Profiling the thermodynamic softness of adenoviral promoters.

We showed previously that anharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of functional significance. The nine known promoters from human adenovirus type 5 were analyzed for inherent DNA softness using the Peyrard-Bishop-Dauxois model and a statistical mechanics approach, using a transfer integral operator. We found a loosely defined pattern of softness peaks distributed both upstream and downstream of the transcriptional start sites, and that early transcriptional regions tended to be softer than late promoter regions. When reported transcription factor binding sites were superimposed on our calculated softness profiles, we observed a close correspondence in many cases, which suggests that DNA duplex breathing dynamics may play a role in protein recognition of specific nucleotide sequences and protein-DNA binding. These results suggest that genetic information is stored not only in explicit codon sequences, but also may be encoded into local dynamic and structural features, and that it may be possible to access this obscured information using DNA dynamics calculations.

Genes invoked in the ovarian transition to menopause.

Menopause and the associated declines in ovarian function are major health issues for women. Despite the widespread health impact of this process, the molecular mechanisms underlying the aging-specific decline in ovarian function are almost completely unknown. To provide the first gene-protein analysis of the ovarian transition to menopause, we have established and contrasted RNA gene expression profiles and protein localization and content patterns in healthy young and perimenopausal mouse ovaries. We report a clear distinction in specific mRNA and protein levels that are noted prior to molecular evidence of steroidogenic failure. In this model, ovarian reproductive aging displays similarities with chronic inflammation and increased sensitivity to environmental cues. Overall, our results indicate the presence of mouse climacteric genes that are likely to be major players in aging-dependent changes in ovarian function.

Capacitance-derived dielectric constants demonstrate differential preinitiation complexes in TBP-independent and TBP-dependent transcription.

The electronic properties of proteins and DNA may change dramatically upon complex formation, yet there are not many experimental methods which can be used to measure these properties. It has been previously shown that measuring the capacitance of a solution containing interacting DNA and protein species can yield information about changing dipole moments. The measured dielectric constant relates directly to the dipole moment of the complexes in solution. Here, we apply this method to partial transcription initiation complexes in order to investigate the changing electronic properties in the transcriptional preinitiation complex. These experiments are the first reported observations relating to the overall dipole moment and its changes in preinitiation complex formation. Comparing results from TBP-independent and TBP-dependent transcriptional systems shows a divergence in the electronic properties of built-up transcription complexes, suggesting that they initiate transcription by significantly different electronic and structural pathways.

DNA dynamically directs its own transcription initiation.

It has long been known that double-stranded DNA is subject to temporary, localized openings of its two strands. Particular regions along a DNA polymer are destabilized structurally by available thermal energy in the system. The localized sequence of DNA determines the physical properties of a stretch of DNA, and that in turn determines the opening profile of that DNA fragment. We show that the Peyrard-Bishop nonlinear dynamical model of DNA, which has been used to simulate denaturation of short DNA fragments, gives an accurate representation of the instability profile of a defined sequence of DNA, as verified using S1 nuclease cleavage assays. By comparing results for a non-promoter DNA fragment, the adenovirus major late promoter, the adeno-associated viral P5 promoter and a known P5 mutant promoter that is inactive for transcription, we show that the predicted openings correlate almost exactly with the promoter transcriptional start sites and major regulatory sites. Physicists have speculated that localized melting of DNA might play a role in gene transcription and other processes. Our data link sequence-dependent opening behavior in DNA to transcriptional activity for the first time.

Auto-acetylation of transcription factors as a control mechanism in gene expression.

We have shown that the human general transcriptional factor IB (TFIIB) auto-acetylates specifically at lysine 238 in the presence of acetyl coenzyme A in vitro. This is the first case of acetylation of a transcription factor in the absence of a factor acetyltransferase (FAT). Acetylation of TFIIB results in a stronger interaction with transcription factor IIF (TFIIF) and activated transcription in vitro. Cells transfected with mutant TFIIB incapable of auto-acetylation show decreased levels of transcription in vitro. If auto-acetylation of TFIIB occurs in cells, acetyl coenzyme A levels may play an important role in the regulation of transcription. In addition, we report for the first time that the RAP30 subunit of TFIIF is also auto-acetylated in the presence of acetyl coenzyme A in a pH-dependent manner, similarly to TFIIB. This finding strongly suggests that auto-acetylation may be more important in regulating gene expression than previously believed.

Transcription factor IIB acetylates itself to regulate transcription.

Acetylation is a well-known regulatory post-translational modification, but a biological function for acetylation in regulating basal transcription factors has not been reported. Here we show that the general transcription factor TFIIB, which is required for the initiation of eukaryotic polymerase II transcription, is acetylated. TFIIB is also an autoacetyltransferase, although it shares no sequence homology with any known acetyltransferases. In the absence of other enzymes, it binds acetyl-coenzyme A (acetyl-CoA), and catalyses the transfer of the acetyl group onto a specific lysine residue (K238). Both recombinant and cellular TFIIB can autoacetylate, markedly stabilizing the interaction between TFIIB and transcription factor TFIIF and activating transcription in vitro and in cells. A K238A mutant, which cannot be autoacetylated, does not show this activation of transcription. Our findings suggest that there is a regulatory pathway controlling acetylation of TFIIB, and they link acetyl-CoA with basal gene transcription.

YY1 is regulated by O-linked N-acetylglucosaminylation (O-glcNAcylation).

YY1 is a zinc finger DNA-binding transcription factor that influences expression of a wide variety of cellular and viral genes. YY1 is essential for the development of mammalian embryos. It regulates the expression of genes with important functions in DNA replication, protein synthesis, and cellular response to external stimuli during cell growth and differentiation. How YY1 accomplishes such a variety of functions is unknown. Here, we show that a subset of the nuclear YY1 appears to be O-GlcNAcylated regardless of the differentiation status of the cells. We found that glucose strongly stimulates O-linked N-acetylglucosaminylation (O-GlcNAcylation) on YY1. Glycosylated YY1 no longer binds the retinoblastoma protein (Rb). Upon dissociation from Rb, the glycosylated YY1 is free to bind DNA. The ability of the O-glycosylation on YY1 to disrupt the complex with Rb leads us to propose that O-glycosylation might have a profound effect on cell cycle transitions that regulate the YY1-Rb heterodimerization and promote the activity of YY1. Our observations provide strong evidence that YY1-regulated transcription is very likely connected to the pathway of glucose metabolism that culminates in the O-GlcNAcylation on YY1, changing its function in transcription.

YY1-DNA interaction results in a significant change of electronic context as measured by capacitance.

The detailed mechanism behind the processes of DNA-dependent RNA transcription initiation is largely unknown. When transcription initiation factors bind DNA, a significant change in the electrostatic state of the complex can result. Using electrical capacitance measurements of solutions of the YY1 zinc finger transcription initiation factor and the adeno-associated viral P5 promoter DNA, we observed a specific dielectric change when a protein-DNA complex was formed. We propose that complexation results in electrostatic changes that may trigger the markedly different electrical behavior, and offer a possible explanation for our results.