Project description:This study compares gene expression in three strains (CPL2H1, CPL2H1 gtf1/gtf1 and CPL2H1 otf1/otf1) with the genetic background of Candida parapsilosis CLIB 214 (CBS 604). Total RNA was isolated using hot acid phenol extraction. A TruSeq stranded mRNA library was sequenced on an Illumina NovaSeq 6000 system.

2021-10-02 | E-MTAB-9442 | biostudies-arrayexpress

RNA-seq of Candida parapsilosis CLIB 214 (CBS 604) grown on different hydroxyaromatic substrates

Project description:Candida parapsilosis CLIB 214 (CBS 604) was grown on synthetic media containing hydroxyaromatic compounds as a sole carbon source. The cells cultivated in medium containing galactose were used as a control. Total RNA was isolated using hot acid phenol extraction. A TruSeq stranded mRNA library was sequenced on an Illumina NovaSeq 6000 system.

2021-10-02 | E-MTAB-9443 | biostudies-arrayexpress

Draft Genome Sequence of Candida railenensis Strain CLIB 1423, Isolated from Papaya Fruit in French Guiana.

Project description: Not available

| S-EPMC9753702 | biostudies-literature

Genome-wide determinants of sequence-specific DNA binding

Project description:DNA binding protein are generally thought to bind specific DNA sequences through selective interactions with DNA bases. However, it is now becoming more widely appreciated that DNA shape, which may not be specified by a unique base sequence, also contributes to site-specific binding. Here we elucidate how DNA sequence and shape confer site specificity on a genomic scale, and relate this to specificity imparted indirectly through occlusion of sequences by the in vivo environment. For simplicity, we focus on the set of General Regulatory Factors (GRFs) that do not rely on other factors for binding. They also serve a related function in organizing chromatin. Remarkably, we find that GRFs will not bind to their cognate motif if the DNA surrounding that sequence lacks a specific shape. While proper DNA sequence/shape properties tend to be restricted to promoter regions, weaker sites that are still binding-competent reside in gene bodies, but are prevented from binding by resident chromatin. Thus, site-specificity is achieved across a genome in vivo by the combined action of favorable DNA sequence and shape interactions, and occlusion by chromatin.

2018-01-16 | GSE93662 | GEO

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