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1.  Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics 
We reveal how the RXRα−RARγ heterodimer upon activation by ATRA sets up a sequence of temporally controlled events that generate different subsets of primary and secondarily induced gene networks.We established RARγ and RXRα chromatin immunoprecipitation (ChIP) analyses coupled with massive parallel sequencing (ChIP-seq) together with the corresponding microarray transcriptomics at five time points during differentiation using pan-RAR and RAR isotype-selective ligands.Gene-regulatory decisions were inferred in silico from the dynamic changes of the transcriptomics patterns that correlated with the expression of RXRα−RARγ and other annotated transcription factors (TFs).Our analysis provides a temporal view of retinoic acid (RA) signalling during F9 cell differentiation, reveals RA receptor (RAR) heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.
Nuclear receptors are ligand-inducible transcription factors, which upon induction by their cognate ligand induce complex temporally controlled physiological programs. Retinoic acid (RA) and its receptors are key regulators of multiple physiological processes, including embryogenesis, organogenesis, immune functions, reproduction and organ homeostasis. While insight into (some of) the physiological functions of the various RA receptor (RAR) and retinoid X receptor (RXR) subtypes has been obtained by exploiting mouse genetics (for a review, see Mark et al, 2006) we are far from an understanding of the molecular circuitries and gene networks that are at the basis of these physiological events.
RAs act by interacting with a complex receptor system that comprises heterodimers formed by one of the three RXR (RARα, β and γ) and RAR (RARα, β and γ) isotypes. While insight into the role of heterodimerization on response element preference and contribution of RAR and RXR to transcription activation of model genes has been obtained (for review, see Gronemeyer et al, 2004) very little is known about the role and dynamics of target gene interaction of the various RXR–RAR heterodimers at a global scale in the context of a biological program.
More fundamentally, in order to develop a systems biology of nuclear receptors we need to establish approaches that reveal how the initial event, the information embedded in the chemical structure of a small molecular weight compound, is propagated through binding to cognate receptor(s), recruitment of co-regulatory factors, epigenetic modulators and additional complexes/machineries to establish temporally controlled gene programs. In this respect, a recent study has revealed the impact of epigenetic modulator crosstalk in the setting up of subprograms for oestrogen receptor signalling (Ceschin et al, 2011).
In the present study, we have used mouse F9 EC cells, a homogeneous cell system which is known to differentiate upon RA exposure and require RARγ for this response (Taneja et al, 1996), in order to integrate at a genome-wide scale (i) the dynamics of RXRα and RARγ binding by chromatin immunoprecipitation (ChIP) analyses coupled with massive parallel sequencing (ChIP-seq), (ii) the correlated temporal regulation of gene programs by global transcriptomics analyses, including (iii) the response to isotype-selective RAR ligands (Box 1). Our study revealed an unexpected highly dynamic association of the RXRα–RARγ with target chromatin and an unexpected dynamics of the heterodimer composition itself, which is indicative of partner swapping.
Inspired by early works on the dynamics of Drosophila puffing patterns during ecdysone-induced metamorphosis (Ashburner et al, 1974) our working hypothesis was that diversification of gene programming is achieved by the sequential activation of separable gene cohorts that constitute the various facets of differentiation, such as altered proliferation, cell physiology, signalling and finally terminal apoptogenic differentiation. To identify these temporally activated subroutines within the overall program, we inferred gene-regulatory decisions in silico from dynamically altered global gene expression patterns that occurred due to the action of RXRα−RARγ and other annotated TFs (Ernst et al, 2007). This dynamic regulatory map was used to reconstruct RXRα–RARγ signalling networks by integration of functional co-citation. Altogether we present a genome-wide view of the temporal gene-regulatory events and the corresponding gene programs elicited by the RXRα–RARγ during F9 cell differentiation. Our study deciphers some of the mechanisms by which the chemical information encoded in RA is diversified to regulate different cohorts of genes.
Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors (TFs) comprising retinoic acid receptor (RARα, β, γ) and retinoid X receptor (RXRα, β, γ). How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model, we defined the temporal changes in the genome-wide binding patterns of RARγ and RXRα and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRα heterodimers targeting identical loci. Comparison of RARγ and RXRα co-binding at RA-regulated genes identified putative RXRα–RARγ target genes that were validated with subtype-selective agonists. Gene-regulatory decisions during differentiation were inferred from TF-target gene information and temporal gene expression. This analysis revealed six distinct co-expression paths of which RXRα–RARγ is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRα–RARγ regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RAR heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.
This study provides a dynamic view of retinoic acid signalling during cell differentiation, reveals RAR/RXR heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.
PMCID: PMC3261707  PMID: 21988834
ChIP-seq; retinoic acid-induced differentiation; RXR–RAR heterodimers; temporal control of gene networks; transcriptomics
2.  Specific and Redundant Functions of Retinoid X Receptor/Retinoic Acid Receptor Heterodimers in Differentiation, Proliferation, and Apoptosis of F9 Embryonal Carcinoma Cells  
The Journal of Cell Biology  1997;139(3):735-747.
