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Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [ChIP-seq]

ABSTRACT: Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [ChIP-seq]

PROVIDER: PRJNA1071639 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27822300_1.fastq.gz	Fastqsanger.gz
	SRR27822300_2.fastq.gz	Fastqsanger.gz
	SRR27822301_1.fastq.gz	Fastqsanger.gz
	SRR27822301_2.fastq.gz	Fastqsanger.gz
	SRR27822284_1.fastq.gz	Fastqsanger.gz

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Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes

Project description:Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes

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Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [RNA-seq]

Project description:Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [RNA-seq]

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Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [ChIP-seq]

Project description:Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex which is part of the spliceosomal U6 snRNP complex. Here we employ ChIP-seq of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3´-exons. During late exponential phase, we observe a near complete transition of Mediator from these promoters to a position in their 3´-ends, overlapping the Lsm3 binding sites approximately 250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA-seq approach we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their mRNA levels and splicing ratios, indicating that the Mediator and Lsm complexes co-operate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription initiation and splicing.

2024-03-26 | GSE254759 | GEO

Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [RNA-seq]

2024-03-26 | GSE254760 | GEO

Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes

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

2024-03-26 | GSE254761 | GEO

Analysis of ribosomal occupancy with ribosome profiling.

Project description:Analysis of ribosomal occupancy with ribosome profiling.

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Growth regulated co-occupancy of Mediator and Lsm3 at intron-containing ribosomal protein genes

Project description:By employing ChIP-seq of chromatin associated with the Lsm3 subunit of the spliceosomal U6 snRNP complex and Med1 or Med15, subunits of the middle and tail modules of Mediator, respectively, we identified 86 genes co-occupied by both Lsm3 and Mediator.

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Chromatin immunoprecipitation of wide type fission yeast to identify intronic and exonic DNA regions with respect to RNA polymerase II occupancy, histone density and H3K36me3 patterns

Project description:Differential marking of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, histone density and H3K36me3 patterns in fission yeast

2011-03-16 | E-TABM-946 | biostudies-arrayexpress

Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

Project description:The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well-known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). We have previously reported that in the absence of SIR2, a derepressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both, activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.

2025-01-09 | GSE285768 | GEO

MEDIATOR subunit med8 binding in Saccharomyces cerevisiae

Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. Med8-TAP strain ChIPed with IgG beads vs. Input in Saccharomyces cerevisiae

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