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Heat shock: genomic run-on (GRO) analysis

ABSTRACT: Heat shock: genomic run-on (GRO) analysis

PROVIDER: PRJNA132523 | ENA |

REPOSITORIES: ENA

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Heat shock: genomic run-on (GRO) analysis

Project description:This SuperSeries is composed of the following subset Series: GSE24483: TR heat-shock GSE24484: RA heat-shock Refer to individual Series

2011-04-19 | E-GEOD-24488 | biostudies-arrayexpress

TR heat-shock

2011-04-19 | GSE24483 | GEO

Heat shock stimulates genomic instability and phenotypic variations in yeast

Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genomic instability. In this study, heat-shock-induced genomic alterations were explored in the heterozygous diploid yeast strain JSC25-1. In combination of the whole-genome microarray, the patterns of chromosomal instability induced by heat shock could also be explored at a whole genome level. Using this system, we found heat-shock treatment resulted in hundreds-fold higher rate of genomic alterations, including aneuploidy and loss of heterozygosity (LOH).

2020-05-18 | GSE150711 | GEO

Immediate transcriptional responses to heat shock of plant leaf

Project description:Ambient temperature is one of the most important environment factors that direct all organisms for morphogenesis, metabolisms and growth. Plants have evolved efficient mechanisms adapting temperature fluctuation such as heat stress response (HSR). Although transcriptional regulatory network of plant HSR has been established, little is known on the genome-wide transcriptional changes within first several minutes upon heat shock (HS). To precisely measure the very first wave of transcriptional response to HS, we investigated the nascent RNA and mature mRNA from plant leaf tissue exposure to 5-min HS treatment using global run-on sequencing (GRO-seq) and RNA sequencing (RNA-seq) methods. We found that only a small group of genes were both up- or down-regulated at nascent RNA and mRNA levels. Primed plants that already exposed to a mild heat stress induced a more drastic transcriptomic alteration than naïve plants which had not experienced a heat stress. Group A1 HEAT SHOCK TRANSCRIPTION FACTORs (HsfA1s) are the major transcription factors in charge of the very early transcriptional HSR. Within 5-minute HS, we also observed that: 1) Engaged RNA polymerase II (Pol II) was accumulated downstream of transcription start sites; 2) 5' pause-release is a rate limiting step for induction of some heat shock protein genes; 3) A good number of genes switched transcription modes; 4) Pervasive read-through was induced at terminators. Plants' HSR is transcriptionally very quick. GRO-seq is sensitive and robust to detect quick response to HS. Heat stress memory takes place at multiple steps of transcription cycles such as Pol II recruitment, 5' pausing, elongation and termination.

2020-07-11 | GSE128698 | GEO

TR heat-shock

Project description:Within a GRO experiment, samples for Transcription rate (TR) analysis were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC) and subjected to run-on. Analysis was done in filters also used for RA analysis of aliquots from the same cultures. The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.

2011-04-19 | E-GEOD-24483 | biostudies-arrayexpress

Heat shock: genomic run-on (GRO) analysis

Project description:This SuperSeries is composed of the SubSeries listed below.

2011-04-19 | GSE24488 | GEO

GRO analysis of rap1-sil, tpk1 & tpk2.

Project description:GRO (Genomic run-on) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome. Keywords: Genomic run-on GRO

2009-08-24 | GSE14080 | GEO

Heat shock stimulates genomic instability and phenotypic variations in yeast

Project description:Heat shock stimulates genomic instability and phenotypic variations in yeast

| PRJNA633359 | ENA

Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain required for efficient transcription of heat shock genes

Project description:RNA polymerase II is decreased on heat shock-induced genes when the CTD phosphatase Fcp1 is knocked down in Drosophila S2 cells. We examined transcriptionally-engaged Pol II genome-wide with GRO-seq to determine if other genes are similarly affected.

2012-06-29 | GSE38748 | GEO

Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster during heat shock

Project description:Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster. Heat shock factor IP DNA or Mock IP DNA from heat shocked Kc 167 cells compared to whole cell extract on Agilent 2x244k tiling arrays.

2011-01-05 | GSE19744 | GEO

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