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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Saccharomyces cerevisiae S288C

SUBMITTER: Amna LAIDIN

PROVIDER: E-MTAB-9038 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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: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

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

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

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

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

MAF1 Represses CDKN1A through a Pol III-Dependent Mechanism

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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

Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [seq]

Project description:Nuclear pores associate with active protein-coding genes in yeast and have been implicated in transcriptional regulation. Here, we show that in addition to transcriptional regulation, key components of C. elegans nuclear pores are required for processing of a subset of small nucleolar RNAs (snoRNAs) and tRNAs transcribed by RNA Polymerase (Pol) III. Chromatin immunoprecipitation of NPP-13 and NPP-3, two integral nuclear pore components, and importin-M-CM-^_ IMB-1, provides strong evidence that this requirement is direct. All three proteins associate specifically with tRNA and snoRNA genes undergoing Pol III transcription. These pore components bind immediately downstream of the Pol III pre-initiation complex, but are not required for Pol III recruitment. Instead, NPP-13 is required for cleavage of tRNA and snoRNA precursors into mature RNAs, whereas Pol II transcript processing occurs normally. Our data suggest that integral nuclear pore proteins act to coordinate transcription and processing of Pol III transcripts in C. elegans. Genome-wide ChIP-seq and ChIP-chip were performed in mixed-stage C. elegans embryos for nuclear pore proteins NPP-13, NPP-3, IMB-1 and chromatin proteins Pol III (RPC-1), TBP-1, TFC-1 (SFC-1), TFC-4 (TAG-315), and Pol II (AMA-1). For RPC-1 and TBP-1 ChIP-seq, embryos depleted for NPP-13 were also used. Total RNAs from wild-type, NPP-13 RNAi, and IMB-1 RNAi embryos were analyzed by RNA-seq.

2013-09-05 | E-GEOD-42714 | biostudies-arrayexpress

Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [array]

2013-09-05 | E-GEOD-42651 | biostudies-arrayexpress

MAF1 Represses CDKN1A through a Pol III-Dependent Mechanism

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2015-06-10 | E-GEOD-42239 | biostudies-arrayexpress

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