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Genome sequencing and annotation studies clearly highlight the impact of transcriptional regulation in plants. However, functional characterization of the majority of transcriptional regulators remains elusive. Hence, high-throughput techniques are required to facilitate their molecular analysis. Here, we provide a detailed protocol to conduct a high-throughput protoplast trans-activation (PTA) screening, which enables simultaneous analysis of up to 95 individual transcription factor activities on a customizable promoter:LUCIFERASE reporter. This system is well suited to decipher complex transcriptional networks such as that triggered by the phytohormone auxin.

Antimicrobial peptides and proteins (AMPs) are tools of the innate immune system employed at injury sites to protect the host from invading microbes and to promote wound repair. In this issue, Roupé et al. characterize epidermal innate immune responses induced by skin injury and the involvement of EGFR for distinct AMPs and IL-8 induction.

In this study, we examine the role of three highly conserved putative binding sites for Myc-associated zinc finger protein (MAZ) in regulation of the human SOX3 gene expression. Electrophoretic mobility shift and supershift assays indicate that complexes formed at two out of three MAZ sites of the human SOX3 promoter involve ubiquitously expressed MAZ protein. Furthermore, in cotransfection experiments we demonstrate that MAZ acts as a positive regulator of SOX3 gene transcription in both undifferentiated and RA-differentiated NT2/D1 cells. Although MAZ increased both basal and RA-induced promoter activity, our results suggest that MAZ does not contribute to RA inducibility of the SOX3 promoter during neuronal differentiation of NT2/D1 cells.

The interaction and binding abilities between the trans -activation response (TAR) element, residues 1–59 of the human immunodeficiency virus type 1 (HIV-1) mRNA, and four computer-simulated designed potentially small-molecule drugs were studied by capillary zone electrophoresis (CZE). Experimental results indicated that these computer-simulated small-molecule drugs could specifically bind to TAR RNA and effectively inhibit the complex formation of HIV-1 trans -activator of transcription (Tat) protein to TAR RNA – an essential component for HIV-1 transcription. The small molecular inhibitors and TAR RNA could be baselinely separated for each individual drug under optimized CE experimental conditions. Their binding constants were quantitatively determined and the data were used for the drug evaluation and screen in lead discovery.

Attempts to demonstrate trans-activation activity by the Drosophila myb gene product (D-Myb) have been unsuccessful so far. We demonstrate that co-transfection of Schneider cells with a plasmid expressing the Drosophila homologue of transcriptional co-activator CBP (dCBP) results in trans-activation by D-Myb. Using this assay system, the functional domains of D-Myb were analyzed. Two domains located in the N-proximal region, one of which is required for DNA binding and the other for dCBP binding, are both necessary and sufficient for trans-activation. In this respect, D-Myb is similar to c-Myb and A-Myb, but different from mammalian B-Myb. These results shed light on how the myb gene diverged during the course of evolution.

Background Human bocavirus (HBoV), a parvovirus, is suspected to be an etiologic agent of respiratory disease and gastrointestinal disease in humans. All mRNAs of HBoV1 are transcribed from a single promoter. Methods In this study, we constructed EGFP and luciferase reporter gene vectors under the control of the HBoV1 full promoter (nt 1–252) and its mutated variants, respectively. Fluorescence microscopy was used to observe expression activities of the EGFP. Dual-luciferase reporter vectors were employed in order to evaluate critical promoter elements and the effect of NS1 protein on promoter activity. Results The HBoV1 promoter activity was about 2.2-fold and 1.9-fold higher than that of the CMV promoter in 293 T and HeLa cells, respectively. The putative transcription factor binding region of the promoter was identified to be located between nt 96 and nt 145. Mutations introduced in the CAAT box of the HBoV1 promoter reduced promoter activity by 34%, whereas nucleotide substitutions in the TATA box had no effect on promoter activity. The HBoV1 promoter activities in 293 T and HeLa cells, in the presence of NS1 protein, were 2- to 2.5-fold higher than those in the absence of NS1 protein. Conclusion The HBoV1 promoter was highly active in 293 T and HeLa cell lines, and the sequence from nt 96 to nt 145 was critical for the activity of HBoV1 promoter. The CAAT box, in contrast to the TATA-box, was important for optimum promoter activity. In addition, the transcriptional activity of this promoter could be trans-activated by the viral nonstructural protein NS1 in these cells.

