TATA Box-binding Protein Binding Research Articles

TBP facilitates RNA Polymerase I transcription following mitosis

ABSTRACT The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II and III). Although TBP is central to transcription by the three RNA Pols in various species, the emergence of TBP paralogs throughout evolution has expanded the complexity in transcription initiation. Furthermore, recent studies have emerged that questioned the centrality of TBP in mammalian cells, particularly in Pol II transcription, but the role of TBP and its paralogs in Pol I transcription remains to be re-evaluated. In this report, we show that in murine embryonic stem cells TBP localizes onto Pol I promoters, whereas the TBP paralog TRF2 only weakly associates to the Spacer Promoter of rDNA, suggesting that it may not be able to replace TBP for Pol I transcription. Importantly, acute TBP depletion does not fully disrupt Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.

Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation

RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here, we use cryoelectron microscopy (cryo-EM) to visualize the S.cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Gene-specific factor TFIIIA interacts with DNA and acts as an adaptor for TFIIIC-promoter interactions. We also visualize DNA binding of TFIIIB subunits, Brf1 and TBP (TATA-box binding protein), which results in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA within the complex undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the transcription initiation complex assembly on the 5S rRNA promoter and allow us to directly compare Pol III and Pol II transcription adaptations.

Study on Interaction Between TATA-Box Binding Protein (TBP), TATA-Box and Multiprotein Bridging Factor 1(MBF1) in Beauveria bassiana by Graphene-Based Electrochemical Biosensors.

The regulation of transcription level is an important step in gene expression process. Beauveria bassiana is a broad-spectrum insecticidal fungi widely used in the biologic control of arthropod. The regulation of its transcription level is a multilevel complex process. Multiprotein bridging factor 1(MBF1) is a transcriptional co-activator that bridges sequence-specific activators and the TATA-box binding protein(TBP), Little is known about the interaction between MBF1, TBP, and TBP binding to DNA(TATA-sequences)in filamentous fungi of Beauveria bassiana, The binding of TBP to TATA-box and TBP to MBF1 was investigated via electrochemical biosensor. Graphene oxide has an electronic mobility that is unattainable for any metal, so it will be highly sensitive as a test electrode. Hence, we developed a simple, sensitive and specific sensor based on an TBP probe and graphene oxide that successfully detected the interaction of TBP and TATA-box or MBF1. From the electrochemical impedance spectroscopy (EIS), we find that the radius will increase when adding TATA-box or MBF1 buffer to the modified TBP protein electrode. When adding no TATA-box or no MBF1, the radius is relatively unchanged. The interaction between TBP and TATA-box or MBF1 was proved based on the results. These data confirmed the specificity of the interactions, (1) our developed graphene-based electrochemical biosensor can be used for monitoring the interaction between TBP and TATA-box or MBF1, (2) TBP can bind to TATA-box, (3) TBP can bind to MBF1, and (4) TBP mediates the interactions of MBF1 to DNA. Therefore, this work provided a label-free, low-cost and simple detection method for the complex process of eukaryotic gene transcription regulation.

TATA-Box Binding Protein O-GlcNAcylation at T114 Regulates Formation of the B-TFIID Complex and Is Critical for Metabolic Gene Regulation.

In eukaryotes, gene expression is performed by three RNA polymerases that are targeted to promoters by molecular complexes. A unique common factor, the TATA-box binding protein (TBP), is thought to serve as a platform to assemble pre-initiation complexes competent for transcription. Here, we describe a novel molecular mechanism of nutrient regulation of gene transcription by dynamic O-GlcNAcylation of TBP. We show that O-GlcNAcylation at T114 of TBP blocks its interaction with BTAF1, hence the formation of the B-TFIID complex, and its dynamic cycling on and off of DNA. Transcriptomic and metabolomic analyses of TBPT114A CRISPR/Cas9-edited cells showed that loss of O-GlcNAcylation at T114 increases TBP binding to BTAF1 and directly impacts expression of 408 genes. Lack of O-GlcNAcylation at T114 is associated with a striking reprogramming of cellular metabolism induced by a profound modification of the transcriptome, leading to gross alterations in lipid storage.

