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

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

PROVIDER: PRJNA1071636 | 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
	SRR27822238_1.fastq.gz	Fastqsanger.gz

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Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [RNA-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 | GSE254760 | GEO

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

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

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

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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.

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 that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (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 the 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 ∼250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.

| S-EPMC11194063 | biostudies-literature

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

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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

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