Human immunodeficiency virus (HIV types 1 and 2) replication is controlled by the interaction of viral-encoded regulatory proteins and host cellular proteins with the viral long terminal repeat (LTR). The presence of HIV-1 and HIV-2 trans-activator proteins, tat1 and tat2, respectively, greatly increases viral gene expression from their homologous LTRs. It is unclear if the cellular factors that support tat1-directed trans-activation of the HIV-1 LTR are the same for tat2 trans-activation of the HIV-2 LTR. Human-Chinese hamster ovary hybrid cell clones were used to probe for human chromosomes involved in regulating HIV-1 and HIV-2 tat-directed transactivation. DNA transfection experiments showed that the presence of human chromosome 12 in human-hamster hybrid clones was necessary for high-level tat-directed trans-activation of the HIV-1 and -2 LTR. Cross-trans-activation of the HIV-2 LTR by tat1 was found to be chromosome 12 independent. In addition, chromosome 12 did not support trans-activation of another human retrovirus (human T-cell leukemia virus type I). Our results suggest that HIV-1 and -2 have evolved to employ a cellular pathway(s) encoded on human chromosome 12 for supporting homologous tat-directed trans-activation. Trans-activation of the HIV-2 LTR by tat1 in chromosome 12-minus cells suggests that multiple cellular pathways can be recruited to trans-activate the HIV-2 LTR and that these pathways may have been important in an HIV-like progenitor virus.

Replication of human immunodeficiency virus type 1 (HIV-1) is controlled by a variety of viral and host proteins. The viral protein Tat acts in concert with host cellular factors to stimulate transcriptional elongation from the viral long terminal repeat (LTR) through a specific interaction with a 59-residue stem-loop RNA known as the trans-activation responsive element (TAR). Inhibitors of Tat-TAR recognition are expected to block transcription and suppress HIV-1 replication. In previous studies, we showed that 2'-O-methyl (OMe) oligonucleotide mixmers containing locked nucleic acid (LNA) residues are powerful steric block inhibitors of Tat-dependent trans-activation in a HeLa cell reporter system. Here we compare OMe/LNA mixmer oligonucleotides with oligonucleotides containing tricyclo-DNAs and their mixmers with OMe residues in four different assays: (1) binding to the target TAR RNA, (2) Tat-dependent in vitro transcription from an HIV-1 DNA template directed by HeLa cell nuclear extract, (3) trans-activation inhibition in HeLa cells containing a stably integrated firefly luciferase reporter gene under HIV-1 LTR control, and (4) an anti-HIV beta-galactosidase reporter assay of viral infection. Although tricyclo-DNA oligonucleotides bound TAR RNA more weakly, they were as good as OMe/LNA oligonucleotides in suppressing in vitro transcription and trans-activation in HeLa cells when delivered by cationic lipid. No inhibition of in vitro transcription and trans-activation in HeLa cells was observed for tricyclo-DNA/OMe mixmers, even though their affinities to TAR RNA were strong and their cell distributions did not differ from oligonucleotides containing all or predominantly tricyclo-DNA residues. Tricyclo-DNA 16-mer showed sequence-specific inhibition of beta-galactosidase expression in an anti-HIV HeLa cell reporter assay.

We have previously identified two homologous groups of BnDREBs in Brassica napus, the trans-active BnDREBI and the trans-inactive BnDREBII, which provided an ideal system to study the trans-activation of DREB1/CBF. Deletion analysis indicated that the two additional regions in BnDREBI contributed little to the transcriptional activity. Domain swapping analysis indicated that all the domains contributed to the activity of BnDREBI, including the ERF/AP2 DNA binding domain. Through site-directed mutagenesis, we identified nine residues that were involved in the activity of BnDREBI, among which six residues are specific to BnDREBI, and three are common to DREB1A.

