Biomedical subjects

Sara J Zanton

Publications and source records attributed to Sara J Zanton.

6 recordsLinked to original sources

PubMed2006

Nucleosome positions predicted through comparative genomics.

DNA sequence has long been recognized as an important contributor to nucleosome positioning, which has the potential to regulate access to genes. The extent to which the nucleosomal architecture at promoters is delineated by the underlying sequence is now being worked out. Here we use comparative genomics to report a genome-wide map of nucleosome positioning sequences (NPSs) located in the vicinity of all Saccharomyces cerevisiae genes. We find that the underlying DNA sequence provides a very good predictor of nucleosome locations that have been experimentally mapped to a small fraction of the genome. Notably, distinct classes of genes possess characteristic arrangements of NPSs that may be important for their regulation. In particular, genes that have a relatively compact NPS arrangement over the promoter region tend to have a TATA box buried in an NPS and tend to be highly regulated by chromatin modifying and remodeling factors.

DNA, Fungal↗

PubMed2006

Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock.

Eukaryotic genes are controlled by sequence-specific DNA-binding proteins, chromatin regulators, general transcription factors, and elongation factors. Here we examine the genome-wide location of representative members of these groups and their redistribution when the Saccharomyces cerevisiae genome is reprogrammed by heat shock. As expected, assembly of active transcription complexes is coupled to eviction of H2A.Z nucleosomes, and disassembly is coupled to the return of nucleosomes. Remarkably, a large number of promoters assemble into partial preinitiation complexes (partial PICs), containing TFIIA, TFIID (and/or SAGA), TFIIB, TFIIE, and TFIIF. However, RNA polymerase II and TFIIH are generally not recruited, and nucleosomes are not displaced. These promoters may be preparing for additional stress that naturally accompany heat stress. For example, we find that oxidative stress, which often occurs with prolonged exposure of cells to high temperature, converts partial PICs into full PICs. Partial PICs therefore represent novel regulated intermediates that assemble at promoters in the midst of chromatin.

Chromatin↗

PubMed2004

Changes in genomewide occupancy of core transcriptional regulators during heat stress.

Organisms respond to heat stress by reprogramming gene expression. In Saccharomyces cerevisiae, heat-induced genes tend to be regulated by factors that belong to the Spt-Ada-Gcn5 acetyltransferase (SAGA) transcription regulatory pathway, whereas heat-repressed genes tend to be regulated by a parallel pathway involving transcription factor IID (TFIID). Here, we examine whether heat stress affects the occupancy of representative factors of each pathway at promoter regions throughout the yeast genome. Representatives of the SAGA pathway include the TATA binding protein, Spt3, and Mot1. Representatives of the TFIID pathway include the TATA binding protein, TAF1, and Bdf1. We find that heat stress causes disassembly of the TFIID pathway at genes that are inhibited by stress. In contrast, heat induces assembly of the SAGA pathway at stress-induced genes, although many also assemble along the TFIID pathway. Other genes were found to assemble almost exclusively along the TFIID pathway. Strikingly, these genes are lowly transcribed and are generally not induced. Thus, heat stress leads to factor assembly along each pathway but with distinct transcriptional outcomes. Further investigation of these pathways reveals that Bdf1 and Mot1 negatively regulate the SAGA pathway in different ways. The findings suggest that Bdf1 blocks assembly, whereas Mot1 promotes disassembly of the transcription machinery.

Genome, Fungal↗

PubMed2004

Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1.

The Brf1 subunit of TFIIIB plays an important role in recruiting the TATA-binding protein (TBP) to the up-stream region of genes transcribed by RNA polymerase III. When TBP is not bound to promoters, it sequesters its DNA binding domain through dimerization. Promoter assembly factors therefore might be required to dissociate TBP into productively binding monomers. Here we show that Saccharomyces cerevisiae Brf1 induces TBP dimers to dissociate. The high affinity TBP binding domain of Brf1 is not sufficient to promote TBP dimer dissociation but in addition requires the TFIIB homology domain of Brf1. A model is proposed to explain how two distinct functional domains of Brf1 work in concert to dissociate TBP into monomers.

Alleles↗

PubMed2004

Identification and distinct regulation of yeast TATA box-containing genes.

Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive. Applying criteria associated with TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G). Approximately 20% of yeast genes contain a TATA box. Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters. Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions.

Chromatin↗

PubMed2003

Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system.

BACKGROUND: With the invention of the DNA chip, genome-wide analysis is now a reality. Unfortunately, solid-phase detection systems such as the DNA chip suffer from a narrow range in quantification and sensitivity. Today the best methodology for sensitive, wide dynamic range quantification and genotyping of nucleic acids is real-time PCR. However, multiplexed real-time PCR technologies require complicated and costly design and manufacturing of separate detection probes for each new target. METHODS: We developed a novel real-time PCR technology that uses universal energy transfer probes constructed from An Expanded Genetic Information System (AEGIS) for both quantification and genotyping analyses. RESULTS: RNA quantification by reverse transcription-PCR was linear over four orders of magnitude for the simultaneous analysis of beta-actin messenger RNA and 18S ribosomal RNA. A single trial validation study of 176 previously genotyped clinical specimens was performed by endpoint analysis for factor V Leiden and prothrombin 20210A mutation detection. There was concordance for 173 samples between the genotyping results from Invader tests and the AEGIS universal energy transfer probe system for both factor V Leiden and prothrombin G20210A. Two prothrombin and one factor V sample gave indeterminate results (no calls). CONCLUSION: The AEGIS universal probe system allows for rapid development of PCR assays for nucleic acid quantification and genotyping.

Actins↗