The homeodomain proteins PBX and MEIS1 are accessory factors that enhance thyroid hormone regulation of the malic enzyme gene in hepatocytes

Posttranslational Modifications in Conserved Transcription Factors: A Survey of the TALE-Homeodomain Superclass in Human and Mouse

Transcription factors (TFs) guide effector proteins like chromatin-modifying or -remodeling enzymes to distinct sites in the genome and thereby fulfill important early steps in translating the genome’s sequence information into the production of proteins or functional RNAs. TFs of the same family are often highly conserved in evolution, raising the question of how proteins with seemingly similar structure and DNA-binding properties can exert physiologically distinct functions or respond to context-specific extracellular cues. A good example is the TALE superclass of homeodomain-containing proteins. All TALE-homeodomain proteins share a characteristic, 63-amino acid long homeodomain and bind to similar sequence motifs. Yet, they frequently fulfill non-redundant functions even in domains of co-expression and are subject to regulation by different signaling pathways. Here we provide an overview of posttranslational modifications that are associated with murine and human TALE-homeodomain proteins and discuss their possible importance for the biology of these TFs.

Influence of neonatal hypothyroidism on hepatic gene expression and lipid metabolism in adulthood

Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology, but its specific influence in liver is less understood. Here, we studied how CH influences the liver gene expression program in adulthood. Pregnant rats were given the antithyroid drug methimazole (MMI) from GD12 until PND30 to induce CH in male offspring. Growth defects due to CH were evident as reductions in body weight and tail length from the second week of life. Once the MMI treatment was discontinued, the feed efficiency increased in CH, and this was accompanied by significant catch-up growth. On PND80, significant reductions in body mass, tail length, and circulating IGF-I levels remained in CH rats. Conversely, the mRNA levels of known GH target genes were significantly upregulated. The serum levels of thyroid hormones, cholesterol, and triglycerides showed no significant differences. In contrast, CH rats showed significant changes in the expression of hepatic genes involved in lipid metabolism, including an increased transcription of PPARα and a reduced expression of genes involved in fatty acid and cholesterol uptake, cellular sterol efflux, triglyceride assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to the onset of hypothyroidism in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters and to T3 replacement with an enhanced activation of malic enzyme. In summary, we provide in vivo evidence that neonatal hypothyroidism influences the hepatic transcriptional program and tissue sensitivity to hormone treatment in adulthood. This highlights the critical role that a euthyroid state during development plays on normal liver physiology in adulthood.

PBX1 genomic pioneer function drives ERα signaling underlying progression in breast cancer

Altered transcriptional programs are a hallmark of diseases, yet how these are established is still ill-defined. PBX1 is a TALE homeodomain protein involved in the development of different types of cancers. The estrogen receptor alpha (ERα) is central to the development of two-thirds of all breast cancers. Here we demonstrate that PBX1 acts as a pioneer factor and is essential for the ERα-mediated transcriptional response driving aggressive tumors in breast cancer. Indeed, PBX1 expression correlates with ERα in primary breast tumors, and breast cancer cells depleted of PBX1 no longer proliferate following estrogen stimulation. Profiling PBX1 recruitment and chromatin accessibility across the genome of breast cancer cells through ChIP-seq and FAIRE-seq reveals that PBX1 is loaded and promotes chromatin openness at specific genomic locations through its capacity to read specific epigenetic signatures. Accordingly, PBX1 guides ERα recruitment to a specific subset of sites. Expression profiling studies demonstrate that PBX1 controls over 70% of the estrogen response. More importantly, the PBX1-dependent transcriptional program is associated with poor-outcome in breast cancer patients. Correspondingly, PBX1 expression alone can discriminate a priori the outcome in ERα-positive breast cancer patients. These features are markedly different from the previously characterized ERα-associated pioneer factor FoxA1. Indeed, PBX1 is the only pioneer factor identified to date that discriminates outcome such as metastasis in ERα-positive breast cancer patients. Together our results reveal that PBX1 is a novel pioneer factor defining aggressive ERα-positive breast tumors, as it guides ERα genomic activity to unique genomic regions promoting a transcriptional program favorable to breast cancer progression.

