James Chuang
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View article: Context-dependent neocentromere activity in synthetic yeast chromosome VIII
Context-dependent neocentromere activity in synthetic yeast chromosome VIII Open
Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synt…
View article: Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in <i>Saccharomyces cerevisiae</i>
Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in <i>Saccharomyces cerevisiae</i> Open
Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans as an integral member of the RNA polymerase II elongation complex. Several studies have shown that Spn1 functions as a histone chap…
View article: Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in <i>Saccharomyces cerevisiae</i>
Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in <i>Saccharomyces cerevisiae</i> Open
Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans as an integral member of the RNA polymerase II elongation complex. Several studies have shown that Spn1 functions as a histone chap…
View article: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability
Cooperative assembly confers regulatory specificity and long-term genetic circuit stability Open
In eukaryotes, links in gene regulatory networks are often maintained through cooperative self-assembly between transcriptional regulators (TRs) and DNA cis-regulatory motifs, a strategy widely thought to enable highly specific regulatory …
View article: Essential histone chaperones collaborate to regulate transcription and chromatin integrity
Essential histone chaperones collaborate to regulate transcription and chromatin integrity Open
Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. Three conserved and essential chaperones, Spt6, Spn1/Iws1, and FACT, associate with elongating RNA polymerase II and…
View article: Essential histone chaperones collaborate to regulate transcription and chromatin integrity
Essential histone chaperones collaborate to regulate transcription and chromatin integrity Open
SUMMARY Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. We have discovered that the physical interaction between two essential histone chaperones, Spt6 and Spn1/Iws…
View article: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae Open
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broa…
View article: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in<i>Saccharomyces cerevisiae</i>
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in<i>Saccharomyces cerevisiae</i> Open
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in S. cerevisiae, we demonstrate that Spn1 broadly influen…
View article: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae Open
All data analyses supporting our preprint "The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae". Reproduce the figures of the paper starting from raw da…
View article: Spt6 Is Required For The Fidelity Of Promoter Selection
Spt6 Is Required For The Fidelity Of Promoter Selection Open
All data analyses supporting our publication "Spt6 is required for the fidelity of promoter selection". Reproduce the figures of the paper starting from raw data, as well as thousands of figures and analyses that aren't shown. See README.m…
View article: Spt6 Is Required For The Fidelity Of Promoter Selection
Spt6 Is Required For The Fidelity Of Promoter Selection Open
All data analyses supporting our preprint "Spt6 is required for the fidelity of promoter selection". Reproduce the figures of the paper starting from raw data, as well as thousands of figures and analyses that aren't shown. See README.md f…
View article: Spt6 is required for the fidelity of promoter selection
Spt6 is required for the fidelity of promoter selection Open
SUMMARY Spt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although Spt6 is viewed as an elongation factor, spt6 mutations in Saccharomyces cerevisiae allow elevated levels of transcripts from…
View article: Spt6 Is Required For The Fidelity Of Promoter Selection
Spt6 Is Required For The Fidelity Of Promoter Selection Open
All data analyses supporting our preprint "Spt6 is required for the fidelity of promoter selection". Reproduce the figures of the paper starting from raw data, as well as thousands of figures and analyses that aren't shown. See README.md f…
View article: Coordinated regulation of acid resistance in Escherichia coli
Coordinated regulation of acid resistance in Escherichia coli Open
Our data suggest that the regulatory network underlying AR is complex and deeply interconnected with the regulation of GABA and glutamate metabolism, nitrogen metabolism. These connections underlie and experimentally validated model of AR1…
View article: Additional file 3: of Coordinated regulation of acid resistance in Escherichia coli
Additional file 3: of Coordinated regulation of acid resistance in Escherichia coli Open
Peaks called and bound and gene expression data for Nac. (XLSX 466 kb)
View article: Additional file 4: of Coordinated regulation of acid resistance in Escherichia coli
Additional file 4: of Coordinated regulation of acid resistance in Escherichia coli Open
Peaks called for NtrC. (XLSX 11.1 kb)
View article: Additional file 2: of Coordinated regulation of acid resistance in Escherichia coli
Additional file 2: of Coordinated regulation of acid resistance in Escherichia coli Open
Peaks called and bound and gene expression data for CsiR. (XLSX 410 kb)
View article: Additional file 5: of Coordinated regulation of acid resistance in Escherichia coli
Additional file 5: of Coordinated regulation of acid resistance in Escherichia coli Open
Peaks called and gene expression data for ompR. (XLSX 28.0 kb)
View article: Versatile genetic assembly system (VEGAS) to assemble pathways for expression in<i>S. cerevisiae</i>
Versatile genetic assembly system (VEGAS) to assemble pathways for expression in<i>S. cerevisiae</i> Open
We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae. Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform …