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ABSTRACT: A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration to tRNA genes

PROVIDER: PRJNA597319 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10759005_1.fastq.gz	Fastqsanger.gz
	SRR10759005_2.fastq.gz	Fastqsanger.gz
	SRR10759006_1.fastq.gz	Fastqsanger.gz
	SRR10759006_2.fastq.gz	Fastqsanger.gz
	SRR10759007_1.fastq.gz	Fastqsanger.gz

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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

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern.

2012-01-01 | GSE33986 | GEO

Saccharomyces cerevisiae

Project description:Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

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Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

2012-01-01 | E-GEOD-33986 | biostudies-arrayexpress

LTR-retrotransposon control by tRNA-derived small RNA

Project description:LTR-retrotransposon control by tRNA-derived small RNA

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Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site (Rpc34)

Project description:The Gypsy-like element Ty3 inserts proximal to the transcription start sites of genes transcribed by RNA polymerase 3 (RNAP3). In this study, a random-barcode Ty3 was used to count Ty3 insertions at specific sites. Surprisingly, saturation transposition of the yeast genome showed that tDNAs even within isoacceptor families are targeted at widely different frequencies. Ectopic expression of Ty3 integrase showed that it localizes to integration targets independent of other Ty3 proteins. Binding of integrase, RNAP3 and factor Brf1 at individual targets did not differ to the same extent as integration. Metadata analysis showed that histone modification H3K4Ac correlated positively with insertion frequency. Targeting frequency could be reconstituted on high copy plasmids containing only 75 bp of 5’ flanking sequence plus the tDNA target. Weighting of insertions according to frequency identified an A/T-rich sequence followed by C as the site of gene-proximal strand transfer. This site lies immediately adjacent to the adenines of the RNAP3 transcription start site motif (CAA). Recent structures of DNA in RNAP3 initiation complexes show that in the initiation complex the transcription start site is sharply bent at the position adjacent to the gene-proximal Ty3 strand transfer. We propose that Ty3 integration occurs in two steps: in the first, host Brf1 engages integrase; in the second, integrase exploits YR flexibility, and that together, these steps determine the wide range of Ty3 targeting frequencies.

2018-04-15 | GSE97893 | GEO

Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site (Integrase)

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Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site (Brf1)

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Arabidopsis thaliana

Project description:Centrophilic retrotransposon integration via targeting CENH3 chromatin in Arabidopsis

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