Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Polygenic and directional regulatory evolution across pathways in Saccharomyces

ABSTRACT: We assess the prevalence of polygenic evolution in pathways between the yeasts S. cerevisiae and S. bayanus. We first established short-read sequencing methods to detect cis-regulatory variation in a diploid hybrid between the species. We then formulated an analytic strategy to test for the scenario in which selective pressure in one species, to increase or decrease the activity of a pathway, has driven the accumulation of cis-regulatory variants that act in the same direction on gene expression. Application of this test revealed a variety of yeast pathways with evidence for directional regulatory evolution. Measurement of allele-specific expression of each ortholog in a diploid hybrid between Saccharomyces species

ORGANISM(S): Saccharomyces bayanus x Saccharomyces cerevisiae

SUBMITTER: Rachel Brem

PROVIDER: E-GEOD-19837 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Polygenic and directional regulatory evolution across pathways in Saccharomyces.

Bullard James H JH Mostovoy Yulia Y Dudoit Sandrine S Brem Rachel B RB

Proceedings of the National Academy of Sciences of the United States of America 20100301 11

The search to understand how genomes innovate in response to selection dominates the field of evolutionary biology. Powerful molecular evolution approaches have been developed to test individual loci for signatures of selection. In many cases, however, an organism's response to changes in selective pressure may be mediated by multiple genes, whose products function together in a cellular process or pathway. Here we assess the prevalence of polygenic evolution in pathways in the yeasts Saccharomy ...[more]

PMID: 20194736

Similar Datasets

Ribo-seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation to determine effects on translation.

2021-09-30 | E-MTAB-9094 | biostudies-arrayexpress

Genome-wide mapping of meiotic double-strand breaks by sequencing Spo11 oligos.

Project description:The nonrandom distribution of meiotic recombination shapes patterns of inheritance and genome evolution, but chromosomal features governing this distribution are poorly understood. Formation of the DNA double-strand breaks (DSBs) that initiate recombination results in accumulation of Spo11 protein covalently bound to small DNA fragments. We show here that sequencing these fragments provides a genome-wide DSB map of unprecedented resolution and sensitivity. We use this map to explore the influence of large-scale chromosome structures, chromatin, transcription factors, and local sequence composition on DSB distributions. Our analysis supports the view that the recombination terrain is molded by combinatorial and hierarchical interaction of factors that work on widely different size scales. Mechanistic aspects of DSB formation and early processing steps are also uncovered. This map illuminates the occurrence of DSBs in repetitive DNA elements, repair of which can lead to chromosomal rearrangements. We discuss implications for evolutionary dynamics of recombination hotspots. We deep sequenced 4 samples of Spo11 oligos on Roche 454 platform. Three samples are technical replicates of Spo11 oligo products prepared from one meiotic culture and the fourth sample was prepared from an independent culture.

2011-03-07 | E-GEOD-26449 | biostudies-arrayexpress

Identification of Golgin Imh1 phosphorylation residues under ER stress in yeast

Project description:The accumulation of misfolded proteins in the endoplasmic reticulum (ER) induces the unfolded protein response (UPR), which acts through various mechanisms to reduce ER stress. We previously found ER stress induced by tunicamycin (TM) treatment promotes the activation of small GTPase Arl1 and thereby increasing the recruitment of downstream effector golgin Imh1 to the late-Golgi. However, the role of Imh1 under ER stress remains unknown. In this study, we found Imh1 is required for the recycling of two SNAREs, Snc1 and Tlg1, upon TM-induced ER stress. Due to Imh1 is already known as phosphorylation protein, we wonder whether phosphorylation play roles in regulating the function of Imh1 under ER stress. We utilized SILAC method to identify the phosphorylation sites on Imh1 upon TM treatment through MS analysis and found several sites increased phosphorylation under ER stress. We finally selected the predominant S25/T27 phosphorylated residues and study the mechanism of how S25/T27 phosphorylation regulates the function of Imh1 in SNARE transport upon TM treatment.

