Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Z-DNA underlies the target choice of Aire by facilitating promoter poising [CUT&Tag]

ABSTRACT: We profiled Pol II-pS5 binding in medullary thymic epithelial cells using CUT&Tag to investigate the logic of Aire's target choices

ORGANISM(S): Mus musculus

PROVIDER: GSE224555 | GEO | 2024/03/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Z-DNA underlies the target choice of Aire by facilitating promoter poising [ChIPmentation]

Project description:We profiled NELF and Aire binding in medullary thymic epithelial cells using ChIPmentation to investigate the logic of Aire's target choices

2024-03-11 | GSE224554 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising [ATAC-seq]

Project description:We profiled chromatin accessibility of medullary thymic epithelial cells to investigate the logic of Aire's target choices

2024-03-11 | GSE224551 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising [ChIP-seq]

Project description:We profiled Pol II binding in medullary thymic epithelial cells using ChIP-seq to investigate the logic of Aire's target choices

2024-03-11 | GSE224553 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising [RNA-seq]

Project description:We profiled transcriptome of medullary thymic epithelial cells from mice of various treatments and genotypes to investigate the logic of Aire's target choices

2024-03-11 | GSE224556 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising [BLISS]

Project description:We profiled DNA double-strand break (DSB) formation genome-wide in medullary thymic epithelial cells to investigate how DSBs regulate Aire's target choices

2024-03-11 | GSE224552 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising [scRNA-Seq]

Project description:Aire is an unconventional transcription factor (TF) that enhances the expression of thousands of genes in medullary thymic epithelial cells (mTECs), which promotes clonal deletion or phenotypic diversion of self-reactive T cells. The biological logic of Aire’s target specificity remains largely unknown as, unlike many TFs, it does not bind to a particular DNA-sequence motif. We implemented two orthogonal approaches to investigate Aire’s cis-regulatory mechanisms: construction of a convolutional neural network and leveraging of natural genetic variation via analysis of F1-hybrid mice. Both approaches nominated Z-DNA and Nfe2•Maf as putative positive influences on Aire’s target choices. Genome-wide mapping studies revealed that Z-DNA-forming and Nfe2l2-binding motifs were positively associated with the inherent ability of a gene’s promoter to generate DNA double-strand breaks (DSBs), and promoters showing strong DSB generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, Aire preferentially targeted genes with poised promoters. We propose a model whereby Z-DNA anchors the Aire-mediated transcriptional program by enhancing DSB generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest previously unexplored routes of manipulating T-cell tolerance.

2024-03-11 | GSE253215 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-03-11 | GSE224557 | GEO

Z-DNA underlies the target choice of Aire by facilitating promoter poising [CUT&Tag]

Project description:Z-DNA underlies the target choice of Aire by facilitating promoter poising [CUT&Tag]

| PRJNA934446 | ENA

Z-DNA underlies the target choice of Aire by facilitating promoter poising

Project description:Z-DNA underlies the target choice of Aire by facilitating promoter poising

| PRJNA931740 | ENA

Analysis of Aire effects on individual mice of different genetic backgrounds

Project description:We compared gene expression profiles of aire-deficient and wild-type littermate thymic medullary epithelial cells. This was done in order to determine whether Aire's effects differed among strains, and also among individuals of the same strain. Keywords: genetic modification

2008-07-22 | GSE8564 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data