We have generated F9 murine embryonal carcinoma cells in which either the retinoid X receptor (RXR)α and retinoic acid receptor (RAR)α genes or the RXRα and RARγ genes are knocked out, and compared their phenotypes with those of wild-type (WT), RXRα−/−, RARα−/−, and RARγ−/− cells. RXRα−/−/ RARα−/− cells were resistant to retinoic acid treatment for the induction of primitive and parietal endodermal differentiation, as well as for antiproliferative and apoptotic responses, whereas they could differentiate into visceral endodermlike cells, as previously observed for RXRα−/− cells. In contrast, RXRα−/−/RARγ−/− cells were defective for all three types of differentiation, as well as antiproliferative and apoptotic responses, indicating that RXRα and RARγ represent an essential receptor pair for these responses. Taken together with results obtained by treatment of WT and mutant F9 cells with RAR isotype– and panRXR-selective retinoids, our observations support the conclusion that RXR/ RAR heterodimers are the functional units mediating the retinoid signal in vivo. Our results also indicate that the various heterodimers can exert both specific and redundant functions in differentiation, proliferation, and apoptosis. We also show that the functional redundancy exhibited between RXR isotypes and between RAR isotypes in cellular processes can be artifactually generated by gene knockouts. The present approach for multiple gene targeting should allow inactivation of any set of genes in a given cell.
PMCID: PMC2141719  PMID: 9348290
3.  Two Novel Drosophila TAFIIs Have Homology with Human TAFII30 and Are Differentially Regulated during Development 
Molecular and Cellular Biology  2000;20(5):1639-1648.
TFIID is a multiprotein complex composed of the TATA binding protein (TBP) and TBP-associated factors (TAFIIs). The binding of TFIID to the promoter is the first step of RNA polymerase II preinitiation complex assembly on protein-coding genes. Yeast (y) and human (h) TFIID complexes contain 10 to 13 TAFIIs. Biochemical studies suggested that the Drosophila (d) TFIID complexes contain only eight TAFIIs, leaving a number of yeast and human TAFIIs (e.g., hTAFII55, hTAFII30, and hTAFII18) without known Drosophila homologues. We demonstrate that Drosophila has not one but two hTAFII30 homologues, dTAFII16 and dTAFII24, which are encoded by two adjacent genes. These two genes are localized in a head-to-head orientation, and their 5′ extremities overlap. We show that these novel dTAFIIs are expressed and that they are both associated with TBP and other bona fide dTAFIIs in dTFIID complexes. dTAFII24, but not dTAFII16, was also found to be associated with the histone acetyltransferase (HAT) dGCN5. Thus, dTAFII16 and dTAFII24 are functional homologues of hTAFII30, and this is the first demonstration that a TAFII-GCN5-HAT complex exists in Drosophila. The two dTAFIIs are differentially expressed during embryogenesis and can be detected in both nuclei and cytoplasm of the cells. These results together indicate that dTAFII16 and dTAFII24 may have similar but not identical functions.
PMCID: PMC85347  PMID: 10669741
4.  Subregions of the adenovirus E1A transactivation domain target multiple components of the TFIID complex. 
Molecular and Cellular Biology  1995;15(11):6283-6290.
Transcriptional activation by the adenovirus E1A 289R protein requires direct contacts with the TATA box-binding protein (TBP) and also displays a critical requirement for TBP-associated factors (TAFs) (T.G. Boyer and A. J. Berk, Genes Dev. 7:1810-1823, 1993; J. V. Geisberg, W. S. Lee, A. J. Berk, and R. P. Ricciardi, Proc. Natl. Acad. Sci. USA 91:2488-2492, 1994; W. S. Lee, C. C. Kao, G. O. Bryant, X. Liu, and A. J. Berk, Cell 67:365-376, 1991; and Q. Zhou, P. M. Lieberman, T. G. Boyer, and A. J. Berk, Genes Dev. 6:1964-1974, 1992). In this report, we demonstrate that the activation domain of E1A (CR3) specifically binds to two TAFs, human TAFII250 (hTAFII250) and Drosophila TAFII110 (dTAFII110). These interactions can take place both in vivo and in vitro and require the carboxy-terminal region of CR3; the zinc finger region of CR3, which binds TBP, is not needed to bind these TAFs. We mapped the E1A-binding sites on hTAFII250 to an internal region that contains a number of structural motifs, including an HMG box, a bromodomain, and direct repeats. This represents the first demonstration that hTAFII250 may serve as a target of a transcriptional activator. We also mapped the E1A binding on dTAFII110 to its C-terminal region. This is of significance since, by contrast, Sp1-mediated activation requires binding to the N-terminal domain of dTAFII110. Thus, distinct surfaces of dTAFII110 can serve as target sites for different activators. Our results indicate that E1A may activate transcription, in part, through direct contacts of the CR3 subdomains with selected components of the TFIID complex.
PMCID: PMC230880  PMID: 7565781
5.  Gene Expression Profiling Elucidates a Specific Role for RARγ in the Retinoic Acid Induced Differentiation of F9 Teratocarcinoma Stem Cells 
Biochemical pharmacology  2007;75(5):1129-1160.
The biological effects of all-trans-retinoic acid (RA), a major active metabolite of retinol, are mainly mediated through its interactions with retinoic acid receptor (RARs α, β, γ) and retinoid X receptor (RXRs α, β, γ) heterodimers. RAR/RXR heterodimers activate transcription by binding to RA-response elements (RAREs or RXREs) in the promoters of primary target genes. Murine F9 teratocarcinoma stem cells have been widely used as a model for cellular differentiation and RA signaling during embryonic development. We identified and characterized genes that are differentially expressed in F9 wild type (Wt) and F9 RAR γ−/− cells, with and without RA treatment, through the use of oligonucleotide based microarrays. Our data indicate that RARγ, in the absence of exogenous RA, modulates gene expression. Genes such as Sfrp2, Tie1, Fbp2, Emp1, and Emp3 exhibited higher transcript levels in RA treated Wt, RARα−/− and RARβ2−/− lines than in RA-treated RARγ−/− cells, and represent specific RARγ targets. Other genes, such as Runx1, were expressed at lower levels in both F9 RARβ2−/− and RARγ−/− cell lines then in F9 Wt and RARα−/−. Genes specifically induced by RA at 6h with the protein synthesis inhibitor cycloheximide in F9 Wt, but not in RARγ−/− cells, included Hoxa3, Hoxa5, Gas1, Cyp26a1, Sfrp2, Fbp2, and Emp1. These genes represent specific primary RARγ targets in F9 cells. Several genes in the Wnt signaling pathway were regulated by RARγ. Delineation of the receptor specific actions of RA with respect to cell proliferation and differentiation should result in more effective therapies with this drug.
