Defective transcriptional activation by diverse VP16 mutants associated with a common inability to form open promoter complexes

SNPD-CRISPR: Single Nucleotide Polymorphism-Distinguishable Repression or Enhancement of a Target Gene Expression by CRISPR System

A wide range of diseases, including cancer, autoimmune diseases, or neurodegenerative diseases, have been associated with single nucleotide mutations in their causative genes. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system is a flexible and efficient genome engineering technology widely used for researches and therapeutic applications which offers immense opportunity to treat genetic diseases. The complex of Cas9 and the guide RNA acts as an RNA-guided endonuclease. Cas9 recognizes a sequence motif known as a protospacer adjacent motif (PAM), and then the guide RNA base pairs with its proximal target region of 20 nucleotides with sequence complementarity. Here we describe the procedure named single nucleotide polymorphism-distinguishable (SNPD)-CRISPR system which can suppress or enhance the expression of disease-causative gene with single nucleotide mutation distinguished from its wild-type. In this study, we used HRAS, one of most famous cancer-causative genes, as an example of a target gene.

Improved transcriptional activators and their use in mis-expression traps in Arabidopsis

The synthetic transcription factor LhG4 has been used in numerous mis-expression studies in plants. We show that the sequence encoding the LhG4 activation domain, derived from Saccharomyces cerevisiae GAL4, contains several cryptic polyadenylation signals in Arabidopsis. The GAL4-derived sequence was modified according to preferred Arabidopsis codon usage, generating LhG4AtO which was faithfully transcribed in Arabidopsis plants. In protoplasts, LhG4AtO achieved maximum transactivation of the pOp promoter with 10-fold less input DNA than LhG4. The same methods were used to compare 10 other LhG4 derivatives that carried alternative natural or synthetic activation domains. Lh214 and Lh314, which contain synthetic activation domains comprising trimers of a core acidic activation domain, directed threefold more GUS expression from the pOp promoter with 20-fold less input DNA than LhG4. In contrast, when expressed from the CaMV 35S promoter in transgenic plants carrying a pOp-GUS reporter, Lh214 and Lh314 yielded transformants with substantially lower GUS activities than other constructs including LhG4AtO and LhG4 which performed similarly. When incorporated into an enhancer-trapping vector, however, LhG4AtO and Lh314 yielded enhancer traps with approximately twice the frequency of LhG4, suggesting that the modified activation domains offer improved performance when expressed from weaker transcription signals. To increase the number of LhG4 patterns available for mis-expression studies, we describe a population of enhancer-trap lines obtained with LhG4AtO in a pOp-GUS background. We show that enhancer-trap lines can transactivate an unlinked pOp-green fluorescent protein (pOp-GFP) reporter in the pattern predicted by staining for GUS activity.

RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits

We have programmed human cells to express physiological levels of recombinant RNA polymerase II (RNAPII) subunits carrying tandem affinity purification (TAP) tags. Double-affinity chromatography allowed for the simple and efficient isolation of a complex containing all 12 RNAPII subunits, the general transcription factors TFIIB and TFIIF, the RNAPII phosphatase Fcp1, and a novel 153-kDa polypeptide of unknown function that we named RNAPII-associated protein 1 (RPAP1). The TAP-tagged RNAPII complex is functionally active both in vitro and in vivo. A role for RPAP1 in RNAPII transcription was established by shutting off the synthesis of Ydr527wp, a Saccharomyces cerevisiae protein homologous to RPAP1, and demonstrating that changes in global gene expression were similar to those caused by the loss of the yeast RNAPII subunit Rpb11. We also used TAP-tagged Rpb2 with mutations in fork loop 1 and switch 3, two structural elements located strategically within the active center, to start addressing the roles of these elements in the interaction of the enzyme with the template DNA during the transcription reaction.

Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms

The topological organization of a TATA binding protein-TFIIB-TFIIF-RNA polymerase II (RNAP II)-TFIIE-promoter complex was analyzed using site-specific protein-DNA photo-cross-linking of gel-purified complexes. The cross-linking results for the subunits of RNAP II were used to determine the path of promoter DNA against the structure of the enzyme. The results indicate that promoter DNA wraps around the mobile clamp of RNAP II. Cross-linking of TFIIF and TFIIE both upstream of the TATA element and downstream of the transcription start site suggests that both factors associate with the RNAP II mobile clamp. TFIIE alpha closely approaches promoter DNA at nucleotide -10, a position immediately upstream of the transcription bubble in the open complex. Increased stimulation of transcription initiation by TFIIE alpha is obtained when the DNA template is artificially premelted in the -11/-1 region, suggesting that TFIIE alpha facilitates open complex formation, possibly through its interaction with the upstream end of the partially opened transcription bubble. These results support the central roles of the mobile clamp of RNAP II and TFIIE in transcription initiation.

The H1 and H2 regions of the activation domain of herpes simplex virion protein 16 stimulate transcription through distinct molecular mechanisms

BACKGROUND

The Herpes Simplex Virion Protein 16 (VP16) contains a strong activation domain which can be subdivided into two regions, H1 and H2, both of which independently activate transcription in vivo. Several components of the basal transcription machinery have been shown to interact with the activation domain of VP16, mostly through the H1 region.

RESULTS

We show that the H2 region binds directly to histone acetyltransferase, CBP (CREB (cAMP Responsive Element Binding Protein) Binding Protein) both in vivo and in vitro. The sites of interaction with the H2 region were mapped to both the amino- and carboxy-terminal segments of CBP. A mutation in the H2 region disrupts the interaction with CBP and abolishes the ability of VP16 to mediate in vitro transactivation from chromatin templates in an acetyl-CoA dependent manner. In contrast, human Mediator, another co-activator complex, binds specifically to both the H1 and H2 regions.

CONCLUSION

The H1 and H2 regions of the VP16 activation domain activate transcription via distinct pathways. The H2 requires CBP for activation, whereas the H1 may function through Mediator and general transcription factors.

Mechanism of promoter melting by the xeroderma pigmentosum complementation group B helicase of transcription factor IIH revealed by protein-DNA photo-cross-linking

The p89/xeroderma pigmentosum complementation group B (XPB) ATPase-helicase of transcription factor IIH (TFIIH) is essential for promoter melting prior to transcription initiation by RNA polymerase II (RNAPII). By studying the topological organization of the initiation complex using site-specific protein-DNA photo-cross-linking, we have shown that p89/XPB makes promoter contacts both upstream and downstream of the initiation site. The upstream contact, which is in the region where promoter melting occurs (positions -9 to +2), requires tight DNA wrapping around RNAPII. The addition of hydrolyzable ATP tethers the template strand at positions -5 and +1 to RNAPII subunits. A mutation in p89/XPB found in a xeroderma pigmentosum patient impairs the ability of TFIIH to associate correctly with the complex and thereby melt promoter DNA. A model for open complex formation is proposed.

Characterization of the transactivation domain of the equine herpesvirus type 1 immediate-early protein