Regulation of the SOX3 gene expression by retinoid receptors

Sox3/SOX3 gene is considered to be one of the earliest neural markers in vertebrates. Despite the mounting evidence that Sox3/SOX3 is one of the key players in the development of the nervous system, limited data are available regarding the transcriptional regulation of its expression. This review is focused on the retinoic acid induced regulation of SOX3 gene expression, with particular emphasis on the involvement of retinoid receptors. Experiments with human embryonal carcinoma cells identified two response elements involved in retinoic acid/retinoid X receptor-dependent activation of the SOX3 gene expression: distal atypical retinoic acid-response element, consisting of two unique G-rich boxes separated by 49 bp, and proximal element comprising DR-3-like motif, composed of two imperfect hexameric half-sites. Importantly, the retinoic acid-induced SOX3 gene expression could be significantly down-regulated by a synthetic antagonist of retinoid receptors. This cell model provides a solid base for further studies on mechanism(s) underlying regulation of expression of SOX3 gene, which could improve the understanding of molecular signals that induce neurogenesis in the stem/progenitor cells both during development and in adulthood.

Pbx homeodomain proteins: TALEnted regulators of limb patterning and outgrowth

Limb development has long provided an excellent model for understanding the genetic principles driving embryogenesis. Studies utilizing chick and mouse have led to new insights into limb patterning and morphogenesis. Recent research has centered on the regulatory networks underlying limb development. Here, we discuss the hierarchical, overlapping, and iterative roles of Pbx family members in appendicular development that have emerged from genetic analyses in the mouse. Pbx genes are essential in determining limb bud positioning, early bud formation, limb axes establishment and coordination, and patterning and morphogenesis of most elements of the limb and girdle. Pbx proteins directly regulate critical effectors of limb and girdle development, including morphogen-encoding genes like Shh in limb posterior mesoderm, and transcription factor-encoding genes like Alx1 in pre-scapular domains. Interestingly, at least in limb buds, Pbx appear to act not only as Hox cofactors, but also in the upstream control of 5' HoxA/D gene expression.

PBX1 and MEIS1 up-regulate SOX3 gene expression by direct interaction with a consensus binding site within the basal promoter region

Sox3/SOX3 [SRY (sex determining region Y)-box 3] is considered to be one of the earliest neural markers in vertebrates, playing a role in specifying neuronal fate. We have previously reported characterization of the SOX3 promoter and demonstrated that the general transcription factors NF-Y (nuclear factor-Y), Sp1 (specificity protein 1) and USF (upstream stimulatory factor) are involved in transcriptional regulation of SOX3 promoter activity. In the present study we provide the first evidence that the TALE (three-amino-acid loop extension) transcription factors PBX1 (pre-B-cell leukaemia homeobox 1) and MEIS1 (myeloid ecotropic viral integration site 1 homologue) participate in regulating human SOX3 gene expression in NT2/D1 cells by direct interaction with the consensus PBX/MEIS-binding site, which is conserved in all mammalian orthologue promoters analysed. PBX1 is present in the protein complex formed at this site with nuclear proteins from uninduced cells, whereas both PBX1 and MEIS1 proteins were detected in the complex created with extract from RA (retinoic acid)-induced NT2/D1 cells. By functional analysis we also showed that mutations of the PBX1/MEIS1-binding sites resulted in profound reduction of SOX3 promoter responsiveness to RA. Finally, we demonstrated that overexpressed PBX1 and MEIS1 increased endogenous SOX3 protein expression in both uninduced and RA-induced NT2/D1 cells. With the results of the present study, for the first time, we have established a functional link between the TALE proteins, PBX1 and MEIS1, and expression of the human SOX3 gene. This link is of particular interest since both TALE family members and members of the SOX superfamily are recognized as important developmental regulators.

Role of CCAAT/enhancer-binding protein, histone acetylation, and coactivator recruitment in the regulation of malic enzyme transcription by thyroid hormone