Elucidating the Molecular Binding Mechanism of the Tata-Binding Protein using Pie-Pife

The TATA-box binding protein (TBP) plays an important regulatory role in regulating gene expression by mediating the formation of the pre-initiation complex on promotor DNA. When binding to DNA, TBP melts the double helix and forms a stable complex while bending the dsDNA by ∼90o along the TATA sequence. In vitro single molecule experiments based on single-pair Förster resonance energy transfer (FRET) have recently revealed a dynamic, step-wise binding process via different intermediate conformations of the dsDNA. In vivo, TBP exists in different forms, e.g. as dimerbound to the dsDNA, or as part of different co-activator/deactivator complexes in the subsequent steps of pre-initiation complex formation. These states however are only observed at cellular concentration of TBP in the micromolar range, which is too high for in vitro single molecule fluorescence imaging. In this contribution, we present a new strategy to visualizes unlabelled TBP binding on DNA with changes in DNA conformation at high concentrations: binding of TBP is monitored via protein-induced fluorescence enhancement (PIFE) while single-pair FRET reports on ongoing conformational changes in the DNA/TBP complex simultaneously. We combine this label-free PIFE-FRET approach with pulsed interleaved excitation (PIE) spectroscopy, to investigate conformational dynamics of freely diffusing protein-DNA complexes in solution at the focus of a confocal microscope. Without the need of surface immobilization it can overcome concentration limitations of multi-colour assays by monitoring two parameters, binding and conformation rearrangement at the same.

Crystal structure of the full Swi2/Snf2 remodeler Mot1 in the resting state.

Swi2/Snf2 ATPases remodel protein:DNA complexes in all of the fundamental chromosome-associated processes. The single-subunit remodeler Mot1 dissociates TATA box-binding protein (TBP):DNA complexes and provides a simple model for obtaining structural insights into the action of Swi2/Snf2 ATPases. Previously we reported how the N-terminal domain of Mot1 binds TBP, NC2 and DNA, but the location of the C-terminal ATPase domain remained unclear (Butryn et al., 2015). Here, we report the crystal structure of the near full-length Mot1 from Chaetomium thermophilum. Our data show that Mot1 adopts a ring like structure with a catalytically inactive resting state of the ATPase. Biochemical analysis suggests that TBP binding switches Mot1 into an ATP hydrolysis-competent conformation. Combined with our previous results, these data significantly improve the structural model for the complete Mot1:TBP:DNA complex and suggest a general mechanism for Mot1 action.

TFIIA transcriptional activity is controlled by a 'cleave-and-run' Exportin-1/Taspase 1-switch.

Transcription factor TFIIA is controlled by complex regulatory networks including proteolysis by the protease Taspase 1, though the full impact of cleavage remains elusive. Here, we demonstrate that in contrast to the general assumption, de novo produced TFIIA is rapidly confined to the cytoplasm via an evolutionary conserved nuclear export signal (NES, amino acids 21VINDVRDIFL30), interacting with the nuclear export receptor Exportin-1/chromosomal region maintenance 1 (Crm1). Chemical export inhibition or genetic inactivation of the NES not only promotes TFIIA's nuclear localization but also affects its transcriptional activity. Notably, Taspase 1 processing promotes TFIIA's nuclear accumulation by NES masking, and modulates its transcriptional activity. Moreover, TFIIA complex formation with the TATA box binding protein (TBP) is cooperatively enhanced by inhibition of proteolysis and nuclear export, leading to an increase of the cell cycle inhibitor p16INK, which is counteracted by prevention of TBP binding. We here identified a novel mechanism how proteolysis and nuclear transport cooperatively fine-tune transcriptional programs.

Transcriptional regulation of follicle-stimulating hormone β-subunit in marmoset by an alternate distal promoter

Follicle-stimulating hormone (FSH) is essential for mammalian folliculogenesis and spermatogenesis. Common marmoset (Callithrix jacchus) is a New World primate which exhibits an unusual FSH profile across the ovarian cycle with a mid-follicular FSH peak that is not observed in Catarrhini primates like humans. Since transcription of FSH β-subunit gene (FSHβ) is a rate-limiting step in the production of mature FSH, this study aimed to investigate the regulation of marmoset FSHβ gene expression in comparison to human. In silico analysis of the FSHβ promoter sequences identified a TATA box element upstream of the conventional TATA box element in marmoset but not in human sequence. FSHβ mRNA transcript longer than the conventional transcript was detected in marmoset pituitary implying presence of a distal transcription start site. In luciferase reporter assays, the marmoset putative distal promoter had higher activity than the corresponding human region even in absence of the conventional proximal promoter. Indeed higher affinity binding of TATA box-binding protein to the putative distal TATA box element was obtained in electrophoretic mobility shift assay. This suggests existence of a differential regulation of FSHβ transcription in marmoset compared to humans.

