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Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

ABSTRACT: Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

PROVIDER: PRJNA523738 | ENA |

REPOSITORIES: ENA

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Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

Project description:These experiments identify the primary response genes of ZNF143 in HEK-293T cells and the transcriptional response that results from treating cells with 500μM auxin.

2019-02-23 | GSE126919 | GEO

Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

Project description:Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

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Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

Project description:We used SLAM-seq approach to define a contribution of RNA synthesis into RNA abundance changes after Tpr loss. Basket nucleoporin Tpr was AID-tagged and depleted through Auxin Induced Degradation system. Loss of Tpr led to rapid changes in rates of RNA synthesis. The majority of transcripts were downregulated. Analysis of RNA-seq and SLAM-seq indicated that the changes in RNA abundance of most of Tpr-dependent up- and downregulated genes resulted from increased or decreased rates of RNA synthesis, respectively.

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High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [PRO-seq]

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Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [PRO-seq]

Project description:Interactions between distal loci in mammalian genomes, including those involving enhancers and promoters, are thought to be a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. The zinc finger transcription factor ZNF143/ZFP143 has been strongly implicated as a factor that regulates chromatin interactions, functioning either with or without CTCF. However, ZNF143/ZFP143’s role in this process and its function with or without CTCF are not well understood. Here, we tagged both CTCF and ZNF143/ZFP143 with dual-purpose degron/imaging tags to combinatorically assess their loop function and effect on each other. We find that ZNF143/ZFP143 possesses no general looping function, and that it largely functions independently to CTCF. Instead, ZNF143/ZFP143 is an essential and highly conserved transcription factor possessing an extremely stable chromatin residence time (>20 min) that regulates an important subset of mitochondrial and ribosomal genes.

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SNP analysis AID-low vs AID-high

Project description:SNP analysis AID-low vs AID-high

2009-07-20 | GSE13612 | GEO

RNA-seq on ES cells where DDX6 was knocked down by the AID method

Project description:To degrade DDX6 acutely, we adopted an advanced protein degradation method, the auxin-induced degron (AID) system. For this purpose, we prepared an AID-tagged DDX6 and E3 ligase subunit of OsTIR1 in an engineered ES (D6AdP cell line). These deposited data are RNA-seq data on these D6AdP ES cells treated with the auxin analog (IAA) treatment for 0, 3, and 6 hours.

2022-11-01 | GSE200483 | GEO

Transcription profiling of mouse AID-GFP-positive vs AID-GFP-negative animals

Project description:Affymetrix gene expression AID-GFP-positive vs AID-GFP-negative Experiment Overall Design: Affymetrix gene expression AID-GFP-positive vs AID-GFP-negative

2009-08-22 | E-GEOD-13611 | biostudies-arrayexpress

AID BioID data for Methot et al, "A licensing step links AID to transcriptional elongation for mutagenesis in B cells", Nat. Commun. 2018

Project description:These files represent the raw spectrum files obtained from the AID BioID experiments described in "A licensing step links AID to transcriptional elongation for mutagenesis in B cells", Nat. Commun. 2018. Detailed description of the BioID experiment protocol is available in the article. Briefly, APOBEC2, AID, AID-R171Y or AID-R178D were C-terminally tagged with BirA* and the constructs were expressed in AID-/- mouse primary B cells ex vivo. These cells were activated with LPS+IL4. After 24hrs, the cells were supplemented with biotin. 24hr later cells were harvested and biotinylated proteins were captured with Streptavidin sepharose beads, followed by on-bead trypsinization. Trypsinized peptides were identified by LC-MS/MS using Thermo Orbitrap Fusion, employing HCD fragmentation.

2018-01-24 | MSV000081963 | MassIVE

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