P-TEFb, cyclin T1 + CDK9, is needed for the expression of cellular promoters and primate lentiviral long terminal repeats (LTRs). Curiously, cellular and lentiviral promoters differ dramatically in the requirements for positive transcriptional elongation factor (P-TEF) b activity. Lentiviral LTRs, but not cellular promoters, need an RNA-associated P-TEFb/Tat/TAR (trans-activation-responsive) RNA ternary complex. Ternary complex defective murine cycT1 is apparently inactive for lentiviral transcription. Why P-TEFb requires Tat/TAR for LTRs but not for cellular promoters remains unknown. To explore this question, we sought to determine whether DNA targeting of murine and human cyclin T1 can reconstitute a Tat/TAR-independent activity to the HIV-1 LTR. In the absence of Tat and TAR, we found that both HuCycT1 and MuCycT1 can robustly activate the HIV-1 LTR. We further showed that Sp1 is necessary and sufficient for this DNA-targeted activity. Thus, like cellular promoters, HIV-1 LTR can use P-TEFb function without a Tat/TAR RNA complex. This activity could explain recent findings of robust HIV-1 replication in rat cells that cannot form a P-TEFb/Tat/TAR moiety.

Skeletal muscle is an attractive target for gene therapies to treat either local or systemic disorders, as well as for genetic vaccination. An ideal expression system for skeletal muscle would be characterized by high level, extended duration of expression and muscle specificity. Viral promoters, such as the cytomegalovirus (CMV) promoter, produce high levels of transgene expression, which last for only a few days at high levels. Moreover, many promoters lack muscle tissue specificity. A muscle-specific skeletal alpha-actin promoter (SkA) has shown tissue specificity but lower peak activity than that of the CMV promoter in vivo. It has been reported in vitro that serum response factor (SRF) can stimulate the transcriptional activity of some muscle-specific promoters. In this study, we show that co- expression of SRF in vivo is able to up-regulate SkA promoter-driven expression about 10-fold and CMV/SkA chimeric promoter activity by five-fold in both mouse gastrocnemius and tibialis muscle. In addition, co-expression of transactivator with the CMV/SkA chimeric promoter in muscle has produced significantly enhanced duration of expression compared with that shown by the CMV promoter-driven expression system. A dominant negative mutant of SRF, SRFpm, abrogated the enhancement to SkA promoter activity, confirming the specificity of the response. Since all the known muscle-specific promoters contain SRF binding sites, this strategy for enhanced expression may apply to other muscle-specific promoters in vivo.

Acquired immunodeficiency syndrome (AIDS) is a result of replication of the human immunodeficiency virus type 1 (HIV-1) predominantly in CD4+ T lymphocytes and macrophages. However, most of these cells in vivo are immunologically quiescent, a condition restricting HIV-1 replication. Vpr is an HIV-1 virion protein suspected to enhance HIV-1 replication in vivo. We demonstrate in this report that Vpr specifically activates HIV-1 long terminal repeat (LTR)-directed transcription. This effect is most pronounced on a minimal promoter from HIV-1 LTR containing the TATA box and binding motifs for the ubiquitous cellular transcription factor Sp1. Evidence is presented that Vpr interacts with Sp1 when Sp1 is bound to the Sp1 motifs within the HIV-1 LTR Both Vpr-Sp1 interaction and Vpr trans-activation require a central Leu/Ile-rich domain in Vpr. Our findings suggest that Vpr trans-activation through Sp1 is most critical for the immediate early transcription of HIV-1 when other positive regulators, such as NF-kappa B, are limited or inactive, a condition presumably present in vivo. By interacting with Sp1, Vpr also has the potential to influence cellular gene expression and cellular functions. Thus, therapeutic approaches directed toward blocking the Vpr trans-activation function could prove valuable in treating AIDS.

The regulation of HIV gene expression is a complex process involving the interaction of viral regulatory gene products and host cell factors. The Tat gene has been shown to play an essential role in the positive regulation of viral gene expression (6, 9). HIV-1 Tat mediates its effect through a sequence termed TAR, which has been genetically defined to reside in the R region of the LTR (19). The TAR region is present in the leader sequence of all viral encoded RNAs, as well as both ends the proviral DNA. The boundaries of HIV-1 TAR are +1 to +80 (where +1 indicates the initiation of transcription). The TAR region has the potential to fold into a stem-loop secondary structure when transcribed into RNA.

