Similar Datasets
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
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
Project description:Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes
| PRJNA1071636 | ENA
Project description:Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [RNA-seq]
| PRJNA1071641 | ENA
Project description:Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [ChIP-seq]
| PRJNA1071639 | ENA
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.
| PRJEB64306 | ENA
Project description:Transcription factors (TFs) act as powerful levers to regulate neural physiology and can be targeted to improve cellular responses to injury or disease. Because TFs often depend on cooperative activity, a major challenge is to identify and deploy optimal sets. Here we developed a bioinformatics pipeline, centered on TF co-occupancy of regulatory DNA, and used it to predict factors that potentiate the effects of pro-regenerative Klf6 in vitro. High content screens of neurite outgrowth identified cooperative activity by 12 candidates, and systematic testing in a mouse model of corticospinal tract (CST) damage substantiated three novel instances of pairwise cooperation. Combined Klf6 and Nr5a2 drove the strongest growth, and transcriptional profiling of CST neurons identified Klf6/Nr5a2-responsive gene networks involved in macromolecule biosynthesis and DNA repair. These data identify TF combinations that promote enhanced CST growth, clarify the transcriptional correlates, and provide a bioinformatics approach to detect TF cooperation.
| S-EPMC8099911 | biostudies-literature
Project description:Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants) and tissue-specifically, have not been successful. We report here the molecular cloning and characterization of seven mouse rDNA variants (v-rDNA). The identification of these v-rDNAs was based on restriction fragment length polymorphisms (RFLPs), which are conserved among individuals and mouse strains. The total copy number of the identified variants is less than 100 and the copy number of each individual variant ranges from 4 to 15. Sequence analysis of the cloned v-rDNA identified variant-specific single nucleotide polymorphisms (SNPs) in the transcribed region. These SNPs were used to develop a set of variant-specific PCR assays, which permitted analysis of the v-rDNAs' expression profiles in various tissues. These profiles show that three v-rDNAs are expressed in all tissues (constitutively active), two are expressed in some tissues (selectively active), and two are not expressed (silent). These expression profiles were observed in six individuals from three mouse strains, suggesting the pattern is not randomly determined. Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA.
| S-EPMC2266999 | biostudies-literature
Project description:Coordinated regulation of ribosomal RNA (rRNA) synthesis and ribosomal protein gene (RPG) transcription by eukaryotic RNA polymerases (RNAP) is a key requirement for growth control. Although evidence for balance between RNPI-dependent 35S rRNA production and RNAPII-mediated RPG transcription have been described, the molecular basis is still obscure. Here, we found that Rph1 modulates the transcription status of both rRNAs and RPGs in yeast. We show that Rph1 widely associates with RNAPI and RNAPII-transcribed genes. Deletion of RPH1 remarkably alleviates cell slow growth caused by TORC1 inhibition via derepression of rRNA and RPG transcription under nutrient stress conditions. Mechanistically, Rim15 kinase phosphorylates Rph1 upon rapamycin treatment. Phosphorylation-mimetic mutant of Rph1 exhibited more resistance to rapamycin treatment, decreased association with ribosome-related genes, and faster cell growth compared to the wild-type, indicating that Rph1 dissociation from chromatin ensures cell survival upon nutrient stress. Our results uncover the role of Rph1 in coordination of RNA polymerases-mediated transcription to control cell growth under nutrient stress conditions.
| S-EPMC7470948 | biostudies-literature
Project description:Parathyroid hormone (PTH) is the major hormone regulating bone remodeling. Binding of PTH to the PTH1 receptor (PTH1R), a heterotrimeric G protein coupled receptor (GPCR), can potentially trigger multiple signal transduction pathways mediated through several different G proteins. In this study, we employed G protein antagonist minigenes inhibiting G?(s), G?(q) or G??? to selectively dissect out which of these G proteins were responsible for effects of PTH(1-34) in targeted signaling and osteogenesis arrays consisting of 159 genes. Among the 32 genes significantly regulated by 24h PTH treatment in UMR-106 osteoblastic cells, 9 genes were exclusively regulated through G(s), 6 genes were solely mediated through G(q), and 3 genes were only controlled through G??. Such findings support the concept that there is some absolute specificity in downstream responses initiated at the G protein level following binding of PTH to the PTH1R. On the other hand, 6 PTH-regulated genes were regulated by both G(s) and G(q), 3 genes were regulated by both G(s) and G??, and 3 genes were controlled by G(s), G(q) and G??. These findings indicate potential overlapping or sequential interactions among different G protein-mediated pathways. In addition, two PTH-regulated genes were not regulated through any of the G proteins examined, suggesting that additional signaling mechanisms may be involved. Selectivity was largely maintained over a 2-48-hour time period. The minigene effects were mimicked by downstream inhibitors. The dissection of the differential effects of multiple G protein pathways on gene regulation provides a more complete understanding of PTH signaling in osteoblastic cells.
| S-EPMC3031163 | biostudies-literature