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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE181701 | GEO | 2022/11/07

REPOSITORIES: GEO

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

Project description:BackgroundMammalian cells have three types of RNA polymerases (Pols), Pol I, II, and III. However, the extent to which these polymerases are cross-regulated and the underlying mechanisms remain unclear.ResultsWe employ genome-wide profiling after acute depletion of Pol I, Pol II, or Pol III to assess cross-regulatory effects between these Pols. We find that these enzymes mainly affect the transcription of their own target genes, while certain genes are transcribed by the other polymerases. Importantly, the most active type of crosstalk is exemplified by the fact that Pol III depletion affects Pol II transcription. Pol II genes with transcription changes upon Pol III depletion are enriched in diverse cellular functions, and Pol III binding sites are found near their promoters. However, these Pol III binding sites do not correspond to transfer RNAs. Moreover, we demonstrate that Pol III regulates Pol II transcription and chromatin binding of the facilitates chromatin transcription (FACT) complex to alter local chromatin structures, which in turn affects the Pol II transcription rate.ConclusionsOur results support a model suggesting that RNA polymerases show cross-regulatory effects: Pol III affects local chromatin structures and the FACT-Pol II axis to regulate the Pol II transcription rate at certain gene loci. This study provides a new perspective for understanding the dysregulation of Pol III in various tissues affected by developmental diseases.

| S-EPMC9703767 | biostudies-literature

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

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

2022-11-07 | GSE181698 | GEO

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

2022-11-07 | GSE181697 | GEO

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

2022-11-07 | GSE181696 | GEO

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

Project description: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 | GSE217478 | GEO

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

2022-11-07 | GSE217477 | GEO

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

Project description:Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture

| PRJNA753068 | ENA

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

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

| PRJNA753069 | ENA

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

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

| PRJNA753072 | ENA

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