In chick embryo hepatocytes, activation of malic enzyme gene transcription by triiodothyronine (T3) is mediated by a T3 response unit (T3RU) that contains five T3 response elements (T3REs) plus five accessory elements that enhance T3 responsiveness conferred by the T3REs. Results from in vitro binding assays indicate that one of the accessory elements (region F) binds CCAAT/enhancer-binding protein-alpha (C/EBPalpha). Here, we investigated the role of C/EBPalpha in the regulation of malic enzyme transcription by T3. Transfection analyses demonstrated that the stimulation of T3RE function by region F did not require the presence of additional malic enzyme gene promoter sequences. Expression of a dominant negative C/EBP inhibited the ability of region F to stimulate T3 responsiveness. In chromatin immunoprecipitation assays, C/EBPalpha and TR associated with the malic enzyme T3RU in the absence and presence of T3 with the extent of the association being greater in the presence of T3. These observations indicate that C/EBPalpha interacts with TR on the malic enzyme T3RU to enhance T3 regulation of malic enzyme gene transcription. T3 treatment increased the acetylation of histones, decreased the recruitment of nuclear receptor corepressor and increased the recruitment of steroid receptor coactivator-1, CREB binding protein, and the thyroid hormone associated protein/mediator complex at the malic enzyme T3RU. In contrast, T3 treatment had no effect on the acetylation of histones and the recruitment of corepressors and coactivators at the T3RU that mediates the T3 activation of acetyl-CoA carboxylase-alpha gene transcription. We propose that differences between the malic enzyme T3RU and the ACCalpha T3RU in the ability of T3 to modulate histone acetylation and coregulatory protein recruitment are due to differences in the composition of the nuclear receptor complexes that bind these regulatory regions.

The CYP2B2 phenobarbital response unit contains binding sites for hepatocyte nuclear factor 4, PBX-PREP1, the thyroid hormone receptor beta and the liver X receptor

A 163 bp enhancer in the CYP2B2 5' flank confers PB (phenobarbital) inducibility and constitutes a PBRU (PB response unit). The PBRU contains several transcription factor binding sites, including NR1, NR2 and NR3, which are direct repeats separated by 4 bp of the nuclear receptor consensus half-site AGGTCA, as well as an ER (everted repeat) separated by 7 bp (ER-7). Constitutive androstane receptor (CAR)-RXR (retinoic X receptor) heterodimers are known to bind to NR1, NR2 and NR3. Electrophoretic mobility-shift analysis using nuclear extracts from livers of untreated or PB-treated rats revealed binding of several other proteins to different PBRU elements. Using supershift analysis and in vitro coupled transcription and translation, the proteins present in four retarded complexes were identified as TRbeta (thyroid hormone receptor beta), LXR (liver X receptor), HNF-4 (hepatocyte nuclear factor 4) and heterodimers of PBX-PREP1 (pre-B cell homoeobox-Pbx regulatory protein 1). LXR-RXR heterodimers bound to NR3 and TRbeta bound to NR3, NR1 and ER-7, whereas the PBX-PREP1 site is contained within NR2. The HNF-4 site overlaps with NR1. A mutation described previously, GRE1m1, which decreases PB responsiveness, increased the affinity of this site for HNF-4. The PBRU also contains a site for nuclear factor 1. The PBRU thus contains a plethora of transcription factor binding sites. The profiles of transcription factor binding to NR1 and NR3 were quite similar, although strikingly different from, and more complex than, that of NR2. This parallels the functional differences in conferring PB responsiveness between NR1 and NR3 on the one hand, and NR2 on the other.

The homeodomain protein PBX participates in JH-related suppressive regulation on the expression of major plasma protein genes in the silkworm, Bombyx mori

In the silkworm, Bombyx mori, major plasma proteins referred to as 30K proteins are the most abundant proteins in the hemolymph of final (fifth) instar larvae. Surgical extirpation of corpora allata, the source of a juvenile hormone (JH), causes rapid accumulation of 30K proteins in the hemolymph of fourth instar larvae. The 30K protein 6G1 (30K6G1) gene was repressed in primary cultured fat body cells treated with a JH analog (JHA), methoprene. To identify the JH response element present in the promoter region of the 30K6G1 gene, we performed transfection analyses of the 5'-deletion mutants of the 30K6G1 gene using primary cultured fat body cells, gel retardation assays and in vivo footprinting analysis. The results from those analyses revealed that a JH response element exists in the sequence between positions -147 and -140. When the promoter construct mutated at positions -143, -142, and -141 was transfected to fat body primary cultured cells, the suppression effect on the reporter gene expression caused by JHA was reduced. Gel retardation assay using specific antibody revealed that a PBX protein binds to the JH response element. Northern blot analysis revealed that the gene expression of Bombyx PBX is enhanced in the fat body cells by JHA treatment. These results indicate that PBX proteins are involved in the JH signaling pathway and play an important role in suppressing 30K protein gene expression in the fat body of B. mori.

