Mechanisms of transcriptional activation and repression can both involve TFIID

Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity

Background

Hox proteins finely coordinate antero-posterior axis during embryonic development and through their action specific target genes are expressed at the right time and space to determine the embryo body plan. As master transcriptional regulators, Hox proteins recognize DNA through the homeodomain (HD) and interact with a multitude of proteins, including general transcription factors and other cofactors. HD binding specificity increases by protein–protein interactions with a diversity of cofactors that outline the Hox interactome and determine the transcriptional landscape of the selected target genes. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but its precise mechanism remains to be elucidated.

Results

Here we report Antennapedia (Antp) Hox protein–protein interaction with the TATA-binding protein (TBP) and the formation of novel trimeric complexes with TFIIEβ and Extradenticle (Exd), as well as its participation in transcriptional regulation. Using Bimolecular Fluorescence Complementation (BiFC), we detected the interaction of Antp-TBP and, in combination with Förster Resonance Energy Transfer (BiFC-FRET), the formation of the trimeric complex with TFIIEβ and Exd in living cells. Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. The trimeric complexes of Antp-TBP with TFIIEβ and Exd were validated using different Antp mutations to disrupt the trimeric complexes. Interestingly, the trimeric complex Antp-TBP-TFIIEβ significantly increased the transcriptional activity of Antp, whereas Exd diminished its transactivation.

Conclusions

Our findings provide important insights into the Antp interactome with the direct interaction of Antp with TBP and the two new trimeric complexes with TFIIEβ and Exd. These novel interactions open the possibility to analyze promoter function and gene expression to measure transcription factor binding dynamics at target sites throughout the genome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-022-00239-8.

Deletions in the 3' part of the NFIX gene including a recurrent Alu-mediated deletion of exon 6 and 7 account for previously unexplained cases of Marshall-Smith syndrome

Marshall-Smith syndrome (MSS) is a very rare malformation syndrome characterized by typical craniofacial anomalies, abnormal osseous maturation, developmental delay, failure to thrive, and respiratory difficulties. Mutations in the nuclear factor 1/X gene (NFIX) were recently identified as the cause of MSS. In our study cohort of 17 patients with a clinical diagnosis of MSS, conventional sequencing of NFIX revealed frameshift and splice-site mutations in 10 individuals. Using multiplex ligation-dependent probe amplification analysis, we identified a recurrent deletion of NFIX exon 6 and 7 in five individuals. We demonstrate this recurrent deletion is the product of a recombination between AluY elements located in intron 5 and 7. Two other patients had smaller deletions affecting exon 6. These findings show that MSS is a genetically homogeneous Mendelian disorder. RT-PCR experiments with newly identified NFIX mutations including the recurrent exon 6 and 7 deletion confirmed previous findings indicating that MSS-associated mutant mRNAs are not cleared by nonsense-mediated mRNA decay. Predicted MSS-associated mutant NFIX proteins consistently have a preserved DNA binding and dimerization domain, whereas they grossly vary in their C-terminal portion. This is in line with the hypothesis that MSS-associated mutations encode dysfunctional proteins that act in a dominant negative manner.

The presence of TATA-binding protein in the brainstem, correlated with sleep apnea in SIDS victims

BACKGROUND

Recent reports have indicated that the presence of transcription factors and RNA polymerase decreases in rat brains that suffer perinatal asphyxia from hypoxia. As hypoxia has been proposed as a causative factor in the Sudden Infant Death Syndrome (SIDS), the correlation between TATA-binding protein (TBP) in the brainstem of SIDS victims as a marker of transcription and the incidence of sleep apnea was investigated.

MATERIALS AND METHODS

A total of 38 infants, including 26 cases of SIDS, died under 6 months of age, in a cohort of 27,000 infants studied prospectively to characterize their sleep-wake behavior. The frequency and duration of sleep apnea was analyzed. Brainstem material was collected and immunohistochemistry of TBP was carried out. The density of TBP-positive neurons was measured quantitatively. Correlation analyses were carried out between the density of TBP-positive neurons and the data concerning sleep apnea.

RESULTS

One SIDS-specific positive correlation occurred between the density of TBP-positive neurons in the dorsal raphe nucleus of the midbrain and the duration of central apnea (p=0.049) and two SIDS-specific negative correlations between the density of TBP-positive neurons in the pars compacta and dissipata of the pedunculopontine tegmentum nucleus (PPTNc, PPTNd) in the midbrain and the duration of apnea (p=0.035).