PMCID: PMC2988767  PMID: 18164278
retinoic acid receptor; gene expression profiles; differentiation; retinol; sfrp5; Tie1
6.  Positive and Negative TAFII Functions That Suggest a Dynamic TFIID Structure and Elicit Synergy with TRAPs in Activator-Induced Transcription 
Molecular and Cellular Biology  2001;21(20):6882-6894.
Human transcription factor TFIID contains the TATA-binding protein (TBP) and several TBP-associated factors (TAFIIs). To elucidate the structural organization and function of TFIID, we expressed and characterized the product of a cloned cDNA encoding human TAFII135 (hTAFII135). Comparative far Western blots have shown that hTAFII135 interacts strongly with hTAFII20, moderately with hTAFII150, and weakly with hTAFII43 and hTAFII250. Consistent with these observations and with sequence relationships of hTAFII20 and hTAFII135 to histones H2B and H2A, respectively, TFIID preparations that contain higher levels of hTAFII135 also contain higher levels of hTAFII20, and the interaction between hTAFII20 and hTAFII135 is critical for human TFIID assembly in vitro. From a functional standpoint, hTAFII135 has been found to interact strongly and directly with hTFIIA and (within a complex that also contains hTBP and hTAFII250) to specifically cooperate with TFIIA to relieve TAFII250-mediated repression of TBP binding and function on core promoters. Finally, we report a functional synergism between TAFIIs and the TRAP/Mediator complex in activated transcription, manifested as hTAFII-mediated inhibition of basal transcription and a consequent TRAP requirement for both a high absolute level of activated transcription and a high and more physiological activated/basal transcription ratio. These results suggest a dynamic TFIID structure in which the switch from a basal hTAFII-enhanced repression state to an activator-mediated activated state on a promoter may be mediated in part through activator or coactivator interactions with hTAFII135.
PMCID: PMC99865  PMID: 11564872
7.  The TFIID Components Human TAFII140 and Drosophila BIP2 (TAFII155) Are Novel Metazoan Homologues of Yeast TAFII47 Containing a Histone Fold and a PHD Finger 
Molecular and Cellular Biology  2001;21(15):5109-5121.
The RNA polymerase II transcription factor TFIID comprises the TATA binding protein (TBP) and a set of TBP-associated factors (TAFIIs). TFIID has been extensively characterized for yeast, Drosophila, and humans, demonstrating a high degree of conservation of both the amino acid sequences of the constituent TAFIIs and overall molecular organization. In recent years, it has been assumed that all the metazoan TAFIIs have been identified, yet no metazoan homologues of yeast TAFII47 (yTAFII47) and yTAFII65 are known. Both of these yTAFIIs contain a histone fold domain (HFD) which selectively heterodimerizes with that of yTAFII25. We have cloned a novel mouse protein, TAFII140, containing an HFD and a plant homeodomain (PHD) finger, which we demonstrated by immunoprecipitation to be a mammalian TFIID component. TAFII140 shows extensive sequence similarity to Drosophila BIP2 (dBIP2) (dTAFII155), which we also show to be a component of Drosophila TFIID. These proteins are metazoan homologues of yTAFII47 as their HFDs selectively heterodimerize with dTAFII24 and human TAFII30, metazoan homologues of yTAFII25. We further show that yTAFII65 shares two domains with the Drosophila Prodos protein, a recently described potential dTAFII. These conserved domains are critical for yTAFII65 function in vivo. Our results therefore identify metazoan homologues of yTAFII47 and yTAFII65.
PMCID: PMC87236  PMID: 11438666
8.  Prodos Is a Conserved Transcriptional Regulator That Interacts with dTAFII16 in Drosophila melanogaster 
Molecular and Cellular Biology  2001;21(2):614-623.
The transcription factor TFIID is a multiprotein complex that includes the TATA box binding protein (TBP) and a number of associated factors, TAFII. Prodos (PDS) is a conserved protein that exhibits a histone fold domain (HFD). In yeast two-hybrid tests using PDS as bait, we cloned the Drosophila TAFII, dTAFII16, as a specific PDS target. dTAFII16 is closely related to human TAFII30 and to another recently discovered Drosophila TAF, dTAFII24. PDS and dTAFII24 do not interact, however, thus establishing a functional difference between these dTAFs. The PDS-dTAFII16 interaction is mediated by the HFD motif in PDS and the N terminus in dTAFII16, as indicated by yeast two-hybrid assays with protein fragments. Luciferase-reported transcription tests in transfected cells show that PDS or an HFD-containing fragment activates transcription only with the help of dTAFII16 and TBP. Consistent with this, the eye phenotype of flies expressing a sev-Ras1 construct is modulated by PDS and dTAFII16 in a gene dosage-dependent manner. Finally, we show that PDS function is required for cell viability in somatic mosaics. These findings indicate that PDS is a novel transcriptional coactivator that associates with a member of the general transcription factor TFIID.
