FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry

Area of Science:

• Immunology
• Molecular Biology
• Genetics

Background:

• FOXP3 is a crucial transcription factor (TF) defining regulatory T cells (Treg cells), essential for immune suppression.
• Unlike in mice, human conventional CD4+ T cells (Tconv cells) can transiently express FOXP3 upon stimulation, indicating complex regulatory mechanisms.
• Understanding the distinct regulation of FOXP3 expression between Treg and Tconv cells is vital for immunology research.

Purpose of the Study:

• To identify cis-regulatory elements (CREs) controlling FOXP3 expression in human Treg and Tconv cells.
• To discover trans-acting factors (TFs) that regulate FOXP3 expression.
• To elucidate the cell- and species-specific mechanisms governing FOXP3 transcription.

Main Methods:

• CRISPR screens were employed to tile the FOXP3 locus and target TFs in human Treg and Tconv cells.
• Combinatorial silencing of identified CREs was performed to understand their epistatic relationships.
• Mutagenesis of a murine negative regulatory element (NS- CRE) was conducted to assess its function.

Main Results:

• A subset of Treg cell CREs, along with Tconv-cell-specific positive (NS+) and negative (NS-) CREs, were found to regulate FOXP3 expression in Tconv cells.
• TF circuitry was mapped, identifying key regulators that occupy and control these CREs.
• A murine NS- CRE was essential for restricting FOXP3 expression exclusively to Treg cells.

Conclusions:

• Distinct cis-regulatory elements and trans-acting factors govern FOXP3 expression in a cell- and species-specific manner.
• The study reveals the intricate circuitry controlling FOXP3 transcription, differentiating its expression patterns in Treg and Tconv cells.
• Findings provide a foundation for understanding immune regulation and potential therapeutic targets.