-Campbell BL , GeorgeCL, PooleyJRet al. The HSP90 molecular chaperone cycle regulates cyclical transcriptional dynamics of the glucocorticoid receptor and its co-regulatory molecules CBP/P300 during ultradian ligand treatment. Mol. Endocrinol. 26(6) , 944–954 (2011).
  • Kangaspeska S , StrideB, MétivierRet al. Transient cyclical methylation of promoter DNA. Nature 452(7183) , 112–115 (2008).
  • Métivier R , GallaisR, TiffocheCet al. Cyclical DNA methylation of a transcriptionally active promoter. Nature 452(7183) , 45–50 (2008).
  • Biddie SC , JohnS, HagerGL. Genome-wide mechanisms of nuclear receptor action. Trends in endocrinology and metabolism. Trends Endocrinol. Metabol.21(1) , 3–9 (2010).
  • Delacroix L , MoutierE, AltobelliGet al. Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. Mol. Cell. Biol. 30(1) , 231–244 (2010).
  • John S , SaboPJ, ThurmanREet al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43(3) , 264–268 (2011).
  • Mikkelsen TS , XuZ, ZhangXet al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 143 , 156–169 (2010).
  • Welboren W -J, van Driel MA, Janssen-Megens EM et al. ChIP-seq of ERα and RNA polymerase II defines genes differentially responding to ligands. EMBO J.28(10) , 1418–1428 (2009).
  • Rigaud G , RouxJ, PictetR, GrangeT. In vivo footprinting of rat tat gene: dynamic interplay between the glucocorticoid receptor and a liver-specific factor. Cell67(5) , 977–986 (1991).
  • Lefterova MI , ZhangY, StegerDJet al. PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev. 22(21) , 2941–2952 (2008).
  • Lupien M , EeckhouteJ, MeyerCAet al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132(6) , 958–970 (2008).
  • Heinz S , BennerC, SpannNet al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B-cell identities. Mol. Cell 38(4) , 576–589 (2010).
  • Boyle AP , DavisS, ShulhaHPet al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132(2) , 311–322 (2008).
  • He HH , MeyerCA, ShinHet al. Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 42 , 343–347 (2010).
  • Jin C , FelsenfeldG. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev.21(12) , 1519–1529 (2007).
  • Jin C , ZangC, WeiGet al. H3.3/H2A.Z double variant-containing nucleosomes mark nucleosome-free regions of active promoters and other regulatory regions. Nat. Genet. 41(8) , 941–945 (2009).
  • Carroll JS , LiuXS, BrodskyASet al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122(1) , 33–43 (2005).
  • Kininis M , ChenBS, DiehlAGet al. Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol. Cell. Biol. 27(14) , 5090–5104 (2007).
  • So AY -L, Chaivorapol C, Bolton EC, Li H, Yamamoto KR. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet.3(6) , e94 (2007).
  • Stender JD , KimK, CharnTHet al. Genome-wide analysis of estrogen receptor α DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol. Cell. Biol. 30(16) , 3943–3955 (2010).
  • Wang Q , LiW, LiuXSet al. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol. Cell 27(3) , 380–392 (2007).
  • Reddy TE , PauliF, SprouseROet al. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 19(12) , 2163–2171 (2009).
  • Hakim O , JohnS, LingJQ, BiddieSC, HoffmanAR, HagerGL. Glucocorticoid receptor activation of the Ciz1-Lcn2 locus by long range interactions. J. Biol. Chem.284(10) , 6048–6052 (2009).
  • Tolhuis B , PalstraR, SplinterE, GrosveldF, de Laat W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell10(6) , 1453–1465 (2002).
  • Hakim O , SungM, VossTCet al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21(5) , 697–706 (2011).
  • Fullwood MJ , LiuMH, PanYFet al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462(7269) , 58–64 (2009).
  • Schoenfelder S , ClayI, FraserP. The transcriptional interactome: gene expression in 3D. Curr. Opin. Genet. Develop.20 , 127–133 (2010).
  • Kim K , DoiA, WenBet al. Epigenetic memory in induced pluripotent stem cells. Nature 467(7313) , 285–290 (2010).
  • Lieberman-Aiden E , Van Berkum NL, Williams L et al. Comprehensive mapping of long-range interactions reveals folding principals of the human genome. Science326(5950) , 289–293 (2010).
  • Lupien M , MeyerCA, BaileySTet al. Growth factor stimulation induces a distinct ER(α) cistrome underlying breast cancer endocrine resistance. Genes Dev. 24(19) , 2219–2227 (2010).
  • Hurtado A , HolmesKA, Ross-InnesCS, SchmidtD, CarrollJS. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat. Genet.43(1) , 27–33 (2011).
  • Cirillo LA , LinFR, CuestaI, FriedmanD, JarnikM, ZaretKS. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell9(2) , 279–289 (2002).
