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Multidrug resistance (MDR) is a serious complication during treatment of opportunistic fungal infections that frequently afflict immunocompromised individuals, such as transplant recipients and cancer patients undergoing cytotoxic chemotherapy. Improved knowledge of the molecular pathways controlling MDR in pathogenic fungi should facilitate the development(More)
MOTIVATION For the purpose of locating conserved genes in a whole genome scale, this paper proposes a new structural optimization problem called the Mutated Subsequence Problem, which gives consideration to possible mutations between two species (in the form of reversals and transpositions) when comparing the genomes. RESULTS A practical algorithm called(More)
Thinopyrum intermedium is an important species with potential utilization value in breeding of wheat. In this study, the non-coding intergenic region of trnH-psbA was investigated to assess the genetic diversity and infer the maternal origin within T. intermedium accessions. Eleven haplotypes were distinguished among the thirty-five accessions of T.(More)
Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and(More)
We measured half-lives of 21,248 mRNA 3' isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives,(More)
Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3' ends. Here we show that polyadenylated 3' termini in three yeast species (Saccharomyces cerevisiae, Kluyveromyces lactis, and Debaryomyces hansenii) are remarkably heterogeneous. Instead of a few discrete 3' ends, the average yeast gene has an "end zone," a >200 bp window(More)
BACKGROUND The Mediator complex associates with RNA polymerase (Pol) II, and it is recruited to enhancer regions by activator proteins under appropriate environmental conditions. However, the issue of Mediator association in yeast cells is controversial. Under optimal growth conditions (YPD medium), we were unable to detect Mediator at essentially any S.(More)
Extensive sonication of formaldehyde-crosslinked chromatin can generate DNA fragments averaging 200 bp in length (range 75-300 bp). Fragmentation is largely random with respect to genomic region and nucleosome position. ChIP experiments employing such extensively fragmented samples show 2- to 4-fold increased enrichment of protein binding sites over control(More)