Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

54 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-on-chip of Sgs1 and gammaH2A and DNA:RNA hybrids in wild type and SGS1 mutants

ABSTRACT: Sgs1 is a DNA helicase with roles in DNA replication and repair. DNA repair proteins have been linked to genome instability in part by altering the landscape of DNA:RNA hybrids. Here, we mapped the Sgs1 binding profile along with the profile of DNA:RNA hybrids and gammaH2A genome-wide in an effort to identify direct vs indirect effects of Sgs1 in DNA:RNA hybrid and gammaH2A distribution. The wild type DNA:RNA hybrid sample was reported previously in E-MTAB-2388.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Maria Aristizabal

PROVIDER: E-MTAB-5582 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

MRE11-RAD50-NBS1 activates Fanconi Anemia R-loop suppression at transcription-replication conflicts

Project description:Rad50 is a component of the conserved MRE11-RAD50-NBS1 (MRN) complex, which functions in genome stability and the cell’s ability to deal with stalled DNA replication forks. We identified Rad50 as a factor important for R-loop tolerance and thus mapped DNA:RNA hybrids in Rad50KO cells and compare them to previously reported wild-type and Sgs1KO profiles.

2019-10-31 | E-MTAB-7885 | biostudies-arrayexpress

DNA:RNA Immunoprecipitation and Tiling Microarray (DRIP-chip)

Project description:Experiment to obtain the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation and tiling microarray (DRIP-chip). Samples: wild type, Rnase H deletion mutant, hpr1 deletion mutant, sen1-1 temperature sensitive mutant.

2014-05-06 | E-MTAB-2388 | biostudies-arrayexpress

The RNAPII-CTD Maintains Genome Integrity Through Inhibition of Retrotransposon Gene Expression and Transposition

Project description:ChIP-chip by array of S. cerevisiae cells to investigate the genome wide occupancy of phospho-S2 and phospho-S5 forms of the RNAPII-CTD. ChIP-chip by array of S. cerevisiae cells to investigate the genome wide occupancy of Ste12 and Tec1.

2015-11-28 | E-MTAB-3906 | biostudies-arrayexpress

ChIP-chip by array of H2BK123ub, H3K4me3, H3K36me3, H3K79me3, and H3K79me2 using Affymetrix tiling arrays.

Project description:Genome-wide mapping of H2BK123ub, H3K4me3, H3K36me3, H3K79me3, and H3K79me2 using Affymetrix tiling arrays.

2011-12-08 | E-MEXP-3217 | biostudies-arrayexpress

Dot1 and Histone H3K79 Methylation in Natural Heterochromatic and HML-HMR Silencing

Project description:ChIP-on-Chip of Sir proteins in WT and dot1 deletion strains

2011-02-09 | E-MEXP-3108 | biostudies-arrayexpress

Chromatin immunoprecipitation in dot1 deletion and G1 or G2 arrested yeast cells to identify methylation patterns

Project description:To define the molecular regulators required for differential pattern of H3K79 methylation by Dot1, we performed a GPS screen and discovered that the components of the cell cycle-regulated SBF complex were required for normal levels of H3K79 di- but not trimethylation. Genome-wide mapping revealed that H3K79 di- and trimethylation to present a mutually exclusive pattern on chromatin with M/G1 cell-cycle-regulated genes significantly enriched for H3K79 dimethylation. Since H3K79 trimethylation requires prior monoubiquitination of H2B, we performed genome-wide profiling of H2BK123 monoubiquitination and showed that H2BK123 monoubiquitination is excluded from cell cycle regulated genes and sites containing H3K79me2 but not from H3K79me3 containing regions. A genome-wide screen for factors responsible for the establishment/removal of H3K79 dimethylation resulted in the identification of several genes including NRM1 and WHI3, which both impact the transcription by the SBF, and MBF complexes, further linking the regulation of H3K79's methylation status to the cell cycle.

2009-10-19 | E-MEXP-2273 | biostudies-arrayexpress

Eaf7 identifies a native protein trimer linked to RNA polymerase-coupled nucleosome recycling

Project description:The NuA4 histone acetyltransferase (HAT) complex is required for gene specific regulation, cell cycle progression, and DNA repair. Dissection of the 13-subunit complex reveals that the Eaf7 subunit bridges Eaf5 with Eaf3, a H3K36me3-binding chromodomain protein, and this Eaf5/7/3 trimer is anchored to NuA4 through Eaf5. This subcomplex represents a functional module as deletions of these genes create similar phenotypes and a large portion of the trimer exists in a native form outside the NuA4 complex. Gene-specific and genome-wide location analyses indicate that the Eaf5/7/3 trimer correlates with transcription activity and is enriched over the coding region. In agreement with a role in transcription elongation, the Eaf5/7/3 trimer interacts with phosphorylated RNA polymerase II and helps its progression. In addition, loss of Eaf5/7/3 partially suppresses intragenic cryptic transcription arising in set2 mutant cells, suggesting a role in nucleosome destabilization. Such a function is supported by genetic interactions with the FACT histone chaperone. On the other hand, loss of the trimer leads to an increase of replication-independent histone exchange over the coding region of transcribed genes. Taken together, these results lead to a model where Eaf5/7/3 associates with elongating polymerase and is involved in the disassembly of nucleosomes in front of the polymerase, but also in their recycling in its wake.

2014-09-25 | E-MTAB-1780 | biostudies-arrayexpress

Effect of truncating the RNAPII CTD on RNAPII genome-wide association

Project description:ChIP-chip by array of Rpb3 localization in yeast with different CTD lenghts and with or without CDK8 deletion to determine the role of CTD length and Cdk8 on RNAPII localization

2013-12-30 | E-MTAB-1341 | biostudies-arrayexpress

Genomewide occupancy changes of transcription associated factors as a result of truncating the RNAPII CTD

Project description:ChIP-chip by array localization of Cdk8, TFIIB, Cet1, Elf1 and Histone H3 Lysine 36 trimethylation in yeast

2014-01-21 | E-MTAB-1379 | biostudies-arrayexpress

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq

Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of mRNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.

2011-12-22 | E-GEOD-34655 | 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