  • Eeckhoute J , LupienM, MeyerCAet al. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 19(3) , 372–380 (2009).
  • Polo JM , LiuS, FigueroaMEet al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat. Biotechnol. 28(8) , 848–855 (2010).
  • Hua S , KittlerR, WhiteKP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell137(7) , 1259–1271 (2009).
  • Ross-Innes CS , StarkR, HolmesKAet al. Cooperative interaction between retinoic acid receptor-α and estrogen receptor in breast cancer. Genes Dev. 24(2) , 171–182 (2010).
  • Jonat C , RahmsdorfHJ, ParkKKet al. Antitumor promotion and antiinflammation: down-modulation of AP-1 (Fos/Jun) activity by glucocorticoid hormone. Cell 62(6) , 1189–1204 (1990).
  • Schüle R , RangarajanP, KliewerSet al. Functional antagonism between oncoprotein c-Jun and the glucocorticoid receptor. Cell 62(6) , 1217–1226 (1990).
  • Gaub MP , BellardM, ScheuerI, ChambonP, Sassone-CorsiP. Activation of the ovalbumin gene by the estrogen receptor involves the fos-jun complex. Cell63(6) , 1267–1276 (1990).
  • Nielsen R , PedersenTA, HagenbeekDet al. Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev. 22(21) , 2953–2967 (2008).
  • Diamond M , MinerJ, YoshinagaSK, YamamotoKR. Transcription factor interactions – selectors of positive or negative regulation from a single DNA element. Science249(4974) , 1266–1272 (1990).
  • Nissen RM , YamamotoKR. The glucocorticoid receptor inhibits NFκB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev.14(18) , 2314–2329 (2000).
  • Norris JD , ChangC, WittmannBMet al. The homeodomain protein HOXB13 regulates the cellular response to androgens. Mol. Cell 36(3) , 405–416 (2009).
  • Heldring N , IssacsGD, DiehlAGet al. Multiple sequence-specific DNA-binding proteins mediate estrogen receptor signaling through a tethering pathway. Mol. Endocrinol. 25(4) , 564–574 (2011).
  • Schmidt D , WilsonMD, BallesterBet al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328(5981) , 1036–1040 (2010).
  • Wilson MD , Barbosa-MoraisNL, SchmidtDet al. Species-specific transcription in mice carrying human chromosome 21. Science 322(5900) , 434–438 (2008).
  • Nechushtan H , BenvenistyN, BrandeisR, ReshefL. Glucocorticoids control phosphoenolpyruvate carboxykinase gene expression in a tissue specific manner. Nucleic Acids Res.15 , 6405–6417 (1987).
  • Odom DT , ZizlzpergerN, GordonDBet al. Control of pancreas and liver gene expression by HNF transcription factors. Science 303(5662) , 1378–1381 (2004).
  • Odom DT , DowellRD, JacobsenESet al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 39 , 730–732 (2007).
  • Wakabayashi K -I, Okamura M, Tsutsuni S et al. The peroxisome proliferator-activated receptor γ/retinoid X receptor α heterodimer targets the histone modification enzyme PR-Set7/Setd8 gene and regulates adipogenesis through a positive feedback loop. Mol. Cell. Biol.29(13) , 3544–3555 (2009).
  • Siersbæk R , NielsenR, JohnSet al. Extensive chromatin remodeling and establishment of transcription factor hotspots during early adipogenesis. EMBO J. 30(8) , 1459–1472 (2011).
  • Steger DJ , GrantGR, SchuppMet al. Propagation of adipogenic signals through an epigenomic transition state. Genes Dev. 24(10) , 1035–1044 (2010).
  • Becker PB , RuppertS, SchützG. Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors. Cell51(3) , 435–443 (1987).
  • Heintzman ND , HonGC, HawkinsRDet al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459(7243) , 108–112 (2009).
  • Wang D , Garcia-BassetsI, BennerCet al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474(7351) , 390–394 (2011).
  • Kagey MH , NewmanJJ, BilodeauSet al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467(7314) , 430–435 (2010).
  • Guelen L , PagieL, BrassetEet al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453(7197) , 948–951 (2008).
  • Peric-Hupkes D , MeulemanW, PagieLet al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol. Cell 38(4) , 603–613 (2010).
  • Nader N , ChrousosGP, KinoT. Circadian rhythm transcription factor CLOCK regulates the transcriptional activity of the glucocorticoid receptor by acetylating its hinge region lysine cluster: potential physiological implications. FASEB J.23(5) , 1572–1583 (2009).
  • Fu M , RaoM, WangCet al. Acetylation of androgen receptor enhances coactivator binding and promotes prostate cancer cell growth. Mol. Cell. Biol. 23(23) , 8563–8575 (2003).
