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RNA-seq analysis of the budding yeast set1∆ strain and prp45(1-169) set1∆ double mutant strain

ABSTRACT: RNA-seq analysis of the budding yeast set1∆ strain and prp45(1-169) set1∆ double mutant strain

PROVIDER: PRJEB18555 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1753300_1.fastq.gz	Fastqsanger.gz
	ERR1753300_2.fastq.gz	Fastqsanger.gz
	ERR1753301_1.fastq.gz	Fastqsanger.gz
	ERR1753301_2.fastq.gz	Fastqsanger.gz
	ERR1753302_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

RNA-seq analysis of the budding yeast set1∆ strain and prp45(1-169) set1∆ double mutant strain

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. Because its human ortholog, SNW1/SKIP, is known to functionally and physically interact with factors involved in transcription elongation and chromatin modifications, it was suggested to be one of the coupling factors which functionally connect splicing and transcription. To determine whether yeast Prp45 has this function as well we tested the genetic interactions between prp45(1-169) allele and deletions of histone modifiers and transcription elongation regulators. RNA-seq analysis was performed to address the changes in transcription and/or splicing in strains deleted in set1, a histone methyltransferase responsible for H3K4 methylation, and the corresponding prp45(1-169) set1 double mutant. Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2024-08-30 | E-MTAB-5335 | biostudies-arrayexpress

RNA-seq analysis of the budding yeast rad6 strain and prp45(1-169) rad6 double mutant strain

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. Because its human ortholog, SNW1/SKIP, is known to functionally and physically interact with factors involved in transcription elongation and chromatin modifications, it was suggested to be one of the coupling factors which functionally connect splicing and transcription. To determine whether the yeast Prp45 has this function as well we tested genetic interactions between prp45(1-169) allele and deletions of histone modifiers and transcription elongation regulators. RNA-seq analysis was performed to address the changes in transcription and/or splicing in strains deleted in rad6, a kinase phosphorylating serine 2 of the C-terminal domain of RNA Polymerase II and an E2 enzyme for H2BK123 monoubiquitination, respectively, and the corresponding double mutant with prp45(1-169). Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2024-08-30 | E-MTAB-5336 | biostudies-arrayexpress

Genome-wide maps of Set1 and H3K4me3 in budding yeast

Project description:We report the application of ChIP-sequencing technology for high-throughput profiling of histone modifications in budding yeast. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide maps of Set1 and H3K4me3 in yeast cells. We find that Set1 and H3 lysine 4 trimethylation locate primarily in open reading frame of genes. In addition, we focus on the distribution of Set1 and H3K4me3 in histone gene clusters and found strong similar binding of Set1 and H3K4me3 on all histone genes.

2019-05-02 | GSE115910 | GEO

RNA-seq analysis of the budding yeast prp45(1-169) strain (a scarless truncation)

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. prp45(1-169) is a temperature-sensitive truncation allele expressing only the first 169 amino acids (the full-length protein consists of 379 amino acids). RNA-seq analysis was performed to determine changes in transcription and splicing in cells with prp45(1-169) allele prepared by the CRISPR/Cas9 method as a scarless truncation, i.e. with no tags and with preserved endogenous 3' UTR. Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2024-08-30 | E-MTAB-5334 | biostudies-arrayexpress

Genome-wide maps of Set1 and H3K4me3 in budding yeast

Project description:Genome-wide maps of Set1 and H3K4me3 in budding yeast

| PRJNA476475 | ENA

RNA-seq analysis of the budding yeast ctk1∆ and rad6∆ strains and prp45(1-169) ctk1∆ and prp45(1-169) rad6∆ double mutant strains

Project description:RNA-seq analysis of the budding yeast ctk1∆ and rad6∆ strains and prp45(1-169) ctk1∆ and prp45(1-169) rad6∆ double mutant strains

| PRJEB18556 | ENA

RNA-seq analysis of budding yeast wild type (BY4741) and prp45(1-169) mutant

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. In addition to its documented involvement in the second step of splicing, here we show that it is important in the early stages of co-transcriptional spliceosome assembly as well. To determine the overall splicing efficiency of prp45 mutant cells and to reveal how the efficiency depends on the sequences which define introns (whether they are consensual or non-consensual), we performed RNA-seq analysis of prp45(1-169) and corresponding wild-type cells (two biological replicates each). Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2017-02-10 | E-MTAB-5149 | biostudies-arrayexpress

RNA-seq analysis of the budding yeast prp45(1-169) strain (a "scarless" truncation)

Project description:RNA-seq analysis of the budding yeast prp45(1-169) strain (a "scarless" truncation)

| PRJEB18554 | ENA

Transcriptome analysis of yeast methyltransferase mutants set5∆, set1∆ and set5∆set1∆

Project description:Purpose: Understand the synergistic relationship between the methyltransferases Set1 and Set5 in the regulation of gene expression. Methods: Total mRNA was obtained from two independent biological replicates each of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ S. cerevisiae strains. Libraries were generated and sequenced using an Illumina HiSeq2000 platform. The sequence reads that passed quality filters were mapped using TopHat and expression levels were quantified using Cufflinks. Results: We generated FPKM expression values for each transcript and identified the differentially expressed genes using an FDR-adjusted p-value of 0.05. Subsequent data analysis was restricted to genes with fold-change greater than 1.7 relative to WT. Our results show that Set1 and Set5 have roles primarily in transcription repression. Moreover, lack of both Set1 and Set5 results in a synergistic exhacerbation of the transcriptional derepression observed in the single mutants. Further analysis revealed a specific enrichment of the Set5/Set1-repressed genes near repetitive DNA sequences of the genome. Conclusions: Our study uncovers an unexpected synergistic role of Set1 and Set5 in transcription repression of telomeric regions and Ty retrotransposons. mRNA profiles of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ were generated by sequencing using an Illumina HiSeq2000 platform. Two biological replicates of each strain were used.

2014-01-15 | E-GEOD-52086 | biostudies-arrayexpress

Meiotic DNA double strand breaks in wild-type and set1∆ cells

Project description:In relation with the study of the meiotic dynamic of H3K4 methylation, we determined the meiotic Double Strand Breaks (DSB) profiles of wild-type and set1∆ cells.

2008-11-01 | GSE12879 | GEO

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