CONCLUSIONS

The significant correlation between the findings of TBP-positive neurons in the midbrain arousal pathway and the characteristics of sleep apnea in SIDS victims is in agreement with the both association of apnea and arousal phenomenon in pathophysiology of SIDS.

Groucho augments the repression of multiple Even skipped target genes in establishing parasegment boundaries

Groucho acts as a co-repressor for several Drosophila DNA binding transcriptional repressors. Several of these proteins have been found to contain both Groucho-dependent and -independent repression domains, but the extent to which this distinction has functional consequences for the regulation of different target genes is not known. The product of the pair-rule gene even skipped has previously been shown to contain a Groucho-independent repression activity. In the Even skipped protein, outside the Groucho-independent repression domain, we have identified a conserved C-terminal motif (LFKPY), similar to motifs that mediate Groucho interaction in Hairy, Runt and Huckebein. Even skipped interacts with Groucho in yeast and in vitro, and groucho and even skipped genetically interact in vivo. Even skipped with a mutated Groucho interaction motif, which abolished binding to Groucho, showed a significantly reduced ability to rescue the even skipped null phenotype when driven by the complete even skipped regulatory region. Replacing this motif with a heterologous Groucho interaction motif restored the rescuing function of Even skipped in segmentation. Further functional assays demonstrated that the Even skipped C terminus acts as a Groucho-dependent repression domain in early Drosophila embryos. This novel repression domain was active on two target genes that are normally repressed by Even skipped at different concentrations, paired and sloppy paired. When the Groucho interaction motif is mutated, repression of each target gene is reduced to a similar extent, with some activity remaining. Thus, the ability of Even skipped to repress different target genes at different concentrations does not appear to involve differential recruitment or function of Groucho. The accumulation of multiple domains of similar function within a single protein may be a common evolutionary mechanism that fine-tunes the level of activity for different regulatory functions.

Heterozygous disruption of the TATA-binding protein gene in DT40 cells causes reduced cdc25B phosphatase expression and delayed mitosis

TATA-binding protein (TBP) is a key general transcription factor required for transcription by all three nuclear RNA polymerases. Although it has been intensively analyzed in vitro and in Saccharomyces cerevisiae, in vivo studies of vertebrate TBP have been limited. We applied gene-targeting techniques using chicken DT40 cells to generate heterozygous cells with one copy of the TBP gene disrupted. Such TBP-heterozygous (TBP-Het) cells showed unexpected phenotypic abnormalities, resembling those of cells with delayed mitosis: a significantly lower growth rate, larger size, more G2/-M- than G1-phase cells, and a high proportion of sub-G1, presumably apoptotic, cells. Further evidence for delayed mitosis in TBP-Het cells was provided by the differential effects of several cell cycle-arresting drugs. To determine the cause of these defects, we first examined the status of cdc2 kinase, which regulates the G2/M transition, and unexpectedly observed more hyperphosphorylated, inactive cdc2 in TBP-Het cells. Providing an explanation for this, mRNA and protein levels of cdc25B, the trigger cdc2 phosphatase, were significantly and specifically reduced. These properties were all due to decreased TBP levels, as they could be rescued by expression of exogeneous TBP, including, in most but not all cases, a mutant form lacking the species-specific N-terminal domain. Our results indicate that small changes in TBP concentration can have profound effects on cell growth in vertebrate cells.

Roles of the NFI/CTF gene family in transcription and development

The Nuclear Factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression. The classes of genes whose expression is modulated by NFI include those that are ubiquitously expressed, as well as those that are hormonally, nutritionally, and developmentally regulated. The NFI family is composed of four members in vertebrates (NFI-A, NFI-B, NFI-C and NFI-X), and the four NFI genes are expressed in unique, but overlapping, patterns during mouse embryogenesis and in the adult. Transcripts of each NFI gene are differentially spliced, yielding as many as nine distinct proteins from a single gene. Products of the four NFI genes differ in their abilities to either activate or repress transcription, likely through fundamentally different mechanisms. Here, we will review the properties of the NFI genes and proteins and their known functions in gene expression and development.