  • Ghisletti S , HuangW, OgawaSet al. Parallel SUMOylation-dependent pathways mediate gene- and signal-specific transrepression by LXRs and PPARγ. Mol. Cell 25(1) , 57–70 (2007).
  • Ieda M , FuJ, Delgado-OlguinPet al. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142(3) , 375–386 (2010).
  • Takahashi K , YamanakaS. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell126(4) , 663–676 (2006).
  • Vierbuchen T , OstermeierA, PangZP, KokubuY, SüdhofTC, WernigM. Direct conversion of fibroblasts to functional neurons by defined factors. Nature463(7284) , 1035–1041 (2010).
  • Okamoto K , IwaiY, Oh-HoraMet al. IkappaBzeta regulates regulates T(H)17 development by cooperating with ROR nuclear receptors. Nature 464(7293) , 1381–1385 (2010).
  • Grimaldi B , BelletMM, KatadaSet al. PER2 controls lipid metabolism by direct regulation of PPARγ. Cell Metabol. 12(5) , 509–520 (2010).
  • Schmutz I , RippergerJA, Baeriswyl-AebischerS, AlbrechtU. The mammalian clock component PERIOD2 coordinates circadian output by interaction with nuclear receptors. Genes Dev.24(4) , 345–357 (2010).
  • Climent J , Perez-LosadaJ, QuigleyDAet al. Deletion of the PER3 gene on chromosome 1p36 in recurrent ER-positive breast cancer. J. Clin. Oncol. 28(23) , 3770–3778 (2010).
  • Cermakian N , Waddington Lamont E, Boudreau P, Boivin DB. Circadian clock gene expression in brain regions of Alzheimer‘s disease patients and control subjects. J. Biol. Rhythms26(2) , 160–170 (2011).
  • Asher G , SchiblerU. Crosstalk between components of circadian and metabolic cycles in mammals. Cell Metab.13(2) , 125–137 (2011).
  • Patel R , PatelM, TsaiRet al. LXRβ is required for glucocorticoid-induced hyperglycemia and hepatosteatosis in mice. J. Clin. Invest. 121(1) , 431–441 (2011).
  • Langlais D , CoutureC, BalsalobreA, DrouinJ. Regulatory network analyses reveal genome-wide potentiation of LIF signaling by glucocorticoids and define an innate cell defense response. PLoS Genet.4(10) , e1000224 (2008).
  • Szanto A , BalintBL, NagyZSet al. STAT6 transcription factor is a facilitator of the nuclear receptor PPARγ-regulated gene expression in macrophages and dendritic cells. Immunity 33(5) , 699–712 (2010).
  • Stavreva DA , WienchM, JohnSet al. Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription. Nat. Cell. Biol. 11(9) , 1093–1102 (2009).
  • Lightman SL , Conway-CampbellBL. The crucial role of pulsatile activity of the HPA axis for continuous dynamic equilibration. Nat. Rev. Neurosci.11(10) , 710–718 (2010).
  • Rauch A , SeitzS, BaschantUet al. Glucocorticoids suppress bone formation by attenuating osteoblast differentiation via the monomeric glucocorticoid receptor. Cell Metab. 11(6) , 517–531 (2010).
  • Guiducci C , GongM, XuZet al. TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus. Nature 465(7300) , 937–941 (2010).
  • Tomlins SA , RhodesDR, PernerSet al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310(5748) , 644–648 (2005).
  • Mani RS , TomlinsSA, CallahanKet al. Induced chromosomal proximity and gene fusions in prostate cancer. Science 326(5957) , 1230 (2009).
  • Lin C , YangL, TanasaBet al. Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 139(6) , 1069–1083 (2009).
  • Yu J , YuJ, CaoQet al. An integrated network of androgen receptor, polycomb, and TMPRSS2–ERG gene fusions in prostate cancer progression. Cancer Cell 17(5) , 443–454 (2010).
  • Gévry N , HardyS, JacquesPEet al. Histone H2A.Z is essential for estrogen receptor signaling. Genes Dev. 23(13) , 1522–1533 (2009).
  • Phuc Le P , FriedmanJR, SchugJet al. Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet. 1(2) , e16 (2005).
  • Gao H , FältS, SandelinAet al. Genome-wide identification of estrogen receptor α-binding sites in mouse liver. Mol. Endocrinol. 22(1) , 10–22 (2007).
  • Hu S , YaoG, GuanXet al. Research resource: genome-wide mapping of in vivo androgen receptor binding sites in mouse epididymis. Mol. Endocrinol. 24(12) , 2392–2405 (2010).
  • Zhang C , FriasMA, MeleAet al. Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science 329(5990) , 439–443 (2010).
  • Bandyopadhyay S , MehtaM, KuoDet al. Rewiring of genetic networks in response to DNA damage. Science 330(2009) , 1385–1389 (2010).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.