RNAPII ChIP-Sequencing of A.thaliana tfiis mutant lines under heat stress conditions
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ABSTRACT:
PROVIDER: PRJNA884835 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNAPII ChIP Sequencing in Col-0 and tfiis mutant lines to elucidate the role of TFIIS during RNAPII mediated transcription
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Project description:The expresion of dominant negative version of Arabidopsis TFIIS (TFIISmut) in plants lacking funtional TFIIS leads to severe growth defects. The genome-wide analysis of changes in active RNAPII occupancy upon TFIISmut expression was determined using ChIP-seq in order to better understand the biological importance of TFIIS. 10DAS seedlings of transgenic lines carring inducible GFP-TFIIS or GFP-TFIISmut transgenes were studied by ChIP-seq following plants exposure to 24h b-estradiol or EtOH (mock) induction.
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Project description:Genome-wide changes in active RNAPII occupancy in the presence of mutated TFIIS (TFIISmut)
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Project description:Rats (n=24) were fed ad libitum diets containing either ground endophyte-free (E-) seed or endophyte–infected (E+) seed for five days at thermoneutrality (21°C) or heat stress (32 C) for 21 days. Rats with intraperitonial transmitters were used with core temperature (Tc) and general activity measured every 5 minutes during the study. At treatment end, the liver was removed, weighed and frozen in liquid nitrogen. RNA was extracted from liver samples, converted to cDNA, and hybridized with the printed oligonucleotide slides. Treatments consisted of four treatment groups, E-TN, E+TN, E-HS, E+HS. E-TN IS control at thermoneutral for 26 days , E+TN toxin fed group at thermoneutral for 26 days; E-HS control at thermoneutral for 5 days and heat treatment for 21 days, E+HS is toxin fed group at thermoneutral for 5 days and heat stress for 21 days. Keywords: Stress response
2007-08-14 | GSE8754 | GEO
Project description:The expresion of dominant negative version of Arabidopsis TFIIS (TFIISmut) in plants lacking funtional TFIIS leads to severe growth defects. The genome-wide analysis of transcriptomic changes upon TFIISmut expression was performed by RNA-seq to better understand the biological importance of TFIIS. 10DAS seedlings of transgenic lines carring inducible GFP-TFIIS or GFP-TFIISmut transgenes were studied by RNA-seq following plants exposure to 24h b-estradiol or EtOH (mock) induction.
2020-03-25 | GSE129072 | GEO
Project description:Connections between RNA polymerase II (RNAPII) transcription stress, R-loops, and genome instability have been established however, the underlying mechanisms remain poorly understood. Here we used a mutant version of elongation factor TFIIS (TFIISmut) to specifically induce increased levels of RNAPII pausing, arrest, and/or backtracking in human cells. TFIISmut expression results in slower elongation rates, relative depletion of polymerases from the end of genes, and increased levels of stopped RNAPII. It affects mRNA splicing and termination as well. Remarkably, however, TFIISmut expression also dramatically increases R-loops, which may form at the anterior end of backtracked RNAPII and trigger genome instability, including DNA strand breaks. These results shed new light on the relationship between transcription stress and R-loops, and suggest that different classes of R-loops exist, potentially with distinct consequences for genome instability.
2019-06-13 | GSE132398 | GEO
Project description:Connections between RNA polymerase II (RNAPII) transcription stress, R-loops, and genome instability have been established however, the underlying mechanisms remain poorly understood. Here we used a mutant version of elongation factor TFIIS (TFIISmut) to specifically induce increased levels of RNAPII pausing, arrest, and/or backtracking in human cells. TFIISmut expression results in slower elongation rates, relative depletion of polymerases from the end of genes, and increased levels of stopped RNAPII. It affects mRNA splicing and termination as well. Remarkably, however, TFIISmut expression also dramatically increases R-loops, which may form at the anterior end of backtracked RNAPII and trigger genome instability, including DNA strand breaks. These results shed new light on the relationship between transcription stress and R-loops, and suggest that different classes of R-loops exist, potentially with distinct consequences for genome instability.
2019-06-13 | GSE132395 | GEO
Project description:Connections between RNA polymerase II (RNAPII) transcription stress, R-loops, and genome instability have been established however, the underlying mechanisms remain poorly understood. Here we used a mutant version of elongation factor TFIIS (TFIISmut) to specifically induce increased levels of RNAPII pausing, arrest, and/or backtracking in human cells. TFIISmut expression results in slower elongation rates, relative depletion of polymerases from the end of genes, and increased levels of stopped RNAPII. It affects mRNA splicing and termination as well. Remarkably, however, TFIISmut expression also dramatically increases R-loops, which may form at the anterior end of backtracked RNAPII and trigger genome instability, including DNA strand breaks. These results shed new light on the relationship between transcription stress and R-loops, and suggest that different classes of R-loops exist, potentially with distinct consequences for genome instability.
2019-06-13 | GSE132391 | GEO
Project description:Many transcription-related proteins are known to be modified by SUMO post-translational modification in yeast, plants, humans and other eukaryotes. We are interested in understanding how cells use sumoylation to regulate transcription of specific genes and globally. To explore this, we carried out ChIP-seq analysis to determine how genomic levels of RNA polymerase II (RNAPII) change when cellular levels of sumoylation are greatly reduced in budding yeast. Compared to wild-type yeast, RNAP occupancy in the sumoylation-deficient ubc9-6 strain was significantly altered for hundreds of genes. Among the genes with the most elevated levels of RNAPII are those involved in translation and ribosome biogenesis, including most ribosomal protein genes. On the other hand, many genes involved in small molecule and amino acid metabolism and biosynthesis showed reduced RNAPII levels in ubc9-6. Exposure of yeast to heat shock is known to cause a widespread change to RNAPII occupancy across the genome. To examine whether cellular sumoylation plays a role in this process, RNAPII ChIP-seq was performed in wild-type and ubc9-6 strains after a brief heat shock. Strikingly, the sumoylation deficient strain showed a far more dramatic redistribution of RNAPII across the genome, with significantly more genes showing a heat-shock induced increase or decrease in RNAPII occupancy. These results imply that cellular sumoylation levels have a significant impact on the regulation of transcription genome-wide, and that normal sumoylation levels are needed to restrain the vast redistribution of RNAPII that occurs in response to heat shock.
2021-09-21 | GSE167424 | GEO