Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Short tandem repeats are important contributors to silencer elements in T cells

ABSTRACT: Short tandem repeats are important contributors to silencer elements in T cells

ORGANISM(S): Mus musculus

PROVIDER: GSE219157 | GEO | 2023/02/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Short tandem repeats are important contributors to silencer elements in T cells

| PRJNA836547 | ENA

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Short tandem repeats are important contributors to silencer elements in T cells

| PRJNA907272 | ENA

Short tandem repeats are important contributors to silencer elements in T cells.

Project description:The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.

| S-EPMC10250210 | biostudies-literature

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Analysis of Dnase Hypersensitive Site (DHS) of P5424 mouse cell line using High-throughput reporter assay

2022-05-12 | GSE202547 | GEO

Candidate silencer elements in the human and mouse genome

Project description:STARR-seq assay performed on uncharacterized cis-regulatory elements to find candidate silencer elements in K562 cells.

2019-12-18 | GSE142207 | GEO

Short tandem repeats susceptible to pathogenic instability linked to chromatin domain disruption

Project description:More than 25 inherited human disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas thousands of repeat tracts across the human genome are relatively stable. Here, we discover that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains. We identify a subset of boundaries with markedly higher CpG island density compared to the rest of the genome. daSTRs specifically localize to ultra-high-density CpG island boundaries, suggesting they might be hotspots for epigenetic misregulation or topological disruption upon STR expansion. Fragile X Syndrome (FXS) patients exhibit severe boundary disruption in a manner that correlates with local loss of CTCF occupancy and the degree of FMR1 silencing. Our data uncover higher-order chromatin architecture as a new dimension in understanding repeat expansion disorders.

2018-08-29 | GSE111170 | GEO

DNA polymerase stalling at structured DNA predicts the stability of short tandem repeats

Project description:Short tandem repeats (STRs) significantly contribute to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their low complexity and repetitive nature induces DNA polymerase slippage and stalling, leading to length variation and base substitutions. However, the characterisation of DNA synthesis through STR loci has been restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour. In order to understand the interplay between the ability of a given STR to impair DNA synthesis and its genomic stability, we developed a high-throughput polymerase extension assay that allows monitoring the kinetics of DNA synthesis at all STR permutations in different lengths in parallel. We have used the assay to map at single-nucleotide resolution the movement of a prototypical A-family replicative DNA polymerase (T7 DNA polymerase) through the repeats over time. From this data we can infer the secondary structure adopted by a given STR from the precise manner in which it stalls polymerase and link this to slippage and point mutation during DNA synthesis.

2020-07-27 | GSE144458 | GEO

Short Tandem Repeats - Targeted-Sequencing of human cells for Lineage tracing

Project description:Short Tandem Repeats - Targeted-Sequencing of human cells for Lineage tracing

| PRJEB25050 | ENA

Short Tandem Repeats of Single-Stranded (ATTCC)n in Neutrophil Extracellular Traps Bind Thrombin

Project description:DNA-protein interactions play a pivotal role in a variety of cellular processes. Despite the considerable research dedicated to understanding these interactions, the specific role of single-stranded DNA (ssDNA) remains largely unexplored. Our study aimed to uncover the role of ssDNA in the interplay between neutrophil extracellular traps (NETs) and thrombin, a crucial enzyme involved in both blood clot formation and immune response. Using chromatin immunoprecipitation sequencing (ChIP-seq) and kethoxal-assisted ssDNA sequencing, we identified a specific short tandem repeat (STR) sequence, ss(ATTCC)n, that is highly enriched and forms an iI-motif structure crucial for its interaction with thrombin. We further observed that the binding affinity between ss(ATTCC)n and thrombin is increased under acidic conditions, a condition frequently linked to diseases such as cancer. Our findings not only shed light on the unexplored area of sequence-dependent ssDNA-protein interactions but also pave the way for targeted interventions in thrombosis and coagulation disorders.

2025-05-29 | GSE253483 | GEO

Short tandem repeats susceptible to pathogenic instability linked to chromatin domain disruption

Project description:Short tandem repeats susceptible to pathogenic instability linked to chromatin domain disruption

| PRJNA436095 | ENA