PMCID: PMC86631  PMID: 11134347
9.  Distinct Mutations in Yeast TAFII25 Differentially Affect the Composition of TFIID and SAGA Complexes as Well as Global Gene Expression Patterns 
Molecular and Cellular Biology  2002;22(9):3178-3193.
The RNA polymerase II transcription factor TFIID, composed of the TATA-binding protein (TBP) and TBP-associated factors (TAFIIs), nucleates preinitiation complex formation at protein-coding gene promoters. SAGA, a second TAFII-containing multiprotein complex, is involved in transcription regulation in Saccharomyces cerevisiae. One of the essential protein components common to SAGA and TFIID is yTAFII25. We define a minimal evolutionarily conserved 91-amino-acid region of TAFII25 containing a histone fold domain that is necessary and sufficient for growth in vivo. Different temperature-sensitive mutations of yTAFII25 or chimeras with the human homologue TAFII30 arrested cell growth at either the G1 or G2/M cell cycle phase and displayed distinct phenotypic changes and gene expression patterns. Immunoprecipitation studies revealed that TAFII25 mutation-dependent gene expression and phenotypic changes correlated at least partially with the integrity of SAGA and TFIID. Genome-wide expression analysis revealed that the five TAFII25 temperature-sensitive mutant alleles individually affect the expression of between 18 and 33% of genes, whereas taken together they affect 64% of all class II genes. Thus, different yTAFII25 mutations induce distinct phenotypes and affect the regulation of different subsets of genes, demonstrating that no individual TAFII mutant allele reflects the full range of its normal functions.
PMCID: PMC133751  PMID: 11940675
10.  Human TAFII130 Is a Coactivator for NFATp 
Molecular and Cellular Biology  2001;21(10):3503-3513.
NFATp is one member of a family of transcriptional activators that regulate the expression of cytokine genes. To study mechanisms of NFATp transcriptional activation, we established a reconstituted transcription system consisting of human components that is responsive to activation by full-length NFATp. The TATA-associated factor (TAFII) subunits of the TFIID complex were required for NFATp-mediated activation in this transcription system, since TATA-binding protein (TBP) alone was insufficient in supporting activated transcription. In vitro interaction assays revealed that human TAFII130 (hTAFII130) and its Drosophila melanogaster homolog dTAFII110 bound specifically and reproducibly to immobilized NFATp. Sequences contained in the C-terminal domain of NFATp (amino acids 688 to 921) were necessary and sufficient for hTAFII130 binding. A partial TFIID complex assembled from recombinant hTBP, hTAFII250, and hTAFII130 supported NFATp-activated transcription, demonstrating the ability of hTAFII130 to serve as a coactivator for NFATp in vitro. Overexpression of hTAFII130 in Cos-1 cells inhibited NFATp activation of a luciferase reporter. These studies demonstrate that hTAFII130 is a coactivator for NFATp and represent the first biochemical characterization of the mechanism of transcriptional activation by the NFAT family of activators.
PMCID: PMC100272  PMID: 11313476
11.  Reversal by RARα agonist Am580 of c-Myc-induced imbalance in RARα/RARγ expression during MMTV-Myc tumorigenesis 
Breast Cancer Research : BCR  2012;14(4):R121.
Retinoic acid signaling plays key roles in embryonic development and in maintaining the differentiated status of adult tissues. Recently, the nuclear retinoic acid receptor (RAR) isotypes α, β and γ were found to play specific functions in the expansion and differentiation of the stem compartments of various tissues. For instance, RARγ appears to be involved in stem cell compartment expansion, while RARα and RARβ are implicated in the subsequent cell differentiation. We found that over-expressing c-Myc in normal mouse mammary epithelium and in a c-Myc-driven transgenic model of mammary cancer, disrupts the balance between RARγ and RARα/β in favor of RARγ.
The effects of c-Myc on RAR isotype expression were evaluated in normal mouse mammary epithelium, mammary tumor cells obtained from the MMTV-Myc transgenic mouse model as well as human normal immortalized breast epithelial and breast cancer cell lines. The in vivo effect of the RARα-selective agonist 4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthyl)carboxamido]benzoic acid (Am580) was examined in the MMTV-Myc mouse model of mammary tumorigenesis.
Modulation of the RARα/β to RARγ expression in mammary glands of normal mice, oncomice, and human mammary cell lines through the alteration of RAR-target gene expression affected cell proliferation, survival and tumor growth. Treatment of MMTV-Myc mice with the RARα-selective agonist Am580 led to significant inhibition of mammary tumor growth (~90%, P<0.001), lung metastasis (P<0.01) and extended tumor latency in 63% of mice. Immunocytochemical analysis showed that in these mice, RARα responsive genes such as Cyp26A1, E-cadherin, cellular retinol-binding protein 1 (CRBP1) and p27, were up-regulated. In contrast, the mammary gland tumors of mice that responded poorly to Am580 treatment (37%) expressed significantly higher levels of RARγ. In vitro experiments indicated that the rise in RARγ was functionally linked to promotion of tumor growth and inhibition of differentiation. Thus, activation of the RARα pathway is linked to tumor growth inhibition, differentiation and cell death.
The functional consequence of the interplay between c-Myc oncogene expression and the RARγ to RARα/β balance suggests that prevalence of RARγ over-RARα/β expression levels in breast cancer accompanied by c-Myc amplification or over-expression in breast cancer should be predictive of response to treatment with RARα-isotype-specific agonists and warrant monitoring during clinical trials.
