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Saccharomyces cerevisiae

ABSTRACT: Cryptic transcription is the primary driving force for nucleosome instability in Spt16 mutant cells

PROVIDER: PRJNA276131 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1813970.fastq.gz	Fastqsanger.gz
	SRR1813980.fastq.gz	Fastqsanger.gz
	SRR1813971.fastq.gz	Fastqsanger.gz
	SRR1813981.fastq.gz	Fastqsanger.gz
	SRR1813962.fastq.gz	Fastqsanger.gz

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Similar Datasets

Cryptic transcription is the primary driving force for nucleosome instability in Spt16 mutant cells

Project description:FACT consists of two essential subunits Spt16 and Pob3 and is a histone chaperone. Depletion of Spt16 using a an spt16 mutant results in a global alteration of nucleosome positions as well as aberrant transcription. Here we show that the majority of nucleosomal changes at gene body upon Spt16 depletion are independent of gene activity, but correlates with cryptic gene transcription and are suppressed by inhibition of RNA Polymerase II activities. In addition, A small fraction of nucleosomal changes is resistant to Pol II inhibition, and Spt16 is enriched at this subgroup of nucleosomes. Moreover, nucleosomes surrounding the initiation sites of cryptic transcription in the spt16 mutant cells are more dynamic than other regions. These results support a model that Spt16 maintains nucleosome stability locally to inhibit the initiation from cryptic transcription, which that once initiated drives additional nucleosome loss upon Spt16 depletion.

2016-05-05 | GSE66215 | GEO

Evidence that cryptic promoters occur extensively throughout the Saccharomyces cerevisiae genome

2008-11-14 | GSE12272 | GEO

Evidence that cryptic promoters occur extensively throughout the Saccharomyces cerevisiae genome

Project description:Microarray analysis was used to identify all cryptic promoters in the S. cerevisiae genome that are activated in spt6 and spt16 mutants. These experiments showed that cryptic initiation is widespread, occurring in approximately 1,000 genes. We generated 2 microarray profiles from fluor-reversed replicates of wild-type and spt6-1004 or spt16-197 mutants. See Cheung et al., (2008) in revision.

2010-05-16 | E-GEOD-12272 | biostudies-arrayexpress

tRNA pool analysis of S. cerevisiae using tRNA-HySeq

Project description:For a typical RNA polymerase (pol) II transcribed budding yeast gene, the 5' -end is characterized by a nucleosome-free region (NFR) immediate upstream of the transcription start site (TSS), flanked by two well-positioned nucleosomes (-1 and +1) containing H2A.Z. A similar arrangement of nucleosomes containing H2A.Z is found on the genes transcribed by pol III, which reside in the NFR actively maintained by the chromatin remodeling complexes. We did genome-wide MNase-seq and ChIP-seq experiments to study the nucleosome arrangement near pol III transcribed genes. We also measured the levels of different tRNAs in the tRNA pool of the wild type and Spt16 mutant (*spt16-197*) cells using tRNA-HySeq method. Although, it is difficult to measure the primary transcripts of tRNA due to their quick processing and the sequence degeneracy of the tRNA isogenes; a comparison of the wild type and Spt16 mutant showed both increase or decrease of tRNA transcripts. The result suggest that Spt16 may not be necessary for the transcription per se of tRNA genes.

2023-12-31 | GSE109527 | GEO

A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae [RNA-seq]

Project description:The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which requires a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription in S. cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, CAF-1, Rtt106, Spt6, and FACT, block transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Collectively, these results demonstrate that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.

2023-12-07 | GSE249580 | GEO

A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae [MNase-seq]

2023-12-06 | GSE249469 | GEO

Saccharomyces cerevisiae

Project description:Genome-wide Localization of Mot1, Spt16, and Nucleosomes in mot1, spt16, and mot1 spt16 cells

| PRJNA318371 | ENA

Saccharomyces cerevisiae

Project description:Analysis of Spt16 depletion

| PRJNA114511 | ENA

Genome-wide profiling of histone chaperone FACT in Saccharomyces cerevisiae

Project description:Spt16-TAP ChIP-seq

2020-12-26 | GSE83086 | GEO

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighbouring genes

Project description:Transcription can be quite disruptive for chromatin so cells have evolved mechanisms to preserve chromatin integrity during transcription, hence preventing the emergence of cryptic transcript from spurious promoter sequences. How these transcripts are regulated and processed by cells remains poorly characterized. Notably, very little is known about the termination of cryptic transcription. Here we used RNA-Seq to identify and characterize cryptic transcripts in Spt6 mutant cells (spt6-1004) in Saccharomyces cerevisiae. We found polyadenylated cryptic transcripts running both sense and anti-sense relative to genes in this mutant. Cryptic promoters were enriched for TATA boxes, suggesting that the underlying DNA sequence defines the location of cryptic promoters. While intragenic sense cryptic transcripts terminate at the terminator of the genes that host them, we found that anti-sense cryptic transcripts preferentially terminate at the 3’-end of upstream genes. These findings led us to demonstrate that most terminators in yeast are bidirectional, leading to termination and polyadenylation of transcripts coming from either direction. We propose that S. cerevisiae has evolved this mechanism in order to prevent spurious transcription from invading neighbouring genes, a feature particularly critical for organisms with small compact genomes.

2017-04-03 | GSE89601 | GEO

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