Equine herpesvirus type 1 (EHV-1) possesses a sole diploid immediate early gene (IE) that encodes a major regulatory protein of 1487 amino acids capable of modulating gene expression from both early and late promoters and also of trans-repressing its own promoter. Using a series of GAL-4-IE fusion constructs, we previously demonstrated that the minimal transactivation domain (TAD) of the IE protein maps within amino acids 3-89. Additional studies revealed that that the carboxyl terminus of the IE protein may be required for full transactivation activity in vitro. Analyses of the minimal TAD revealed the presence of 13 acidic amino acids and six basic residues giving the TAD region a net negative charge of -7. In addition, there are conserved hydrophobic residues (Leu(12) and Phe(15)) that may be critical for transactivation function. To identify residues essential for IE transactivation and to ascertain if the overall net negative charge of the TAD or the position of specific hydrophobic residues within the IE TAD are critical for the transactivation function, plasmids expressing mutant forms of the TAD were generated using specifically designed mutagenic oligonucleotides and PCR mutagenesis. Mutagenized TADs in which the acidic and hydrophobic amino acid residues were replaced, singly and in combination, with polar, uncharged amino acids were cloned into a GAL-4/CAT reporter expression system and assayed in transient transfection assays. To determine if the carboxyl terminus is necessary for full transactivation activity, a series of constructs that express forms of the IE protein-containing deletions within this region were generated and assayed for transactivation function in transient transfection assays. These assays demonstrated that mutation of any acidic residue, either singly or in combination, or deletion of the carboxyl terminus of the IE protein resulted in a severe impairment of transactivation activity. These results show that both acidic and hydrophobic residues within the IE TAD are critical for transactivation function and that the carboxyl terminus of the IE protein is required for full transactivation activity.

Promoter opening via a DNA fork junction binding activity

The rate-limiting step in transcriptional initiation typically is opening the promoter DNA to expose the template strand. Opening is tightly regulated, but how it occurs is not known. These experiments identify an activity, recognition of specific DNA fork junctions, and suggest that it is critical to bacterial promoter opening. This activity is both sequence and structure specific; it recognizes the bases that constitute the upstream double-stranded/single-stranded boundary of the open complex. Promoter mutations known to reduce opening rates lead to comparable reductions in fork junction binding affinity. The activity acts to establish the upstream boundary of melted DNA and works in conjunction with two single-stranded DNA binding activities that recognize separately the two melted strands. The junction binding activity is contained within the sigma factor component of the holoenzyme. The activity occurs in both a typical prokaryotic transcription system and in a eukaryotic-like bacterial system that responds to enhancers and needs ATP. Thus DNA opening catalyzed by fork junction binding may occur in a variety of systems in which DNA must be opened to be copied.

Molecular genetics of the RNA polymerase II general transcriptional machinery

Transcription initiation by RNA polymerase II (RNA pol II) requires interaction between cis-acting promoter elements and trans-acting factors. The eukaryotic promoter consists of core elements, which include the TATA box and other DNA sequences that define transcription start sites, and regulatory elements, which either enhance or repress transcription in a gene-specific manner. The core promoter is the site for assembly of the transcription preinitiation complex, which includes RNA pol II and the general transcription fctors TBP, TFIIB, TFIIE, TFIIF, and TFIIH. Regulatory elements bind gene-specific factors, which affect the rate of transcription by interacting, either directly or indirectly, with components of the general transcriptional machinery. A third class of transcription factors, termed coactivators, is not required for basal transcription in vitro but often mediates activation by a broad spectrum of activators. Accordingly, coactivators are neither gene-specific nor general transcription factors, although gene-specific coactivators have been described in metazoan systems. Transcriptional repressors include both gene-specific and general factors. Similar to coactivators, general transcriptional repressors affect the expression of a broad spectrum of genes yet do not repress all genes. General repressors either act through the core transcriptional machinery or are histone related and presumably affect chromatin function. This review focuses on the global effectors of RNA polymerase II transcription in yeast, including the general transcription factors, the coactivators, and the general repressors. Emphasis is placed on the role that yeast genetics has played in identifying these factors and their associated functions.

Viral transactivating proteins

Many viruses utilize the cellular transcription apparatus to express their genomes, and they encode transcriptional regulatory proteins that modulate the process. Here we review the current understanding of three viral regulatory proteins. The adenovirus E1A protein acts within the nucleus to regulate transcription through its ability to bind to other proteins. The herpes simplex type 1 virus VP16 protein acts within the nucleus to control transcription by binding to DNA in conjunction with cellular proteins. The human T-cell leukemia virus Tax protein influences transcription through interactions with cellular proteins in the nucleus as well as the cytoplasm.

