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High-througput sequencing of the rtel1 mutant

ABSTRACT: High-througput sequencing of the rtel1 mutant

PROVIDER: PRJEB7299 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR613759.fastq.gz	Fastqsanger.gz
	ERR613760.fastq.gz	Fastqsanger.gz
	ERR613761.fastq.gz	Fastqsanger.gz
	ERR613762.fastq.gz	Fastqsanger.gz
	ERR613763.fastq.gz	Fastqsanger.gz

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High-througput sequencing of the rtel1 mutant

Project description:RNA sequencing performed on the root tips of rtel1 mutants and Col-0

2016-09-01 | E-MTAB-2943 | biostudies-arrayexpress

RTEL1 is involved in transcriptional gene silencing and inhibition of heterochromatic DNA methylation

Project description:Transcriptional gene silencing is an essential mechanism for controlling the expression of genes and transposable elements (TEs) and is commonly associated with high levels of DNA methylation. Thus, release of silencing is frequently observed in mutants for genes involved in DNA methylation maintenance. However, studies in Arabidopsis thaliana have revealed that transcriptional repression of some DNA-methylated genes and TEs also relies on repressors that operate through pathways largely independent of DNA methylation. One such pathway appears linked to DNA replication and DNA repair and mutations in factors involved in these processes such as the polymerases alpha, delta and epsilon destabilize silencing. Here, we isolate a new mutant allele of the helicase REGULATOR OF TELOMERE ELONGATION 1 (RTEL1) gene from a genetic screen for TGS-deficient mutants. RTEL1 is highly conserved among eukaryotes and plays an important role in the resolution of DNA secondary structures during DNA replication. We show that rtel1 causes release of TGS without loss of DNA methylation or global changes in chromatin accessibility. However, many heterochromatic loci show increased levels of DNA methylation and chromatin accessibility in rtel1 mutants. Our findings reveal a function for RTEL1 in maintaining silencing and in preventing DNA hypermethylation of heterochromatin.

2023-07-04 | GSE197614 | GEO

Comparative genome-wide transcriptional profile after RTEL1 depletion and G4 stabilisation.

Project description:The goal of this study is to compare the transcription profile of mouse embryonic fibroblasts upon deletion of the helicase RTEL1 and stabilisation of G-quadruplexes (G4) with the G4 stabilisation drug TMPyP4.

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RTEL1 modulates H3 occupancy in heterochromatic regions and acts synergistically with MET1/DDM1 to maintain genome integrity

Project description:RTEL1 mainly mediates histone H3 occupancy in heterochromatic regions and functions in parallel with DDM1 and MET1 to maintain genome integrity.

2019-09-06 | GSE86447 | GEO

High throughput sequencing analyzes small RNA profile alteration in the exosomes from lung cancer patients and healthy controls

Project description:Purpose: The goals of this study are to compare the small RNA expression profiles in the peripheral exosomes and try to find biomarkers for early diagnosis of lung adenocarcinoma Methods: Exosome was extracted from peripherial blood samples from 5 patients with lung adenocarcinoma and 5 healthy controls. RNA was extracted and microRNA profile was analyzed by high througput sequencing. Results: The expression of 5 microRNAs was found significantly altered in patients with lung adenocarcinoma

2019-03-14 | GSE111803 | GEO

High-throughput sequencing of zebrafish wild-type and duox mutant larvae

Project description:To determine the molecular basis for the dual oxidase in circulation in duox mutant zebrafish, we performed high-throughput sequencing at 4 dpf. Results revealed 375 up-regulated genes and 360 down-regulated genes in the duox mutant zebrafish compared with wild-type zebrafish. We found that some mitochondrial genes are down-regulated in duox mutant zebrafish, which was reconfirmed with qRT-PCR.

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DRIP-sequencing U2OS

Project description:Here, we identify that a human DNA helicase RTEL1, which is known to play a role in the maintenance of telomeres by interacting with proteins in the shelterin complex by resolving G4 quadruplexes, is essential for prevention of R-loop accumulation during replication and for MiDAS in mitosis at both CFSs and telomeres. Our findings indicate that RTEL1 plays a genome-wide role in preventing the collapse of replication forks at sites of G-quadruplexes and R-loop formation. Considering cancer cells rely on RTEL1 function to resolve the elevated transcription-replication conflicts caused by oncogene activation, RTEL1 is a potential drug target for cancer therapy.

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High-throughput sequencing of zebrafish wild-type and duox mutant larvae

Project description:High-throughput sequencing of zebrafish wild-type and duox mutant larvae

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UV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli

Project description:UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. RNA fragments were isolated and converted to cDNA, PCR amplified and sequenced using Illumina Solexa GAxII and HiSeq2000 platforms.

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Deletion of the helicase RTEL1 in RNA:DNA hybrids throughout the genome and how this may be affected by overexpression of the protein WT RNaseH1GFP in MEFs

Project description:The goal of this study is to assess the effect of the deletion of the helicase RTEL1 in RNA:DNA hybrids throughout the genome and how this may be affected by overexpression of the protein WT RNaseH1GFP in mouse embryonic fibroblasts.

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