Research Article: Simian virus 40 large T antigen-mediated transactivation of the cyclin A promoter is independent of p53 and TBP binding functions

Abstract Simian virus 40 is a small DNA tumor virus capable of transforming cells in culture and causing tumors in animal models. The viral protein large T antigen specifically binds the tumor suppressors p53 and hypophosphorylated retinoblastoma protein (pRb) to prevent G1 arrest. T antigen also transactivates the cyclin-A promoter. This activity is independent of pRb binding, yet dependent upon the J-domain Hsp70-binding region. T antigen also binds transcription factors, including TATA box binding protein (TBP). Thus, we assessed whether cyclin A promoter activation relied on this activity and/or the ability to complex with p53. Using a luciferase reporter assay, we show that T antigen mutant proteins defective in TBP and p53 binding are able to transactivate the cyclin A promoter to wild type levels. These data indicate that T antigen mediated transactivation of the cyclin A promoter uses a p53 and TBP-binding-independent mechanism, yet relies on hsp70 binding to the N-terminal, J-domain. This suggest...

Identification of the relationship between the variability of the expression of signaling pathway genes in the human brain and the affinity of TATA-binding protein to their promoters

Variations in gene expression are the subject of a wide range of research aimed at the reconstruction of regulatory protein binding sites on DNA, regulatory gene regions, gene networks, signaling pathways, and many other entities that are able to modify gene expression. Pearson’s coefficient of variation (Cv, the ratio of the standard deviation to the mean) is the measure of variations in gene expression that is the most used in the fields of intense biomedical and breeding research. In turn, only one common genomic regulatory signal has been identified in all eukaryotes, namely, the TATA box, together with three other, less conservative, obligatory elements of core promoters accompanying it: DPE, BPE, and INR. We applied the equation for TATA box Binding Protein (TBP) affinity to TATA boxes deduced from our experimental data to the analysis of high-throughput sequencing data on 35609 mRNAs in 946 human brain segments taken from the Allen Brain Atlas. The analysis revealed a significant correlation between the affinity of TBP binding to promoters of signaling pathways genes and in silico estimates of Pearson’s Cv of the expression of these genes. This finding may help scientists analyze high-throughput sequencing data in order to identify more candidate factors modifying gene expression.

A Novel Mechanism to Control Cell/Tissue Specific Activities of Glucocorticoid Receptor

Cell/tissue‐specific differential actions of glucocorticoids are mediated by the glucocorticoid receptor (GR) splice variants that possess truncated N‐terminal domain (NTD), which exists in an intrinsically disordered (ID) conformation and consists of GR's major activation function, AF1. Human GR variants lacking AF1 sequences are virtually inactive whereas those lacking amino acids on the NT flanking sequences of AF1 are most active in regulating GR target genes. However, the underlying mechanism of these GR isoform specific effects is largely unknown. We hypothesize that the GR isoform specific activities are allosterically regulated through order‐disorder transition of ID NTD sequences upon interaction with TATA‐box binding protein (TBP). First, using surface plasmon resonance method, we determined the binding kinetics of TBP with different fragments of GR containing AF1 sequences. We found that placing AF1 immediately upstream from the DNA binding domain leads to strongest AF1‐TBP interaction (KD = 0.07 µM) whereas AF1C (a core sub‐domain of AF1, important for AF1 activity) showed the weakest binding (KD = 3.0 µM) when compared to AF1 (KD = 0.5 µM). Interestingly, the GR fragment consisting of entire NTD showed a biphasic binding response to TBP. Our secondary/tertiary structural analyses using biophysical methods showed that upon TBP binding, each GR fragment adopts a compact/stable structure, and the stability is proportional to the TBP binding affinity. Consistent with GR isoform specific activity, TBP‐bound GR fragment lacking NT flanking sequences showed highest AF1‐mediated GR activity. Our studies for the first time have shown a mechanism for differential activities of GR isoforms that could open unique opportunities for cell/tissue‐specific endocrine‐based therapies.

