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

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Gene expression is precisely regulated by cis-regulatory elements, including enhancers (activators) and silencers (repressors).
• While gene activation mechanisms are well-studied, the function and identification of gene silencers remain less understood.
• Silencers are genetic elements that negatively regulate gene transcription independently of their genomic position.

Purpose of the Study:

• To develop and validate a novel high-throughput reporter assay for quantitative assessment of silencer activity in mammals.
• To identify and characterize cis-acting silencers using this new method in a mouse T cell line.
• To explore the genomic and functional associations of identified silencer elements.

Main Methods:

• Repurposed the STARR-seq (Self-Transcribing Activated Regulatory Region sequencing) approach for silencer activity assessment.
• Analyzed silencer activity from DNase hypersensitive sites in a mouse T cell line.
• Utilized CRISPR-mediated genomic deletions for functional validation of identified silencers.

Main Results:

• Identified novel silencer elements associated with both repressive and active chromatin marks.
• Found enriched binding motifs for known transcriptional repressors within identified silencers.
• Validated the repressive function of specific silencers in regulating non-T cell genes and genes involved in T cell differentiation.
• Discovered an association between silencer activity and short tandem repeats (repetitive elements).

Conclusions:

• The developed STARR-seq based strategy provides a robust method for genome-wide identification and characterization of silencer elements.
• Silencers play a significant role in gene repression, impacting normal development and cell differentiation.
• Repetitive elements may contribute to the functional activity of silencers.