Cross-talk between glucocorticoid and retinoic acid signals involving glucocorticoid receptor interaction with the homoeodomain protein Pbx1

Glucocorticoid (GC) signalling influences the response of the cell to a number of other signals via a mechanism referred to as 'cross-talk'. This cross-talk may act at several levels, including an interaction between the transcription factors involved in the signalling pathways. In the present paper, we demonstrate a novel functional interaction between GC and all- trans -retinoic acid (RA) signalling. We show that, in P19 embryonal carcinoma cells, GCs potentiate RA-induced expression of the murine Hoxb -1 gene through an autoregulatory element, b1-ARE, recognized by the Pbx1 and HOXB1 homoeodomain proteins. The synergistic effect of GC did not involve GC receptor (GR) binding to the b1-ARE, and the GC-GR complex alone was unable to activate transcription via the element. Furthermore, the ability of the GR to transactivate was not required, excluding expression of a GC-induced protein as the mechanism for the GC/RA synergy. Additional transfection experiments showed that the Pbx1/HOXB1 heterodimer was the target for the GC effect. Furthermore, functional dissection of the GR demonstrated that the DNA-binding domain (DBD) of the GR was required for the synergy. A physical interaction between the GR and Pbx1 proteins was demonstrated in vivo by co-immunoprecipitation experiments. These results are compatible with a model in which the GC/RA synergy is mediated by a direct interaction between the GR and Pbx1. On the basis of the ubiquitous expression of both GR and Pbx1, a number of genes regulated by Pbx are likely to be important targets for GC-mediated 'cross-talk'.

A thyroid hormone response unit formed between the promoter and first intron of the carnitine palmitoyltransferase-Ialpha gene mediates the liver-specific induction by thyroid hormone

Carnitine palmitoyltransferase-I (CPT-I) catalyzes the rate-controlling step of fatty acid oxidation. CPT-I converts long-chain fatty acyl-CoAs to acylcarnitines for translocation across the mitochondrial membrane. The mRNA levels and enzyme activity of the liver isoform, CPT-Ialpha, are greatly increased in the liver of hyperthyroid animals. Thyroid hormone (T3) stimulates CPT-Ialpha transcription far more robustly in the liver than in non-hepatic tissues. We have shown that the thyroid hormone receptor (TR) binds to a thyroid hormone response element (TRE) located in the CPT-Ialpha promoter. In addition, elements in the first intron participate in the T3 induction of CPT-Ialpha gene expression, but the CPT-Ialpha intron alone cannot confer a T3 response. We found that deletion of sequences in the first intron between +653 and +744 decreased the T3 induction of CPT-Ialpha. Upstream stimulatory factor (USF) and CCAAT enhancer binding proteins (C/EBPs) bind to elements within this region, and these factors are required for the T3 response. The binding of TR and C/EBP to the CPT-Ialpha gene in vivo was shown by the chromatin immunoprecipitation assay. We determined that TR can physically interact with USF-1, USF-2, and C/EBPalpha. Transgenic mice were created that carry CPT-Ialpha-luciferase transgenes with or without the first intron of the CPT-Ialpha gene. In these mouse lines, the first intron is required for T3 induction as well as high levels of hepatic expression. Our data indicate that the T3 stimulates CPT-Ialpha gene expression in the liver through a T3 response unit consisting of the TRE in the promoter and additional factors, C/EBP and USF, bound in the first intron.

The homeodomain Pbx2-Prep1 complex modulates hepatocyte nuclear factor 1alpha-mediated activation of the UDP-glucuronosyltransferase 2B17 gene

UDP glucuronosyltransferases (UGT) are expressed in a wide range of tissues in which their levels of expression and distribution are dependent on cell-type specific regulatory mechanisms. The presence of a hepatocyte nuclear factor (HNF) 1 binding site in the proximal promoters of several UGT2B genes has been shown to contribute to their expression in liver cells and possibly other HNF1-containing cell types. In some of these UGT2B genes, a putative pre-B cell homeobox (Pbx) transcription factor binding site is found directly adjacent to the functional HNF1 site. To determine whether this putative Pbx site contributes to the regulation of UGT2B expression, we chose the UGT2B17 gene and investigated the capacity of its Pbx site to bind specific transcription factors and alter promoter activity. The UGT2B17 Pbx site matches a consensus Pbx site known to bind members of the Pbx, Hox, Meis, and Prep1 families of homeodomain-containing proteins and has previously been shown to bind nuclear proteins in DNaseI footprint assays. In this study, we used gel shift and functional assays to show that a Pbx2-Prep1 heterodimer can bind to the UGT2B17 Pbx site and interfere with the binding of HNF1alpha to its site adjacent to the Pbx site. This interaction of Pbx2-Prep1 and HNF1alpha results in down-regulation of HNF1alpha-mediated activation of the UGT2B17 promoter. Modulation of transcription by restricting the binding of transcriptional effectors to their target site is a novel role for Pbx2-Prep1 complexes.

