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

PROVIDER: PRJEB70781 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12330831_1.fastq.gz	Fastqsanger.gz
	ERR12330831_2.fastq.gz	Fastqsanger.gz
	ERR12330832_1.fastq.gz	Fastqsanger.gz
	ERR12330832_2.fastq.gz	Fastqsanger.gz
	ERR12330833_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.

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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

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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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Analysis of non-coding RNAs in drn1âÂ deletion strains

Project description:The turnover of introns spliced from pre-mRNA occurs first by debranching the lariat intron followed by destruction of the linear intron by other nucleases. We have identified a novel component of intron turnover, DRN1 (YGR093W). In order to identify RNAs affected by Drn1 turnover, we used a microarray containing probes specific to ~400 yeast non-coding RNAs to analyze a strain deleted for Drn1. These data implicated Drn1 in the turnover of a number of introns spliced from ribosomal-protein genes. Two-color experiment with biological replicate and dye swap.

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