See related editorial by Garattini et al
PMCID: PMC3680916  PMID: 22920668
12.  Retinoic Acid Receptor γ1 (RARγ1) Levels Control RARβ2 Expression in SK-N-BE2(c) Neuroblastoma Cells and Regulate a Differentiation-Apoptosis Switch 
Molecular and Cellular Biology  1998;18(11):6482-6492.
Vitamin A and its derivatives (retinoids) have profound effects on the proliferation and differentiation of many cell types and are involved in a diverse array of developmental and physiological regulatory processes, including those responsible for the development of the mature nervous system. Retinoid signals are mediated by retinoic acid (RA) receptors (RARs) and retinoid X receptors (RXRs), which show distinct spatio-temporal patterns of expression during development and in adult tissues. We have used SK-N-BE2(c) neuroblastoma cells to study the effects of reciprocal regulation of expression of various RARs. We show that in these cells RARγ1 acts as a repressor of RARβ2 transcription in the absence of an agonist. In the presence of RA, the expression of RARγ1 is reduced and that of RARβ2 is induced. Overexpression of RARγ1 neutralizes the effects of RA on RARβ induction. Expression of an RARγ1-specific antisense construct leads to the constitutive expression of RARβ2. Although both overexpression of RARγ1 and its reduction of expression can result in inhibition of cell proliferation, they induce different morphological changes. Reduction of RARγ1 (and induction of RARβ) leads to increased apoptosis, whereas RARγ1 overexpression leads to differentiation in the absence of apoptosis. Thus, RARγ1 appears to control a differentiation-apoptosis switch in SK-N-BE2(c) neuroblastoma cells.
PMCID: PMC109234  PMID: 9774664
13.  Synergistic Transcriptional Activation by TATA-Binding Protein and hTAFII28 Requires Specific Amino Acids of the hTAFII28 Histone Fold 
Molecular and Cellular Biology  1999;19(7):5050-5060.
Coexpression of the human TATA-binding protein (TBP)-associated factor 28 (hTAFII28) with the altered-specificity mutant TBP spm3 synergistically enhances transcriptional activation by the activation function 2 of the nuclear receptors (NRs) for estrogen and vitamin D3 from a reporter plasmid containing a TGTA element in mammalian cells. This synergy is abolished by mutation of specific amino acids in the α2-helix of the histone fold in the conserved C-terminal region of hTAFII28. Critical amino acids are found on both the exposed hydrophilic face of this helix and the hydrophobic interface with TAFII18. This α-helix of hTAFII28 therefore mediates multiple interactions required for coactivator activity. We further show that mutation of specific residues in the H1′ α-helix of TBP either reduces or increases interactions with hTAFII28. The mutations which reduce interactions with hTAFII28 do not affect functional synergy, whereas the TBP mutation which increases interaction with hTAFII28 is defective in its ability to synergistically enhance activation by NRs. However, this TBP mutant supports activation by other activators and is thus specifically defective for its ability to synergize with hTAFII28.
PMCID: PMC84343  PMID: 10373554
14.  Retinoid Regulated Association of Transcriptional Coregulators and the Polycomb Group Protein SUZ12 with the Retinoic Acid Response Elements of Hoxa1, RARβ2, and Cyp26A1 in F9 Embryonal Carcinoma Cells 
Journal of molecular biology  2007;372(2):298-316.
Hox gene expression is activated by all-trans retinoic acid (RA), through binding to Retinoic Acid Receptor-Retinoid X Receptor (RAR-RXR) heterodimers bound at RA response elements (RAREs) of target genes. The RARs and RXRs each have three isotypes (α, β, and γ), which are encoded by distinct genes. Hox genes are also repressed by polycomb group proteins (PcG), though how these proteins are targeted is unclear. We used chromatin immunoprecipitation assays to investigate the association of RXRα, RARγ, cofactors, and the PcG protein SUZ12 with the Hoxa1, RARβ2, and Cyp26A1 RAREs in F9 embryonal carcinoma cells (teratocarcinoma stem cells) during RA treatment. We demonstrate that RARγ and RXRα are associated with RAREs prior to and during RA treatment. pCIP, p300, and RNA polymerase II levels increased at target RAREs upon exposure to RA. Conversely, SUZ12 was found associated with all RAREs studied and these associations were attenuated by treatment with RA. Upon RA removal, SUZ12 re-associated with RAREs. H3ac, H3K4me2, and H3K27me3 marks were simultaneously detected at target loci, indicative of a bivalent domain chromatin structure. During RA mediated differentiation, H3K27me3 levels decreased at target RAREs whereas H3ac and H3K4me2 levels remained constant. These studies provide insight into the dynamics of association of coregulators with RAREs and demonstrate a novel link between RA signaling and PcG repression.
PMCID: PMC2972191  PMID: 17663992
SUZ12; polycomb; differentiation; retinoic acid receptors; epigenetic marks
15.  RARγ is critical for maintaining a balance between hematopoietic stem cell self-renewal and differentiation 
The Journal of Experimental Medicine  2006;203(5):1283-1293.