Role of indirect readout mechanism in TATA box binding protein-DNA interaction.

Gene expression generally initiates from recognition of TATA-box binding protein (TBP) to the minor groove of DNA of TATA box sequence where the DNA structure is significantly different from B-DNA. We have carried out molecular dynamics simulation studies of TBP-DNA system to understand how the DNA structure alters for efficient binding. We observed rigid nature of the protein while the DNA of TATA box sequence has an inherent flexibility in terms of bending and minor groove widening. The bending analysis of the free DNA and the TBP bound DNA systems indicate presence of some similar structures. Principal coordinate ordination analysis also indicates some structural features of the protein bound and free DNA are similar. Thus we suggest that the DNA of TATA box sequence regularly oscillates between several alternate structures and the one suitable for TBP binding is induced further by the protein for proper complex formation.

TBP binding-induced folding of the glucocorticoid receptor AF1 domain facilitates its interaction with steroid receptor coactivator-1.

The precise mechanism by which glucocorticoid receptor (GR) regulates the transcription of its target genes is largely unknown. This is, in part, due to the lack of structural and functional information about GR's N-terminal activation function domain, AF1. Like many steroid hormone receptors (SHRs), the GR AF1 exists in an intrinsically disordered (ID) conformation or an ensemble of conformers that collectively appears to be unstructured. The GR AF1 is known to recruit several coregulatory proteins, including those from the basal transcriptional machinery, e.g., TATA box binding protein (TBP) that forms the basis for the multiprotein transcription initiation complex. However, the precise mechanism of this process is unknown. We have earlier shown that conditional folding of the GR AF1 is the key for its interactions with critical coactivator proteins. We hypothesize that binding of TBP to AF1 results in the structural rearrangement of the ID AF1 domain such that its surfaces become easily accessible for interaction with other coactivators. To test this hypothesis, we determined whether TBP binding-induced structure formation in the GR AF1 facilitates its interaction with steroid receptor coactivator-1 (SRC-1), a critical coactivator that is important for GR-mediated transcriptional activity. Our data show that stoichiometric binding of TBP induces significantly higher helical content at the expense of random coil configuration in the GR AF1. Further, we found that this induced AF1 conformation facilitates its interaction with SRC-1, and subsequent AF1-mediated transcriptional activity. Our results may provide a potential mechanism through which GR and by large other SHRs may regulate the expression of the GR-target genes.

Abstract 4532: Induced folding of the glucocorticoid receptor's AF1 domain facilitates its interaction with steroid receptor coactivator-1

Abstract The mechanism by which glucocorticoids brings about apoptotic cell death of lymphoid cells is still not well understood. However, it has been established that ligand-activated glucocorticoid receptor (GR) regulates transcription of target genes by binding to site-specific DNA and/or coregulatory proteins. Like other members of the steroid hormone receptors (SHRs), the GR possesses a modular structure characterized by three major functional domains: N-terminal domain (NTD), DNA binding domain (DBD), and ligand binding domain (LBD). The transactivation activity of SHRs is mainly controlled by two activation function domains, AF1 and AF2 located in the NTD and LBD, respectively. The precise mechanism by which SHRs regulate the transcription of the target genes is largely unknown. This is, in part, due to the lack of structural and functional information about AF1 domain. Due to the availability of the LBD structure, the relevant structural and functional properties of AF2 have been well characterized whereas it is nebulous in case of AF1 due to unavailability of its 3-D structure. The GR AF1 exists as an ensemble of largely unstructured conformers or intrinsically disordered (ID). The GR AF1 recruits other coregulatory proteins, including proteins from the basal transcriptional machinery, e.g. TATA box binding protein (TBP) by creating binding surfaces for these proteins. Other studies have also shown that transactivation domains of several transcription factors including SHRs undergo a disorder/order transition upon interaction with proteins from the basal transcriptional machinery. We have earlier shown that conditional folding of the GR AF1 is the key for its interactions with its critical coactivator proteins. It is interesting that the ID GR AF1 directly interacts with the TBP, the critical protein that forms the basis for the multiprotein transcription initiation complex. However, the precise mechanism of this process is unknown. One possibility may be that TBP binding-induced structured conformation in AF1 is involved in creating a platform for the GR AF1-associated coactivators. In this study we tested whether TBP binding induces structure formation in the GR AF1 such that AF1's interaction with SRC-1, a critical coactivator which is important for GR-mediated transcriptional activity, is facilitated. Our data show that TBP binding induced structure formation in the GR AF1facilitates its interaction with SRC-1, and subsequent AF1-mediated transcriptional activity. Our results provide a potential mechanism through which GR and other SHRs may regulate the expression of the GR-target genes, information essential to understand how specific signals are passed from the receptor to target genes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4532. doi:10.1158/1538-7445.AM2011-4532

