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TranscriptomicsRetrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern. TIP-seq recovery of transposon insertion junctio...
ORGANISM(S): Saccharomyces cerevisiae 
2012-01-01 | E-GEOD-33986 | biostudies-arrayexpress
TranscriptomicsExpression data from the partially synthetic yeasts SynIXR-1D, -6B, -22D, and controls.
We have replaced the right arm of chromosome IX in Saccharomyces cerevisiae with a synthetic version to generate synIXR haploids. The synthetic chromosome features multiple sequeunce modifications. We analyzed gene expression by microarray analysis in three synIXR haploids (1D, 6B, and 22D) to dete...
ORGANISM(S): Saccharomyces cerevisiae 
2011-09-13 | E-GEOD-31326 | biostudies-arrayexpress
GenomicsA high-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast
Under continuous, glucose-limited conditions, budding yeast exhibit robust metabolic cycles associated with major oscillations of gene expression and metabolic state. However, how such fluctuations might be coordinately linked to changes in chromatin status is less well understood. Here, we examine ...
ORGANISM(S): Saccharomyces cerevisiae 
2014-08-31 | E-GEOD-52339 | biostudies-arrayexpress
TranscriptomicsThe Transposon Insertion site Profiling Chip (TIP-chip)
We have developed a microarray intended for use in finding all transposons in a region of interest. By selectively amplifying and hybridizing transposon flanking DNA to our array, we can localize all transposons in the region present on our TIP-chip, a dense tiling array. We have tested our technolo...
ORGANISM(S): Saccharomyces cerevisiae 
2010-07-01 | E-GEOD-5646 | biostudies-arrayexpress
TranscriptomicsGate-Keeping transcription through histone H3 K42, a novel site of methylation in the yeast nucleosome core
A new site of methylation was identified on histone H3 K42 in Saccharomyces cerevisiae. Mutations were engineered at this site to mimic either a constitutively modified state, K42L, or a constitutively unmodified state, K42Q in addition to an alanine substitution. K42A. The effects of these mutation...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-27 | E-GEOD-13889 | biostudies-arrayexpress
TranscriptomicsExpression profiles of histone point mutants
Accurate chromosome segregation requires that sister kinetochores biorient and attach to microtubules from opposite poles. Kinetochore biorientation relies on the underlying centromeric chromatin, which provides a platform to assemble the kinetochore and to recruit the regulatory factors that ensur...
ORGANISM(S): Saccharomyces cerevisiae 
2013-12-04 | E-GEOD-39903 | biostudies-arrayexpress
TranscriptomicsA comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation
Histone acetylation and deacetylation are among the principal mechanisms by which chromatin is regulated during transcription, DNA silencing, and DNA repair. We analyzed patterns of genetic interactions uncovered during comprehensive genome-wide analyses in yeast to probe how histone acetyltransfera...
ORGANISM(S): Saccharomyces cerevisiae 
2008-06-11 | E-GEOD-9771 | biostudies-arrayexpress
TranscriptomicsTrivalent arsenic inhibits the functions of chaperonin complex
The goal of this study was to identify yeast mutants with arsenite hypersensitivity. Keywords: dose response Matched pools of yeast knockout (YKO) mutants were grown in paired growth media lacking or containing arsenite at various concentrations. The relative abundances of the YKO mutants were profi...
ORGANISM(S): Saccharomyces cerevisiae 
2010-07-26 | E-GEOD-5973 | biostudies-arrayexpress
TranscriptomicsA genome-wide genetic interaction screen reveals metabolic roles of human histone deacetylase 1
Dynamic acetylation of metabolic proteins has emerged as a ubiquitous post-translational modification of human metabolic proteins. However, the corresponding modifying enzymes and the functions of the modification await exploration. Using a genome-wide synthetic lethality screen, we constructed a ge...
ORGANISM(S): Homo sapiens 
2012-02-10 | E-GEOD-29662 | biostudies-arrayexpress
ProteomicsThe de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging
In the era of synthetic biology, design, construction, and utilization of synthetic chromosomes with unique features provide a new strategy to study complex cellular processes such as aging. Herein, we successfully constructed the 884 Kb synXIII of Saccharomyces cerevisiae to investigate replicative...
ORGANISM(S): Saccharomyces Cerevisiae 
2024-10-30 | PXD057330 |
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