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Context-dependent effects of Acf1 assessed in high throughput

ABSTRACT: Context-dependent effects of Acf1 assessed in high throughput

PROVIDER: PRJNA417865 | ENA |

REPOSITORIES: ENA

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Context-dependent effects of Acf1 assessed in high throughput

Project description:We applied a multiplexed genomic tethering assay (Brueckner, Epigenetics Chromatin, 2016; PMID:27777628) to elucidate the function of ACF1, the large subunit of the ACF nucleosome sliding complex in drosophila Kc167 cells. Targeting a Gal4DBD-ACF1 fusion to several hundred integrated reporters revealed a context-dependent repressive effect which is modulated by gene activity and chromatin state.

2017-11-10 | GSE106759 | GEO

Context-dependent effects of HP1 assessed in high throughput

Project description:Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporter genes (Akhtar, Cell, 2013; PMID: 23953119) with Gal4-mediated tethering of the protein of interest. We applied the assay to Drosophila Heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein working by a chromatin compaction mechanism but has also been linked to transcriptional activation. Probing the effects of HP1a in more than one thousand genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing loci. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by two-fold. In regions marked by a H3K36me3-rich chromatin signature linked to transcriptional elongation, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a recruitment in any of the loci examined. The multiplexed tethered reporter assay will be a useful tool to dissect combinatorial regulatory interactions in chromatin.

2016-09-20 | GSE83714 | GEO

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

Project description:The abundant RNA modification pseudouridine (Ψ) has been mapped transcriptome-wide by chemically modifying pseudouridines with carbodiimide and detecting the resulting reverse transcription stops in high-throughput sequencing. However, these methods have limited sensitivity and specificity, in part due to the use of reverse transcription stops. We sought to use mutations rather than just stops in sequencing data to identify pseudouridine sites. Here, we identify reverse transcription conditions that allow read-through of carbodiimide-modified pseudouridine (CMC-Ψ), and we show that pseudouridines in carbodiimide-treated human ribosomal RNA have context-dependent mutation and stop rates in high-throughput sequencing libraries prepared under these conditions. Furthermore, accounting for the context-dependence of mutation and stop rates can enhance the detection of pseudouridine sites. Similar approaches could contribute to the sequencing-based detection of many RNA modifications.

2018-05-07 | GSE110247 | GEO

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

Project description:Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

| PRJNA433264 | ENA

ABPP-HT - high-throughput activity-based profiling of deubiquitylating enzyme inhibitors in a cellular context

Project description:The potency and selectivity of a small molecule inhibitor are key parameters to assess during the early stages of drug discovery. In particular, it is very informative for characterizing compounds in a relevant cellular context in order to reveal potential off-target effects and drug efficacy. Activity-based probes (ABPs) are valuable tools for that purpose, however, obtaining cellular target engagement data in a high-throughput format has been particularly challenging. Here, we describe a new methodology named ABPP-HT (high-throughput-compatible activity-based protein profiling), implementing a semi-automated proteomic sample preparation workflow that increased the throughput capabilities of the classical ABPP workflow approximately ten times while preserving its enzyme profiling characteristics. Using a panel of deubiquitylating enzyme (DUB) inhibitors, we demonstrate the feasibility of ABPP-HT to provide compound selectivity profiles of endogenous DUBs in a cellular context at a fraction of time as compared to previous methodologies

2021-02-24 | PXD023036 | Pride

Context-dependent genetic effects on gene expression

Project description:Context-dependent genetic effects on gene expression

| PRJNA853369 | ENA

Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing

Project description:We sought to find if epigenetic drugs had chromatin context-dependent effects on CRISPR-Cas9 efficiency and DNA double-strand break repair. We performed a multiplexed drug screen in a reporter cell line containing 19 sequencing based pathway reporters. This submission contains high throughput sequencing data of the pathway reporters, their mapping and mutation readout. It also contains the raw pA-DamID data for H3K27me3, H3K9me2, H3K9me3 and "Dam-only" samples in RPE-1 cells.

2023-11-30 | GSE248980 | GEO

Drosophila melanogaster

Project description:Context-dependent effects of HP1 assessed in high throughput

| PRJNA326782 | ENA

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.

Project description: Not available

| S-EPMC6161689 | biostudies-literature

Clinical study on diagnosis of colorectal cancer based on high-throughput tumor antigen polypeptides screening

Project description:Interventions: Gold Standard:Pathological diagnosis;Index test:high-throughput tumor antigen polypeptides screening Primary outcome(s): Diagnostic accuracy Study Design: Factorial

| 2704426 | ecrin-mdr-crc

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