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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-Seq of six mammals tissues: liver, muscle, testes with antibody against RNA polymerase III

ABSTRACT: Homologous vertebrate tissues express a highly conserved set of transcribed genes; paradoxically, expression of tRNAs that are required to translate mRNAs into proteins have been reported to be divergent. To resolve this paradox, we mapped the genome-wide occupancy of pol III in primary tissues isolated from six mammals. We confirmed that the specific tRNA genes bound by pol III, as well as the extent and stability of binding, can vary substantially among mammalian tissues, and we discovered that this divergence is far greater between species. We combined pol III occupancy from genomically discrete tRNA loci into collective binding into isoacceptor classes and then into amino acid-based isotype classes, and at each step we found increasing conservation. At the level of amino acid isotypes, pol III binding is almost invariant among all the tissues and species profiled. Thus, the basal transcriptional machinery is constrained collectively in its synthesis of functional tRNA isotypes, despite rapid divergence of polymerase binding to specific tRNA genes. Part of experiment series: RNA-Seq E-MTAB-424, ChIP-Seq E-MTAB-957

ORGANISM(S): Homo sapiens

SUBMITTER: Gordon Brown

PROVIDER: E-MTAB-958 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-Seq of six mammals

Project description:Homologous vertebrate tissues express a highly conserved set of transcribed genes; paradoxically, expression of tRNAs that are required to translate mRNAs into proteins have been reported to be divergent. To resolve this paradox, we mapped the genome-wide occupancy of pol III in primary tissues isolated from six mammals. We confirmed that the specific tRNA genes bound by pol III, as well as the extent and stability of binding, can vary substantially among mammalian tissues, and we discovered that this divergence is far greater between species. We combined pol III occupancy from genomically discrete tRNA loci into collective binding into isoacceptor classes and then into amino acid-based isotype classes, and at each step we found increasing conservation. At the level of amino acid isotypes, pol III binding is almost invariant among all the tissues and species profiled. Thus, the basal transcriptional machinery is constrained collectively in its synthesis of functional tRNA isotypes, despite rapid divergence of polymerase binding to specific tRNA genes. Part of experiment series: RNA-Seq E-MTAB-424, ChIP-Seq E-MTAB-958

2011-07-29 | E-MTAB-424 | biostudies-arrayexpress

[E-MTAB-442] ChIP-seq of mouse liver with no antibody to provide input sequences for ChIP experiments on C57BJ/6J mice

Project description:Odom_mouse_C57BL6J_input This experiment provides chromatin immunoprecipitation input sequences (i.e. no antibody was added during the ChIP protocol), suitable for use as input for ChIP experiments on C57BJ/6J mice. ArrayExpress Release Date: 2011-03-01 Publication Title: Pol III occupancy of tRNA genes is highly divergent between loci but highly conserved by amino acid isotypes Publication Author List: Claudia Kutter; Gordon D. Brown; Stephen Watt; Michael D. Wilson; Angela Goncalves; Robert J. White, Duncan T. Odom Person Roles: submitter Person Last Name: Brown Person First Name: Gordon Person Mid Initials: D Person Email: gordon.brown@cancer.org.uk Person Phone: +44(0)1223404275 Person Address: Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK Person Affiliation: CRUK-CRI

2011-07-14 | GSE30604 | GEO

Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs [ChIP-Seq]

Project description:Alu SINEs are the most numerous frequently occurring transcription units in our genomes and possess sequence competence for transcription by RNA Pol III. However, through poorly understood mechanisms, the Alu RNA levels are maintained at very low levels in normal somatic cells with obvious benefits of low rates of Alu retrotransposition and energy-economical deployment of RNA Pol III to the tRNA genes which share promoter structure and polymerase requirements with Alu SINEs. Using comparative ChIP sequencing, we unveil that a repeat binding protein, CGGBP1, binds to the transcriptional regulatory regions of Alu SINEs thereby impeding Alu transcription by inhibiting RNA Pol III recruitment. We show that this Alu-silencing depends on growth factor stimulation of cells and subsequent tyrosine phosphorylation of CGGBP1. Importantly, CGGBP1 ensures a sequence-specific discriminative inhibition of RNA Pol III activity at Alu promoters, while sparing the structurally similar tRNA promoters. Our data suggest that CGGBP1 contributes to growth-related transcription by preventing the hijacking of RNA Pol III by Alu SINEs. Examination of one DNA binding protein in two different conditions of treatment.