Hematopoietic stem cells (HSCs) sustain lifelong production of all blood cell types through finely balanced divisions leading to self-renewal and differentiation. Although several genes influencing HSC self-renewal have been identified, to date no gene has been described that, when activated, enhances HSC self-renewal and, when activated, promotes HSC differentiation. We observe that the retinoic acid receptor (RAR)γ is selectively expressed in primitive hematopoietic precursors and that the bone marrow of RARγ knockout mice exhibit markedly reduced numbers of HSCs associated with increased numbers of more mature progenitor cells compared with wild-type mice. In contrast, RARα is widely expressed in hematopoietic cells, but RARα knockout mice do not exhibit any HSC or progenitor abnormalities. Primitive hematopoietic precursors overexpressing RARα differentiate predominantly to granulocytes in short-term culture, whereas those overexpressing RARγ exhibit a much more undifferentiated phenotype. Furthermore, loss of RARγ abrogated the potentiating effects of all-trans retinoic acid on the maintenance of HSCs in ex vivo culture. Finally, pharmacological activation of RARγ ex vivo promotes HSC self-renewal, as demonstrated by serial transplant studies. We conclude that the RARs have distinct roles in hematopoiesis and that RARγ is a critical physiological and pharmacological regulator of the balance between HSC self-renewal and differentiation.
PMCID: PMC2121209  PMID: 16682494
16.  EWS, but Not EWS-FLI-1, Is Associated with Both TFIID and RNA Polymerase II: Interactions between Two Members of the TET Family, EWS and hTAFII68, and Subunits of TFIID and RNA Polymerase II Complexes 
Molecular and Cellular Biology  1998;18(3):1489-1497.
The t(11;22) chromosomal translocation specifically linked to Ewing sarcoma and primitive neuroectodermal tumor results in a chimeric molecule fusing the amino-terminus-encoding region of the EWS gene to the carboxyl-terminal DNA-binding domain encoded by the FLI-1 gene. As the function of the protein encoded by the EWS gene remains unknown, we investigated the putative role of EWS in RNA polymerase II (Pol II) transcription by comparing its activity with that of its structural homolog, hTAFII68. We demonstrate that a portion of EWS is able to associate with the basal transcription factor TFIID, which is composed of the TATA-binding protein (TBP) and TBP-associated factors (TAFIIs). In vitro binding studies revealed that both EWS and hTAFII68 interact with the same TFIID subunits, suggesting that the presence of EWS and that of hTAFII68 in the same TFIID complex may be mutually exclusive. Moreover, EWS is not exclusively associated with TFIID but, similarly to hTAFII68, is also associated with the Pol II complex. The subunits of Pol II that interact with EWS and hTAFII68 have been identified, confirming the association with the polymerase. In contrast to EWS, the tumorigenic EWS–FLI-1 fusion protein is not associated with either TFIID or Pol II in Ewing cell nuclear extracts. These observations suggest that EWS and EWS–FLI-1 may play different roles in Pol II transcription.
PMCID: PMC108863  PMID: 9488465
17.  Redundant Role of Tissue-Selective TAFII105 in B Lymphocytes 
Molecular and Cellular Biology  2002;22(18):6564-6572.
Regulated gene expression is a complex process achieved through the function of multiple protein factors acting in concert at a given promoter. The transcription factor TFIID is a central component of the machinery regulating mRNA synthesis by RNA polymerase II. This large multiprotein complex is composed of the TATA box binding protein (TBP) and several TBP-associated factors (TAFIIs). The recent discovery of multiple TBP-related factors and tissue-specific TAFIIs suggests the existence of specialized TFIID complexes that likely play a critical role in regulating transcription in a gene- and tissue-specific manner. The tissue-selective factor TAFII105 was originally identified as a component of TFIID derived from a human B-cell line. In this report we demonstrate the specific induction of TAFII105 in cultured B cells in response to bacterial lipopolysaccharide (LPS). To examine the in vivo role of TAFII105, we have generated TAFII105-null mice by homologous recombination. Here we show that B-lymphocyte development is largely unaffected by the absence of TAFII105. TAFII105-null B cells can proliferate in response to LPS, produce relatively normal levels of resting antibodies, and can mount an immune response by producing antigen-specific antibodies in response to immunization. Taken together, we conclude that the function of TAFII105 in B cells is likely redundant with the function of other TAFII105-related cellular proteins.
PMCID: PMC135626  PMID: 12192054
18.  The Human TFIID Components TAFII135 and TAFII20 and the Yeast SAGA Components ADA1 and TAFII68 Heterodimerize to Form Histone-Like Pairs 
Molecular and Cellular Biology  2000;20(1):340-351.
It has been previously proposed that the transcription complexes TFIID and SAGA comprise a histone octamer-like substructure formed from a heterotetramer of H4-like human hTAFII80 (or its Drosophila melanogaster dTAFII60 and yeast [Saccharomyces cerevisiae] yTAFII60 homologues) and H3-like hTAFII31 (dTAFII40 and yTAFII17) along with two homodimers of H2B-like hTAFII20 (dTAFII30α and yTAFII61/68). However, it has not been formally shown that hTAFII20 heterodimerizes via its histone fold. By two-hybrid analysis with yeast and biochemical characterization of complexes formed by coexpression in Escherichia coli, we showed that hTAFII20 does not homodimerize but heterodimerizes with hTAFII135. Heterodimerization requires the α2 and α3 helices of the hTAFII20 histone fold and is abolished by mutations in the hydrophobic face of the hTAFII20 α2 helix. Interaction with hTAFII20 requires a domain of hTAFII135 which shows sequence homology to H2A. This domain also shows homology to the yeast SAGA component ADA1, and we show that yADA1 heterodimerizes with the histone fold region of yTAFII61/68, the yeast hTAFII20 homologue. These results are indicative of a histone fold type of interaction between hTAFII20-hTAFII135 and yTAFII68-yADA1, which therefore constitute novel histone-like pairs in the TFIID and SAGA complexes.