Promoter activation via a cyclic AMP response element in vitro

Transcription activation via activating transcription factor cyclic AMP response element binding (ATF/CREB) sites in vitro was explored using transcription and permanganate assay for open complex formation. These sites were used to drive transcription from an adenovirus major late core sequence. Under conditions where activation is strong, 20-50-fold, ATF/CREB is required for preinitiation complexes to reach the open complex stage. Complete opening requires activator, ATP, and initiating nucleotides. In exploration of postinitiation steps, no stimulation of promoter clearance was observed but a modest stimulation of the rate of continuous transcription occurred. High amounts of DNA template, commonly used in in vitro studies, allows some templates to open without activator, but leaves the nucleotide requirements intact. This leads to a drastic lowering of the dependence on ATF/CREB. Taken together, the data indicate that ATF/CREB activates this system primarily by stimulating the formation of functional preinitiation complexes.

Synergistic activation of transcription by the mutant and wild-type minimal transcriptional activation domain of VP16

VP16 activates transcription by stimulating initiation, and for this function the aromatic residue at position 442 within its activation domain is critical. Recent studies have suggested that VP16 also stimulates transcriptional elongation. It has been shown that VP16 can activate transcription tethered downstream of the transcription start site to RNA. Here, we analyze the synergistic activation features of hybrid VP16 fusion proteins when tethered simultaneously to RNA downstream of the start site and to DNA upstream of a promoter in order to investigate its role in postinitiation control of transcription. Upon targeting the VP16 activation domain simultaneously to both DNA and RNA, high levels of transcriptional synergism is observed. Importantly, a transcription-defective VP16 minimal activation domain (amino acids 413-453) mutated at critical residue 442 (phenylalanine --> proline) maintained synergism, when bound to RNA, with the DNA-bound wild-type VP16 minimal activation domain. Targeting of this "functionally defective" VP16 minimal activation domain via RNA and an intact activation domain via DNA allowed us to uncover a postinitiation activity for VP16 not previously detected in DNA targeting studies. We suggest that, in addition to stimulating initiation, VP16 also acts at a postinitiation step involving residues other than the critical residue at position 442 within the same 41-amino acid minimal activation domain (amino acids 413-453) required for initiation.

Critical amino acids in the transcriptional activation domain of the herpesvirus protein VP16 are solvent-exposed in highly mobile protein segments. An intrinsic fluorescence study

Eukaryotic transcriptional regulatory proteins typically comprise both a DNA binding domain and a regulatory domain. Although the structures of many DNA binding domains have been elucidated, no detailed structures are yet available for transcriptional activation domains. The activation domain of the herpesvirus protein VP16 has been an important model in mutational and biochemical studies. Here, we characterize the VP16 activation domain using time-resolved and steady-state fluorescence. Unique intrinsic fluorescent probes were obtained by replacing phenylalanine residues with tryptophan at position 442 or 473 of the activation domain of VP16 (residues 413-490, or subdomains thereof), linked to the DNA binding domain of the yeast protein GAL4. Emission spectra and quenching properties of Trp at either position were characteristic of fully exposed Trp. Time-resolved anisotropy decay measurements suggested that both Trp residues were associated with substantial segmental motion. The Trp residues at either position showed nearly identical fluorescence properties in either the full-length activation domain or relevant subdomains, suggesting that the two subdomains are similarly unstructured and have little effect on each other. As this domain may directly interact with several target proteins, it is likely that a significant structural transition accompanies these interactions.