The viral trans-activator protein, tat, stimulates HIV trans-cription by recognizing the transactivation-responsive region (TAR). Genetic experiments have shown that TAR is a cis-acting element which is located immediately downstream of the transcription start site, between nucleotides +1 and +59 (Dayton et al., 1986; Rosen et al., 1986; Fisher et al., 1986; Hauber et al., 1987; Muesing et al., 1987).

Retroviruses first attracted attention as the etiological agents of tumors in various animals, including birds, rodents and primates. The retrovirus-induced tumors comprise above all T- and B-cell leukemias/lymphomas, chronic myelogenous leukemia and mammary carcinomas, and are characterized by a long latent period between infection and manifestation of the disease. Since their detection, oncogenic retroviruses have been the object of intense study contributing to our knowledge of basic mechanisms and molecular events involved in carcinogenesis in general. An essential step in the retrovirus life cycle is the covalent integration of the double-stranded DNA copy of viral RNA into the cellular genome, forming the provirus. The proviruses are quite stable and are generally a permanent acquisition for the cellular genome. Therefore, the presence of the provirus can have profound genetic implications for the host cell. There are at least three main routes that are assumed to lead to retroviral oncogenesis: Transduction of cell-derived oncogenes (v-onc) carried by some retroviruses, activation of cellular proto-oncogenes (c-onc) in cis by insertional mutation or activation of cellular genes in trans by virus encoded transcription factors.

Dynamics of imidazole binding to tetra-p-sulfophenylporphinatochromium(III) have been investigated as a function of hydrogen ion concentration Labile substitution of imidazole at axial position is shown to be due to trans activation by the bound hydroxide ion. Rate of addition of a second dazole, to form a bis complex, was found to be slower than the substitution of the first imidazole. Neither imidazolium nor the anion of imidazole was found to react with the Cr(III) porphyrin.

Human T-cell leukemia virus type I (HTLV-l) is the first human retrovirus to be well established (1, 2) and is associated with a unique T-cell malig­ nancy-adult T-cell leukemia (ATL) (3). Since the ATL and HTLV-l show the same geographic distribution (4, 5, 6) and patients with ATL are always infected with HTLV-I, it has been expected that HTLV-l would provide a direct clue to understanding the mechanism of tumorigenesis in humans. It was also expected that studies on HTLV-l would provide strategies for diagnosis, treatment, and prevention of ATL. Studies on HTL V-I and the related viruses have progressed rapidly, largely as the result of technologies developed in research on animal retroviruses. New aspects of the retroviruses have been discovered, including a novel mech­ anism of leukemogenesis. This chapter reviews recent advances in the molecular biology of HTL V -1, focusing on the activation of viral and cellular gene expression.

The transcription initiation signals for retroviruses lie within the long terminal repeat (LTR) sequences that flank the integrated provirus. This study shows that factors present in cells infected with bovine leukemia virus (BLV) mediate transcriptional trans activation of the BLV LTR. This phenomenon is similar to that reported for the human T-cell leukemia virus LTR and establishes both structural and functional criteria for inclusion of BLV and human T-cell leukemia viruses in the same family of transforming retroviruses., SCOPUS: ar.j, info:eu-repo/semantics/published

Even though transcription factors (TFs) are central players of gene regulation and have been extensively studied, their regulatory trans‐activation domains (tADs) often remain unknown and a systematic functional characterization of tADs is lacking. Here, we present a novel high‐throughput approach tAD‐seq to functionally test thousands of candidate tADs from different TFs in parallel. The tADs we identify by pooled screening validate in individual luciferase assays, whereas neutral regions do not. Interestingly, the tADs are found at arbitrary positions within the TF sequences and can contain amino acid (e.g., glutamine) repeat regions or overlap structured domains, including helix–loop–helix domains that are typically annotated as DNA‐binding. We also identified tADs in the non‐native reading frames, confirming that random sequences can function as tADs, albeit weakly. The identification of tADs as short protein sequences sufficient for transcription activation will enable the systematic study of TF function, which—particularly for TFs of different transcription activating functionalities—is still poorly understood.