PMCID: PMC85089  PMID: 10594036
19.  Retinoic Acid Receptor-Mediated Induction of ABCA1 in Macrophages 
Molecular and Cellular Biology  2003;23(21):7756-7766.
ABCA1, the mutant molecule in Tangier Disease, mediates efflux of cellular cholesterol to apoA-I and is induced by liver X receptor (LXR)/retinoid X receptor (RXR) transcription factors. Retinoic acid receptor (RAR) activators (all-trans-retinoic acid [ATRA] and TTNPB) were found to increase ATP-binding cassette transporter 1 (ABCA1) mRNA and protein in macrophages. In cellular cotransfection assays, RARγ/RXR activated the human ABCA1 promoter, via the same direct repeat 4 (DR4) promoter element as LXR/RXR. Chromatin immunoprecipitation analysis in macrophages confirmed the binding of RARγ/RXR to the ABCA1 promoter DR4 element in the presence of ATRA, with weaker binding of RARα/RXR, and no binding of RARβ/RXR. However, in macrophages from RARγ−/− mice, TTNPB still induced ABCA1, in association with marked upregulation of RARα, suggesting that high levels of RARα can compensate for the absence of RARγ. Dose-response experiments with ATRA in mouse primary macrophages showed that other LXR target genes were weakly induced (ABCG1 and SREBP-1c) or not induced (apoE and LXRα). The more specific RAR activator TTNPB did not induce SREBP-1c in mouse primary macrophages or liver. These studies indicate a direct role of RARγ/RXR in induction of macrophage ABCA1.
PMCID: PMC207565  PMID: 14560020
20.  Human TAFII55 Interacts with the Vitamin D3 and Thyroid Hormone Receptors and with Derivatives of the Retinoid X Receptor That Have Altered Transactivation Properties 
Molecular and Cellular Biology  1999;19(8):5486-5494.
We have identified novel interactions between the human (h)TATA-binding protein-associated factor TAFII55 and the ligand-binding domains (LBDs) of the nuclear receptors for vitamin D3 (VDR) and thyroid hormone (TRα). Following expression in Cos cells, hTAFII55 interacts with the VDR and TRα LBDs in a ligand-independent manner whereas no interactions with the retinoid X receptors (RXRs) or with other receptors were observed. Deletion mapping indicates that hTAFII55 interacts with a 40-amino-acid region spanning α-helices H3 to H5 of the VDR and TRα LBDs but not with the equivalent highly related region of RXRγ. TAFII55 also interacts with chimeric receptors in which the H3-to-H5 region of RXRγ has been replaced with that of the VDR or TRα. Furthermore, replacement of two single amino acids of the RXRγ LBD with their VDR counterparts allows the RXRγ LBD to interact with hTAFII55 while the corresponding double substitution allows a much stronger interaction. In transfection experiments, the single mutated RXRγ LBDs activate transcription to fivefold higher levels than wild-type RXRγ while the double mutation activates transcription to a level comparable to that observed with the VDR. There is therefore a correlation between the ability of the modified RXRs to interact with hTAFII55 and transactivation. These results strongly suggest that the TAFII55 interactions with the modified RXR LBDs modulate transcriptional activation.
PMCID: PMC84390  PMID: 10409738
21.  RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements 
Nucleic Acids Research  2015;43(10):4833-4854.
In mouse embryonic cells, ligand-activated retinoic acid receptors (RARs) play a key role in inhibiting pluripotency-maintaining genes and activating some major actors of cell differentiation.
To investigate the mechanism underlying this dual regulation, we performed joint RAR/RXR ChIP-seq and mRNA-seq time series during the first 48 h of the RA-induced Primitive Endoderm (PrE) differentiation process in F9 embryonal carcinoma (EC) cells. We show here that this dual regulation is associated with RAR/RXR genomic redistribution during the differentiation process. In-depth analysis of RAR/RXR binding sites occupancy dynamics and composition show that in undifferentiated cells, RAR/RXR interact with genomic regions characterized by binding of pluripotency-associated factors and high prevalence of the non-canonical DR0-containing RA response element. By contrast, in differentiated cells, RAR/RXR bound regions are enriched in functional Sox17 binding sites and are characterized with a higher frequency of the canonical DR5 motif. Our data offer an unprecedentedly detailed view on the action of RA in triggering pluripotent cell differentiation and demonstrate that RAR/RXR action is mediated via two different sets of regulatory regions tightly associated with cell differentiation status.
PMCID: PMC4446430  PMID: 25897113
22.  Distinct Subdomains of Human TAFII130 Are Required for Interactions with Glutamine-Rich Transcriptional Activators 
Molecular and Cellular Biology  1998;18(10):5734-5743.
TFIID is a multiprotein complex consisting of the TATA box binding protein and multiple tightly associated proteins (TAFIIs) that are required for transcription by selected activators. We previously reported cloning and partial characterization of human TAFII130 (hTAFII130). The central domain of hTAFII130 contains four glutamine-rich regions, designated Q1 to Q4, that are involved in interactions with the transcriptional activator Sp1. Mutational analysis has revealed specific regions within the glutamine-rich (Q1 to Q4) central region of hTAFII130 that are required for interaction with distinct activation domains. We tested amino- and carboxyl-terminal deletions of hTAFII130 for interaction with Sp1 activation domains A and B (Sp1A and Sp1B) and the N-terminal activation domain of CREB (CREB-N) by using the yeast two-hybrid system. Our results indicate that Sp1B interacts almost exclusively with the Q1 region of hTAFII130. In contrast, Sp1A makes multiple contacts with Q1 to Q4 of hTAFII130, while CREB-N interacts primarily with the Q1-Q2 hTAFII130 subdomain. Consistent with these interaction studies, overexpression of the Q1-to-Q4 region in HeLa cells inhibits Sp1- but not VP16-mediated transcriptional activation. These findings indicate that the Q1-to-Q4 region of hTAFII130 is required for Sp1-mediated transcriptional enhancement in mammalian cells and that different activation domains target distinct subdomains of hTAFII130.