Abortive initiation and first bond formation at an activated adenovirus E4 promoter

Abortive initiation at the adenovirus E4 promoter was studied by following the production of RNA formed from the initiating nucleotides UpA and CTP. Formation of a specific short RNA via a reaction with appropriate alpha-amanitin sensitivity required promoter, activator, and ATP. In the absence of any of these, an alpha-amanitin-resistant reaction led to lower levels of a product of unknown origin. The alpha-amanitin-sensitive reaction required open promoter complexes, as assayed directly by permanganate probing. This reaction was not blocked by the inhibition of polymerase C-terminal domain kinase activity or by the lack of DNA supercoiling. Thus, formation of the initial bond of the mRNA appears to require activator and ATP to open the DNA but not phosphorylation of the polymerase C-terminal domain. In addition, the abortive initiation reaction was strongly suppressed when all elongation substrates were present, suggesting that cycling to produce high amounts of abortive product is strongly disfavored during productive initiation at this promoter.

A role for activator-mediated TFIIB recruitment in diverse aspects of transcriptional regulation

BACKGROUND

Transcription by RNA polymerase II in eukaryotic cells requires the ordered assembly of general transcription factors on the promoter to form a preinitiation complex. Transcriptional activator proteins (activators) stimulate transcription by increasing the rate and/or extent of preinitiation complex assembly. We have shown previously that acidic activators increase the stable association of TFIIB on the promoter, a process we refer to as 'recruitment'. In this study, we provide evidence that diverse activators facilitate TFIIB assembly by a related mechanism. We then investigate the activator-mediated assembly of TFIIB with regard to two aspects of transcription: the distance-dependence of activator function, and reinitiation.

RESULTS

We have previously described amino-acid-substitution mutants of TFIIB that are able to support an activator-independent basal level of transcription but do not respond to acidic activators. We now show that these mutants also do not respond to other classes of activators. We demonstrate that this defect is due to a failure of the activators to recruit the mutant TFIIB to the promoter. Activators often lose activity as their distance from the initiation site is increased. We show that this impaired transcriptional activity correlates with a decrease in TFIIB recruitment. Finally, we find that following the initiation of transcription, TFIIB dissociates from the promoter, requiring the activator-mediated reassembly of TFIIB in the preinitiation complex for each new round of transcription.

CONCLUSION

We have provided evidence that diverse activators recruit TFIIB to the promoter by a related mechanism. This central step in transcriptional activation is sensitive to promoter architecture, and is required for each new round of transcription.

Nucleotide requirements for activated RNA polymerase II open complex formation in vitro

The role of nucleotides in activated RNA polymerase II transcription was studied. Permanganate footprinting confirmed that there is a strict nucleotide requirement for forming open promoter complexes that cannot be overcome by the addition of a dinucleotide primer corresponding to the start site sequence. However, higher concentrations of other nucleoside triphosphates can substitute for ATP in catalyzing open complex formation. Opening catalyzed by these nucleotides is inhibited by the ATP analogue adenosine 5'-O-(thio-triphosphate), suggesting that they may function through cross-binding to the ATP site. The KM for ATP for opening and the involvement of other nucleotides in opening differs from the characteristics reported for TFIIH helicase and C-terminal domain kinase activities. This raises the possibility that opening does not involve these activities. The results alleviate very significantly the considerable current uncertainty concerning the role of ATP in the mammalian mRNA transcription initiation pathway.

Activator-induced conformational change in general transcription factor TFIIB

Transcriptional activator proteins (activators) function, at least in part, by increasing preinitiation complex assembly (for reviews see refs 1-4). Previous studies have shown that an acidic activator forms a contact with the general transcription factor TFIIB (refs 5-7) and recruits it into the preinitiation complex. Mutational studies indicate that this interaction between the acidic activator and TFIIB is required for transcriptional stimulation. We show here that the acidic activator-TFIIB interaction has an additional function in preinitiation complex assembly. We provide evidence that in native TFIIB the amino- and carboxy-terminal domains are engaged in an intramolecular interaction. The acidic activator disrupts this intramolecular interaction to expose binding sites for general transcription factors that enter the preinitiation complex through association with TFIIB. Thus, the acidic activator induces a conformational change in TFIIB that drives preinitiation complex assembly forward.