The human transcription factor IID subunit human TATA-binding protein-associated factor 28 interacts in a ligand-reversible manner with the vitamin D(3) and thyroid hormone receptors

Using coexpression in COS cells, we have identified novel interactions between the human TATA-binding protein-associated factor 28 (hTAF(II)28) component of transcription factor IID and the ligand binding domains (LBDs) of the nuclear receptors for vitamin D3 (VDR) and thyroid hormone (TRalpha). Interaction between hTAF(II)28 and the VDR and TR LBDs was ligand-reversible, whereas no interactions between hTAF(II)28 and the retinoid X receptors (RXRs) or other receptors were observed. TAF(II)28 interacted with two regions of the VDR, a 40-amino acid region spanning alpha-helices H3-H5 and alpha-helix H8. Interactions were also observed with the H3-H5 region of the TRalpha but not with the equivalent highly related region of the RXRgamma. Fine mapping using RXR derivatives in which single amino acids of the RXRgamma LBD have been replaced with their VDR counterparts shows that the determinants for interaction with hTAF(II)28 are located in alpha-helix H3 and are not identical to those previously identified for interactions with hTAF(II)55. We also describe a mutation in the H3-H5 region of the VDR LBD, which abolishes transactivation, and we show that interaction of hTAF(II)28 with this mutant is no longer ligand-reversible.

Repressed expression of the human xanthine oxidoreductase gene. E-box and TATA-like elements restrict ground state transcriptional activity

Studies were initiated to address the basis for the low xanthine oxidoreductase (XOR) activity in humans relative to nonprimate mammalian species. The expression of the XOR in humans is strikingly lower than in mice, and both transcription rates and core promoter activity of the gene are repressed. Analysis of human XOR promoter activity in hepatocytes and vascular endothelial cells showed that the region from -258 to -1 contains both repressor and activator binding regions regulating core promoter activity. The region between -138 and -1 is necessary and sufficient for initiating, and the region between -258 and -228 is critical for restricting core promoter activity. Within the latter region, site-directed mutations identified a consensus sequence "acacaggtgtgg" (-242 to -230) that contains an E-box that binds a repressor. In addition, the TATA-like element is also required to restrict promoter activity and TFIID binds to this site. The results demonstrate that both an E-box and TATA-like element are required to restrict gene activity. A model is proposed to account for human XOR regulation.

The Drosophila TATA binding protein contains a strong but masked activation domain

TATA binding protein (TBP) is a critical transcription factor involved in transcription by all three RNA polymerases (RNAPs). Studies using in vitro systems and yeast have shown that the C-terminal core domain (CTD) of TBP is necessary and sufficient for many TBP functions, but the significance of the N-terminal domain (NTD) of TBP is still obscure. Here, using transient expression assays in Drosophila Schneider cells, we show that the NTD of Drosophila TBP (dTBP) strongly activates transcription when fused to the GAL4 DNA binding domain (DBD). Strikingly, the activity of the NTD is completely repressed in the context of full-length dTBP. In contrast to the much weaker activation obtained by either full-length dTBP or the dTBP CTD fused to the GAL4 DBD, activation by the NTD is dependent on the presence of GAL4 binding sites and is susceptible to the effects of a dominant negative TFIIB mutant, TFIIB deltaC202, a property observed previously with certain authentic activation domains. Activation by the NTD, but not full-length dTBP or the CTD, seems to be mediated by the action of a strong activation domain, likely a glutamine-rich region. In conclusion, the dTBP NTD can behave as a very strong activator that is masked in the full-length protein, suggesting possible roles for the dTBP NTD in RNAP II-mediated transcription.

Evolutionary conserved mechanism of transcriptional repression by even-skipped

Even-skipped (Eve) is a transcriptional repressor involved in segment formation in Drosophila melano-gaster. In order to gain further insights into the mechanism of action of Eve we tested whether it would function as a transcriptional repressor in mammalian cells. We found that Eve was indeed a potent repressor in two different mammalian cell types and at several promoters. In vitro transcription assays confirmed that Eve directly represses transcription initiation when specifically targeted to a promoter. We also found that, unlike the case with transcriptional activators, Eve does not repress transcription synergistically. Analysis of the effect of Eve on preinitiation complex assembly in a crude HeLa cell nuclear extract demonstrated that the Eve repression domain functions by preventing the assembly of TFIID with the promoter. Our data support the hypothesis that Eve contains an active repression domain that functions specifically to prevent preinitiation complex formation.