PMCID: PMC109159  PMID: 9742090
23.  RARγ-induced E-cadherin downregulation promotes hepatocellular carcinoma invasion and metastasis 
Aberrant expression of Retinoic acid receptor γ (RARγ) is implicated in cancer development. Our previous study identified that RARγ functions as a tumor promoter to drive hepatocellular carcinoma (HCC) growth. However, its contribution to HCC invasion and metastasis remains unclear.
RARγ expression in clinical HCC samples was detected by western blot and immunohistochemistry. The relationship between RARγ expression levels and the clinical characteristics were evaluated. HCC cell line MHCC-97H were stably knocked down RARγ using a lentivirus vector-based shRNA technique. The cells were analyzed by migration and invasion assays, and injected into nude mice to assess tumor metastasis. E-cadherin expression regulated by RARγ was examined by qPCR, western blot and immunofluorescence staining.
The expression of RARγ is significantly upregulated in human HCC tissues. Moreover, its expression positively correlates with tumor size, distant metastasis and TNM stage, and negatively correlates with length of survival of HCC patients. Knockdown of RARγ markedly inhibits HCC cell invasion and metastasis both in vitro and in vivo. Mechanistic investigations reveal that RARγ functions through regulation of NF-κB-mediated E-cadherin downregulation to promote HCC invasion and metastasis. Notably, RARγ expression status negatively correlates with E-cadherin expression in HCC cell lines and clinical HCC samples.
These findings demonstrate that RARγ could promote HCC invasion and metastasis by regulating E-cadherin reduction, and implicate new strategies to aggressively treat HCC through targeting RARγ/E-cadherin signaling axis.
Electronic supplementary material
The online version of this article (doi:10.1186/s13046-016-0441-9) contains supplementary material, which is available to authorized users.
PMCID: PMC5069892  PMID: 27756432
RARγ; E-cadherin; Hepatocellular carcinoma; Metastasis
24.  Oncogenic Activity of Retinoic Acid Receptor γ Is Exhibited through Activation of the Akt/NF-κB and Wnt/β-Catenin Pathways in Cholangiocarcinoma 
Molecular and Cellular Biology  2013;33(17):3416-3425.
Aberrant expression and function of retinoic acid receptor γ (RARγ) are often involved in the progression of several cancers. However, the role of RARγ in cholangiocarcinoma (CCA), chemoresistant bile duct carcinoma with a poor prognosis, remains unclear. In the present study, we found that RARγ was frequently overexpressed in human CCA specimens. Its overexpression was associated with poor differentiation, lymph node metastasis, high serum carbohydrate antigen 19-9 level, and poor prognosis of CCA. Downregulation of RARγ reduced CCA cell proliferation, migration, invasion, and colony formation ability in vitro and tumorigenic potential in nude mice. RARγ knockdown resulted in upregulation of cell cycle inhibitor P21, as well as downregulation of cyclin D1, proliferating cell nuclear antigen, and matrix metallopeptidase 9, in parallel with suppression of the Akt/NF-κB pathway. Furthermore, overexpression of RARγ contributed to the multidrug chemoresistance of CCA cells, at least in part due to upregulation of P glycoprotein via activation of the Wnt/β-catenin pathway. Molecular mechanism studies revealed that RARγ interacted with β-catenin and led to β-catenin nuclear translocation. Taken together, our results suggested that RARγ plays an important role in the proliferation, metastasis, and chemoresistance of CCA through simultaneous activation of the Akt/NF-κB and Wnt/β-catenin pathways, serving as a potential molecular target for CCA treatment.
PMCID: PMC3753848  PMID: 23798555
25.  Regulation of Retinoid-Mediated Signaling Involved in Skin Homeostasis by RAR and RXR Agonists/Antagonists in Mouse Skin 
PLoS ONE  2013;8(4):e62643.
Endogenous retinoids like all-trans retinoic acid (ATRA) play important roles in skin homeostasis and skin-based immune responses. Moreover, retinoid signaling was found to be dysregulated in various skin diseases. The present study used topical application of selective agonists and antagonists for retinoic acid receptors (RARs) α and γ and retinoid-X receptors (RXRs) for two weeks on mouse skin in order to determine the role of retinoid receptor subtypes in the gene regulation in skin. We observed pronounced epidermal hyperproliferation upon application of ATRA and synthetic agonists for RARγ and RXR. ATRA and the RARγ agonist further increased retinoid target gene expression (Rbp1, Crabp2, Krt4, Cyp26a1, Cyp26b1) and the chemokines Ccl17 and Ccl22. In contrast, a RARα agonist strongly decreased the expression of ATRA-synthesis enzymes, of retinoid target genes, markers of skin homeostasis, and various cytokines in the skin, thereby markedly resembling the expression profile induced by RXR and RAR antagonists. Our results indicate that RARα and RARγ subtypes possess different roles in the skin and may be of relevance for the auto-regulation of endogenous retinoid signaling in skin. We suggest that dysregulated retinoid signaling in the skin mediated by RXR, RARα and/or RARγ may promote skin-based inflammation and dysregulation of skin barrier properties.
PMCID: PMC3634743  PMID: 23638129

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