35 datasets found

Cells are constantly under attack by a plethora of DNA damaging agents that arise from both exogenous and endogenous sources. To deal with this threat to cell and organism...

Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes

We report the development of a versatile strategy to map nucleosomes in multiple model organisms Overall design: Nucleosome positoining data (MNase-seq) from S. cerevisiae...

The transcriptome profiles of S. cerevisiae S288C and ScL1 knockout strain cultured under normal conditions</p><p>The transcriptome profiles of S. pombe 972h- and...

Arrays of regularly spaced nucleosomes dominate chromatin and are often phased, i.e., aligned at reference sites like active promoters. How distances between nucleosomes and...

Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet mechanistic details of this evolution remain elusive. By comparing the...

Coccidioidomycosis (Valley Fever) is an emerging endemic fungal infection with a rising incidence and an expanding geographic range. It is caused by Coccidiodes, which are...

Most genetic changes have negligible reversion rates. As most mutations that confer resistance to an adversary condition (e.g., drug treatment) also confer a growth defect in...

DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae we demonstrate that centromeric DNA...

We developed a high throughput 5’P sequencing approach (HT-5PSeq) to investigate 5'P mRNA degradome in relation with translation process. This approach is easy and scalable and...

Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these...

Structural analysis of chromosome folding in vivo has been revolutionized by Chromosome Conformation Capture (3C) and related methods, which use proximity ligation to identify...

We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel...

We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq. Overall design: ATAC-seq was performed on...

The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome...

Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe Overall design: Illumina sequencing of mononucleosomal DNA...

APA mechanisms in S. pombe and S. cerevisiae are largely different, distinctly impacting gene expression, antisense transcripts and 3’UTR evolution, and core processing factors...

It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and...

We measured global expression profiles in SFP1 deletion mutants and isogenic wild type strains during lag and log phase growth. To match the physiology of each species as well...

We applied the ribose-seq and Ribose-Map techniques to study biological signatures of ribonucleotide incorporation in the genomic DNA of budding and fission yeast. We found that...