Even-skipped represses transcription by binding TATA binding protein and blocking the TFIID-TATA box interaction

The Drosophila homeodomain protein Even-skipped (Eve) is a transcriptional repressor, and previous studies have suggested that it functions by interfering with the basal transcription machinery. Here we describe experiments indicating that the mechanism of Eve repression involves a direct interaction with the TATA binding protein (TBP) that blocks binding of TBP-TFIID to the promoter. We first compared Eve activities in in vitro transcription systems reconstituted with either all the general transcription factors or only TBP, TFIIB, TFIIF30, and RNA polymerase II. In each case, equivalent and very efficient levels of repression were observed, indicating that no factors other than those in the minimal system are required for repression. We then show that Eve can function efficiently when its recognition sites are far from the promoter and that the same regions of Eve required for repression in vivo are necessary and sufficient for in vitro repression. This includes, in addition to an Ala-Pro-rich region, residues within the homeodomain. Using GAL4-Eve fusion proteins, we demonstrate that the homeodomain plays a role in repression in addition to DNA binding, which is to facilitate interaction with TBP. Single-round transcription experiments indicate that Eve must function prior to TBP binding to the promoter, suggesting a mechanism whereby Eve represses by competing with the TATA box for TBP binding. Consistent with this, excess TATA box-containing oligonucleotide is shown to specifically and efficiently disrupt the TBP-Eve interaction. Importantly, we show that Eve binds directly to TFIID and that this interaction can also be disrupted by the TATA oligonucleotide. We conclude that Eve represses transcription via a direct interaction with TBP that blocks TFIID binding to the promoter.

Different core promoters possess distinct regulatory activities in the Drosophila embryo

There are numerous examples of shared enhancers interacting with just a subset of target promoters. In some cases, specific enhancer-promoter interactions depend on promoter competition, whereby the activation of a preferred target promoter precludes expression of linked genes. Here, we employ a transgenic embryo assay to obtain evidence that promoter selection is influenced by the TATA element. Both the AE1 enhancer from the Drosophila Antennapedia gene complex (ANT-C) and the IAB5 enhancer from the Bithorax complex (BX-C) preferentially activate TATA-containing promoters when challenged with linked TATA-less promoters. In contrast, the rho neuroectoderm enhancer (NEE) does not discriminate between these two classes of promoters. Thus, certain upstream activators, such as Ftz, prefer TATA-containing promoters, whereas other activators, including Dorsal, work equally well on both classes of promoters. These results provide in vivo evidence that different core promoters possess distinct regulatory activities. We discuss the possibility that an invariant TFIID complex can adopt different conformations on the core promoter.

Functional interaction between p53, the TATA-binding protein (TBP), andTBP-associated factors in vivo

The transcriptional activator p53 is known to interact with components of the general transcription factor TFIID in vitro. To examine the relevance of these associations to transcriptional activation in vivo, plasmids expressing a p53-GAL4 chimera and Drosophila TATA-binding protein (dTBP) were transfected into Drosophila Schneider cells. p53-GAL4 and dTBP displayed a markedly synergistic effect on activated transcription from a GAL4 site-containing reporter that was at least 10-fold greater than observed with other activators tested. A mutant p53 previously shown to be defective in both transcriptional activation in vivo and in binding to TBP-associated factors (TAFs) in vitro, although still capable of binding dTBP, did not cooperate with dTBP, suggesting that TAFs may contribute to this synergy. Providing further support for this possibility, transfected dTBP assembled into rapidly sedimenting complexes and could be immunoprecipitated with anti-TAF antibodies. While overexpression of any of several TAFs did not affect basal transcription, in either the presence or the absence of cotransfected dTBP, overexpression of TAFII230 inhibited transcriptional activation mediated by p53-GAL4 as well as by GAL4-VP16 and Sp1. Overexpression of TAFII40 and TAFII60 also inhibited activation by p53-GAL4 but had negligible effects on activation by GAL4-VP16 and Sp1, while TAFII110 did not affect any of the activators. TAF-mediated inhibition of activated transcription could be rescued by high levels of exogenous dTBP, which also restored full synergy. These data demonstrate for the first time that functional interactions can occur in vivo between TBP, TAFs, and p53.