2015-04-29 | E-GEOD-53571 | biostudies-arrayexpress

A Multiplicity of Factors Contributes to Selective RNA polymerase III occupancy of a Subset of RNA polymerase III Genes in Mouse Liver

Project description:The genomic loci occupied by RNA polymerase (pol) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitation experiments followed by deep sequencing (ChIP-Seq). These studies have in particular shown that only about 40 % of the annotated 622 human tRNA genes and pseudogenes are occupied by pol III, and that these genes are often in regions of open chromatin rich in active pol II transcription units. Here we have used ChIP-Seq to characterize pol III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver pol III-occupied loci and point to a conserved pol III-occupied mammalian interspersed repeat (MIR) as a potential regulator of a pol III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse pol III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence can strongly affect pol III occupancy of tRNA genes. They reveal correlations with various genomic features that together describe the pol III occupancy scores over some 50% of tRNA genes. In mouse liver, pol III-occupied loci represented in the NCBI37/mm9 genome assembly comprise fifty 5S genes, fourteen known non-tRNA genes, nine 4.5S genes, and some twenty nine SINEs. In addition, out of the 433 annotated tRNA genes, half are occupied by pol III. Transfer RNA gene expression levels reflect both an underlying genomic organization that is conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes. 12 samples examinded, 4 on pol III, 2 on pol II, 2 on H3K4me3, 2 on H3k36me3, 2 input samples.

2012-01-19 | E-GEOD-33421 | biostudies-arrayexpress

A Multiplicity of Factors Contributes to Selective RNA polymerase III occupancy of a Subset of RNA polymerase III Genes in Mouse Liver

2012-01-19 | GSE33421 | GEO

Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs [ChIP-Seq]

2015-04-29 | GSE53571 | GEO

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.

Project description:RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type–specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico–predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome.

2010-04-14 | GSE20309 | GEO

RNA Pol III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

Project description:RNA polymerase III transcribes many noncoding RNAs (e.g. tRNAs) important for translational capacity and other functions. Here, we localized RNA polymerase III, alternative TFIIIB complexes (BRF1/2) and TFIIIC in HeLa cells, determining the Pol III transcriptome, defining gene classes, and revealing ‘TFIIIC-only’ sites. Pol III localization in other transformed and primary cell lines revealed both novel and cell-type specific Pol III loci, and one occupied miRNA. Surprisingly, only a fraction of the in silico-predicted Pol III loci are occupied. Interestingly, many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer binding proteins such as ETS1 and STAT1. Remarkably, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. Taken together, active promoter and enhancer-like chromatin appears to gate Pol III accessibility to the genome.

2010-04-14 | GSE20609 | GEO

RNA Pol III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

2010-04-14 | E-GEOD-20609 | biostudies-arrayexpress

Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [PRO-seq]

Project description:Genome binding/occupancy profiling by high throughput sequencing ｜ Expression profiling by high throughput sequencing | Other Mammalian nuclei contain Pol I, Pol II, and Pol III. However, to what extent and how they are cross-regulated remains elusive. Here, we performed orthogonal multi-omics profiling after acute degradation of the largest subunits of Pol I, Pol II, and Pol III, and showed that they mainly affect specific genes. In contrast, the loss of Pol I or Pol II causes few changes for other RNA polymerases and confirms those known. The changes of Pol II transcription after Pol III depletion are the largest among all the cross-regulatory types. Meta-analyses reveal that Pol III depletion increases nucleosome positioning, reduces the FACT complex occupancy, and perturbs Pol II elongation for nearby mRNA genes. Furthermore, the nucleosome positioning changes also underpinning the Pol II effects on Pol III-mediated tRNA transcription. Our results suggest that Pol III works together with Pol II to coordinate their transcription activities by maintaining local chromatin architecture.

2022-11-07 | GSE181699 | GEO

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