Binding‐folding induced regulation of the AF1 transactivation domain of the glucocorticoid receptor

The precise mechanism by which the glucocorticoid receptor (GR) regulates the transcription of the target genes is largely unknown. This is, in part, due to the lack of structural and functional information about its AF1 transactivation domain, which exists as an ensemble of largely unstructured conformers or intrinsically disordered (ID). It has been shown that transactivation domains of several transcription factors undergo a disorder/order transition upon interaction with proteins from the basal transcriptional machinery. It is interesting that the ID GR AF1 directly interacts with the TATA box binding protein (TBP), the critical protein that forms the basis for the multiprotein transcription initiation complex. However, the precise mechanism of this process is unknown. In this study we tested whether TBP binding induces structure formation in the GR AF1 such that AF1's interaction with steroid receptor coactivator‐1 (SRC‐1), a critical coactivator which is important for GR‐mediated transcriptional activity, is facilitated. Our data show that TBP binding induces structure formation in otherwise ID AF1such that its interaction with SRC‐1, and subsequent AF1‐mediated transcriptional activity is significantly enhanced. Our results may provide a potential mechanism through which GR passes its signals to regulate the expression of its specific target genes. Supported by a grant from NIH (DK058829).

Unraveling the Dynamics of TBP-NC2 with Hidden Markov Modeling

One of the early steps in initiation of transcription is the binding of the TATA box Binding Protein (TBP) to a core-promoter TATA Box. After binding, the transcription complex is assembled in cooperation with our general transcription factors. The binding of TBP to DNA is also a prime target for regulating gene transcription and many cofactors can interact with TBP at this initial stage.In a recent publication (Schluesche et al), we showed that the binding of the Negative Cofactor 2 (NC2) leads to dynamic behavior of the TBP-NC2 complex along the DNA using single-pair Forster Resonance Energy Transfer (spFRET). To extract detailed kinetic information from the single molecule experiments, we have adapted a Hidden Markov Model to analyze the spFRET data collected using a EMCCD camera. With add of the HMM analysis, it is possible to determine how many states are available which transitions are possible, providing new insights into the origins of these different states.We performed measurements on four DNA strands, two containing the AdML promoter with identical labeling but different DNA lengths and two containing the H2B promoter with labels at two different positions on the DNA. Results of the AdML promoter showed the high reproducibility of the analysis method. Four FRET states were clearly observable. For the H2B promoter, many more states were observable in the HMM analysis showing a high complexity of dynamics but yet very similar patterns as observed for the AdML promoter.Schluesche et al 2007 NSMB 14:1196-1201

Proteomics Reveals a Physical and Functional Link between Hepatocyte Nuclear Factor 4α and Transcription Factor IID

Proteomic analyses have contributed substantially to our understanding of diverse cellular processes. Improvements in the sensitivity of mass spectrometry approaches are enabling more in-depth analyses of protein-protein networks and, in some cases, are providing surprising new insights into well established, longstanding problems. Here, we describe such a proteomic analysis that exploits MudPIT mass spectrometry and has led to the discovery of a physical and functional link between the orphan nuclear receptor hepatocyte nuclear factor 4alpha (HNF4alpha) and transcription factor IID (TFIID). A systematic characterization of the HNF4alpha-TFIID link revealed that the HNF4alpha DNA-binding domain binds directly to the TATA box-binding protein (TBP) and, through this interaction, can target TBP or TFIID to promoters containing HNF4alpha-binding sites in vitro. Supporting the functional significance of this interaction, an HNF4alpha mutation that blocks binding of TBP to HNF4alpha interferes with HNF4alpha transactivation activity in cells. These findings identify an unexpected role for the HNF4alpha DNA-binding domain in mediating key regulatory interactions and provide new insights into the roles of HNF4alpha and TFIID in RNA polymerase II transcription.