Sterol regulatory element-binding protein-1 interacts with the nuclear thyroid hormone receptor to enhance acetyl-CoA carboxylase-alpha transcription in hepatocytes

In previous work, we characterized a 3,5,3'-triiodothyronine response element (T3RE) in acetyl-CoA carboxylase-alpha (ACCalpha) promoter 2 that mediated 3,5,3'-triiodothyronine (T3) regulation of ACCalpha transcription in chick embryo hepatocytes. Sequence comparison analysis revealed the presence of sterol regulatory element-1 (SRE-1) located 5 bp downstream of the ACCalpha T3RE. Here, we investigated the role of this SRE-1 in modulating T3 regulation of ACCalpha transcription. Transfection analyses demonstrated that the SRE-1 enhanced T3-induced ACCalpha transcription by more than 2-fold in hepatocytes. The effect of the SRE-1 on T3 responsiveness required the presence of the T3RE in its native orientation. In pull-down experiments, the mature form of sterol regulatory element-binding protein-1 (SREBP-1) specifically bound the alpha-isoform of the nuclear T3 receptor (TR), and the presence of T3 enhanced this interaction. A region of TRalpha containing the DNA-binding domain plus flanking sequences (amino acids 21-157) was required for interaction with SREBP-1, and a region of SREBP-1 containing the basic helix-loop-helix-leucine zipper domain (amino acids 300-389) was required for interaction with TRalpha. In gel mobility shift experiments, TRalpha, retinoid X receptor-alpha, and mature SREBP-1 formed a tetrameric complex on a DNA probe containing the ACCalpha T3RE and SRE-1, and the presence of T3 enhanced the formation of this complex. Formation of the tetrameric complex stabilized the binding of SREBP-1 to the SRE-1. These results indicate that SREBP-1 directly interacts with TR-retinoid X receptor in an orientation-specific manner to enhance T3-induced ACCalpha transcription in hepatocytes. T3 regulation of ACCalpha transcription in nonhepatic cell cultures such as chick embryo fibroblasts is markedly reduced compared with that of chick embryo hepatocytes. Here, we also show that alterations in SREBP expression play a role in mediating cell type-dependent differences in T3 regulation of ACCalpha transcription.

Chicken ovalbumin upstream-promoter transcription factor and E-box-binding proteins enhance thyroid-hormone responsiveness of the malic enzyme gene in avian hepatocytes

In chick embryo hepatocytes (CEH), stimulation of malic enzyme transcription by 3,3',5-tri-iodothyronine (T3) is mediated by a liver-specific and T3-inducible DNase I hypersensitive region (-3910 to -3640 bp) in the malic enzyme gene. Previous studies have shown that this region contains a cluster of five T3 response elements (T3REs), referred to as a T3 response unit (T3RU), plus three accessory elements that enhance T3 responsiveness conferred by the T3RU. Here we report the identification of two additional accessory elements within the -3910 to -3640 bp region. Each element augments T3 regulation of malic enzyme transcription in CEH. One element, designated region G (-3681/-3666 bp), contains a single nuclear-hormone-receptor half-site that binds the orphan receptor chicken ovalbumin upstream-promoter transcription factor. The other element, designated region H (-3655/-3646 bp), contains an E-box motif that binds proteins of unknown identity. Stimulation of T3RE function by region G or region H does not require the presence of additional malic enzyme sequences. In contrast with the stimulatory effects of regions G and H on T3 responsiveness in CEH, neither of these elements is effective in modulating T3 responsiveness in chick embryo fibroblasts (CEF). Instead, region H functions as a T3-insensitive repressor of transcription in CEF. These results indicate that chicken ovalbumin upstream-promoter transcription factor and E-box-binding proteins interact with nuclear T3 receptors to enhance T3 regulation of malic enzyme transcription in CEH and that alterations in region G and region H activities contribute to diminished T3 regulation of malic enzyme transcription in CEF relative to CEH. As the pattern of protein binding to regions G and H varies substantially between CEH and CEF, the mechanism for cell-type-dependent differences in region G and region H activity may involve alterations in protein binding to these T3 accessory elements.