2022-07-21 | PXD031562 | Pride

Investigating the upstream signaling of Imh1 phosphorylation under ER stress in yeast

Project description:The accumulation of misfolded proteins in the endoplasmic reticulum (ER) induces the unfolded protein response (UPR), which acts through various mechanisms to reduce ER stress. We previously found ER stress induced by tunicamycin (TM) treatment promotes the activation of small GTPase Arl1 and thereby increasing the recruitment of downstream effector golgin Imh1 to the late-Golgi. However, the role of Imh1 under ER stress remains unknown. In this study, we found Imh1 is required for the recycling of two SNAREs, Snc1 and Tlg1, upon TM-induced ER stress and phosphorylation of Imh1 is required for this regulation. Since Ire1 is the sensor of UPR in yeast and we previous found that Ire1 is required for Arl1-Imh1 activation, we wonder whether Ire1 signaling is also responsible for the TM-induced phosphorylation of Imh1 and the subsequent SNARE transport. We compared the phosphorylation signal of Imh1 in WT with that in the absence of Ire1 and further performed SILAC method in a label swap replication. Collectively, this study illustrates the mechanism of how signaling under ER stress promotes Imh1 in cooperation with another tether factor in regulating the SNARE transport to alleviate ER stress in yeast cells.

2022-07-21 | PXD031563 | Pride

Analysis of P-body (Dcp1) and Stress Granule (Pbp1) RNA content

Project description:Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. Here we perform RIP-seq to determine the RNA interactors of Dcp1 (PB marker) and Pbp1 (SG marker) before and after an appropriate glucose stress.

2021-09-30 | E-MTAB-9096 | biostudies-arrayexpress

A high resolution map of a cyanobacterial transcriptome

Project description:Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation (ChIP) sequencing. We report absolute transcript levels, operon identification, and high-resolution mapping of 5' and 3' ends of transcripts. We identify several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination. Furthermore, we identify many putative non-coding transcripts. We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription. RNA Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 RNA polymerase ChIP Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 Tiling Microarray of the cyanobacterium Synechococcus elongatus PCC 7942

2011-05-16 | E-GEOD-29264 | biostudies-arrayexpress

Nucleosomes are context-specific, H2A.Z modulated barriers to RNA polymerase

Project description:Nucleosomes are barriers to transcription in vitro, however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA Polymerase II (RNAPII) at nucleotide resolution. Our results suggest that nucleosomes present significant, context-specific barriers to RNAPII in vivo that can be tuned by the incorporation of H2A.Z. 8 sets of two replicates each of paired-end and 3 sets of two replicates each of single-end samples were sequenced and analyzed.

2014-03-06 | E-GEOD-49106 | biostudies-arrayexpress

Transcription profiling of a S96xSK1 yeast cross and its pool of spores.

Project description:To dissect local regulation into cis and trans contribution, we measured allelic differential expression in a hybrid cross of two yeast strains and compared it against allelic differential expression in a pool of spores of the same cross. RNA- and DNA-seq of a diploid S. cerevisiae hybrid and its haploid spores.

2015-02-04 | E-GEOD-61553 | biostudies-arrayexpress

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [ChIP-Seq data]

Project description:Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks. ChIP Sequencing of the Schizosaccharomyces pombe 972h- transcription factor Pho7-TAP in high-Pi, no-Pi, and csk1M-NM-^T conditions

2013-01-02 | E-GEOD-39498 | biostudies-arrayexpress

Genomic maps of homotypic H2Av, heterotypic H2Av, input and 80mM salt soluble chromatin from Drosophila S2 cells

Project description:Nucleosomes that contain the histone variant H2A.Z are enriched around transcriptional start sites in many organisms. A single octameric nucleosome can contain two H2A.Z histones (homotypic) or one H2A.Z and one canonical H2A (heterotype). We generated high-resolution maps of homotypic and heterotypic Drosophila H2A.Z (H2Av) nucleosomes. Although homotypic and heterotypic H2Av nucleosomes map throughout most of the genome, homotypic nucleosomes are enriched and heterotypic nucleosomes are depleted downstream of active promoters and intron/exon boundaries. The distribution of homotypic H2A.Z nucleosomes resembles that of salt-soluble nucleosomes and shows evidence of displacement during transcriptional elongation. Homotypic nucleosomes are also depleted downstream of paused polymerases, where salt-soluble nucleosomes are conspicuously depleted. Our results suggest a model whereby H2A.Z enrichment patterns result from different structural interactions within the core of heterotypic and homotypic nucleosomes following disruption during transcriptional elongation. We analyzed two replicates for input, heterotypic and homotypic purifications. We sequenced one library for each of the single H2Av pulldown and 80mM salt soluble samples.

2010-11-01 | E-GEOD-21615 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data