Binding of C/EBPβ to the C-Reactive Protein (CRP) Promoter in Hep3B Cells Is Associated with Transcription of CRP mRNA

Expression of the acute phase protein C-reactive protein (CRP) is tightly regulated in hepatocytes. Although very little CRP mRNA is transcribed normally, inflammatory stimuli are followed by a dramatic increase in mRNA synthesis and accumulation. IL-6 and IL-1beta are believed to be the major cytokines responsible for induction of CRP and other acute phase proteins. Our previous studies, using transient transfection and EMSA experiments, implicated involvement of the transcription factors C/EBPbeta, STAT3, Rel p50, and c-Rel in CRP induction. In the current study we used chromatin immunoprecipitation assays to determine the kinetics of transcription factor occupancy of these transcription factors on the endogenous CRP promoter. All of these transcription factors were found bound to the endogenous CRP promoter in the absence of cytokines, but cytokine treatment markedly increased binding of only C/EBPbeta. In addition, c-Rel and TATA box-binding protein (TBP) appeared to occupy the promoter in parallel in the presence of cytokines. In the absence of cytokines, CRP mRNA accumulation was not measurable but began to increase by 3 h after exposure of cells to IL-1beta plus IL-6, peaking at 12 h with secondary peaks at 18 and 24 h. The secondary peaks in mRNA expression paralleled the pattern of binding of c-Rel and TBP to the CRP promoter. We conclude that the CRP promoter has a low level of transcription factor occupancy in the absence of cytokines and induction occurs with binding of C/EBP, and that c-Rel and TBP are important for modulating CRP expression.

Structure and TBP binding of the Mediator head subcomplex Med8–Med18–Med20

The Mediator head module stimulates basal RNA polymerase II (Pol II) transcription and enables transcriptional regulation. Here we show that the head subunits Med8, Med18 and Med20 form a subcomplex (Med8/18/20) with two submodules. The highly conserved N-terminal domain of Med8 forms one submodule that binds the TATA box-binding protein (TBP) in vitro and is essential in vivo. The second submodule consists of the C-terminal region of Med8 (Med8C), Med18 and Med20. X-ray analysis of this submodule reveals that Med18 and Med20 form related beta-barrel folds. A conserved putative protein-interaction face on the Med8C/18/20 submodule includes sites altered by srb mutations, which counteract defects resulting from Pol II truncation. Our results and published data support a positive role of the Med8/18/20 subcomplex in initiation-complex formation and suggest that the Mediator head contains a multipartite TBP-binding site that can be modulated by transcriptional activators.

Cooperation between Small Nuclear RNA-activating Protein Complex (SNAPC) and TATA-box-binding Protein Antagonizes Protein Kinase CK2 Inhibition of DNA Binding by SNAPC

Protein kinase CK2 regulates RNA polymerase III transcription of human U6 small nuclear RNA (snRNA) genes both negatively and positively depending upon whether the general transcription machinery or RNA polymerase III is preferentially phosphorylated. Human U1 snRNA genes share similar promoter architectures as that of U6 genes but are transcribed by RNA polymerase II. Herein, we report that CK2 inhibits U1 snRNA gene transcription by RNA polymerase II. Decreased levels of endogenous CK2 correlates with increased U1 expression, whereas CK2 associates with U1 gene promoters, indicating that it plays a direct role in U1 gene regulation. CK2 phosphorylates the general transcription factor small nuclear RNA-activating protein complex (SNAP(C)) that is required for both RNA polymerase II and III transcription, and SNAP(C) phosphorylation inhibits binding to snRNA gene promoters. However, restricted promoter access by phosphorylated SNAP(C) can be overcome by cooperative interactions with TATA-box-binding protein at a U6 promoter but not at a U1 promoter. Thus, CK2 may have the capacity to differentially regulate U1 and U6 transcription even though SNAP(C) is universally utilized for human snRNA gene transcription.