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ChIP-seq analysis of yeast Ty1 integrase reveal the role of the AC40 interacting domain in the recruitment at both Pol I and Pol III-transcribed genes

ABSTRACT: ChIP-seq analysis of yeast Ty1 integrase reveal the role of the AC40 interacting domain in the recruitment at both Pol I and Pol III-transcribed genes

PROVIDER: PRJEB38222 | ENA |

REPOSITORIES: ENA

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ChIP-seq analysis of yeast Ty1 integrase reveal the role of the AC40 interacting domain in the recruitment at both Pol I and Pol III-transcribed genes

Project description:In budding yeast, the selective integration of the Ty1 LTR retrotransposon upstream of RNA polymerase III (Pol III)-transcribed genes requires the interaction between the AC40, a common subunit of Pol III and Pol I, and Ty1 integrase (IN1). The AC40/IN1 interaction involves a short sequence, the targeting domain (TD), present in the C-terminal part of IN1. Chip-seq analysis using WT or mutated Ty1 integrase demonstrated that TD is responsible for the recruitment of IN1 at both Pol I and Pol III-transcribed genes. Moreover, the introduction of the C-terminal residues of Ty1 in the Ty5 retrotransposon, which preferentially integrates in heterochromatin at silent mating loci (HMR and HML) and near telomeres, leads to its retargeting at Pol III-transcribed genes.

2020-05-11 | E-MTAB-9038 | biostudies-arrayexpress

Retroelement Ty1 Integrase interactome identified using tandem chromatin affinity purification ( TChAP) after in vivo crosslink in yeast Saccharomyces cerevisiae

Project description:To identify yeast proteins associated with Ty1 integrase (IN) that could regulate Ty1 replication, we co-purified IN partners using the tandem chromatin affinity purification procedure after in vivo cross-link (TChAP), which we developed previously (Nguyen et al. 2014). We first identified RNA Pol I and Pol III complexes and also a small subset of additional evolutionary conserved complexes, including PAF1 (Polymerase-Associated Factor 1),FACT (FAcilitates Chromatin Transcription), the proteasome and the CK2 kinase. We next confirmed that CK2 interacts with Ty1 integrase in vivo and repress Ty1 retromobility. We showed that Ty1 IN is a substrate of CK2 in vitro and identified 12 phosphorylated residues. In vivo approaches showed that only part of the protein was phosphorylated in the cells and did not demonstrate any direct evidence between Ty1 IN phosphorylation and retromobility inhibition.

2022-11-17 | PXD027420 | Pride

Ty1 Integrase Interacts with RNA Polymerase III-specific Subcomplexes to Promote Insertion of Ty1 Elements Upstream of Polymerase (Pol) III-transcribed Genes.

Project description: Not available

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Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (I)

Project description:Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of many examples, the transcription of non-coding RNA genes by RNA polymerase (pol) III is less well characterized. Here we profile the epigenetic features of pol III target genes throughout the human genome. This reveals that the chromatin landscape of pol III-transcribed genes resembles that of pol II templates in many ways, although there are also clear differences. Our analysis also discovered an entirely unexpected phenomenon, namely that pol II co-localizes with the majority of genomic loci that are bound by pol III. Chip-Seq experiments for six samples: Pol III, TFIIIB, TFIIIC, H3K4me3 in HeLa cells and Pol III, S2 phos Pol II in CD4+ cells.

2010-04-25 | E-GEOD-20040 | biostudies-arrayexpress

Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (II)

2010-04-25 | E-GEOD-20071 | biostudies-arrayexpress

Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (II)

2010-04-25 | GSE20071 | GEO

Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (I)

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CLIP-seq analysis of integrase-RNA interactions

Project description:Integrase CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitors and IN K264/266A and R269/K273A mutations Integrase CLIP-seq experiments were conducted by immunoprecipitation of integrase-RNA complexes from fully formed mature and eccentric virus particles. Libraries of RNA molecules bound by integrase were generated and sequenced by Illumina Hi-Seq2000 and 2500 platforms.

2016-08-25 | E-GEOD-83588 | biostudies-arrayexpress

CLIP-seq analysis of integrase-RNA interactions

2016-08-25 | GSE83588 | GEO

TY1-RPB9 ChIP seq datasets of Trypanosoma brucei in 2T1 cells, which were depleted of HAT1 or HAT2 over a time period up to 48 h

Project description:Analysis of the genome-wide distribution of RNA Pol II subunit RPB9, endogenously tagged with 2 x TY1, following depletion of HAT1 or HAT2 over a time period up to 48 h and in WT cells

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