# Identification of novel DNA sequence motifs that modulate transcription in T cells

## TL;DR

This study identifies new DNA sequence motifs that influence gene expression in T cells, revealing gaps in our understanding of how genes are regulated in these immune cells.

## Contribution

The paper presents a comprehensive discovery of 2,036 novel DNA motifs that modulate transcription in T cells, surpassing known transcription factor binding sites.

## Key findings

- Novel motifs were found to regulate gene transcription in T cells more effectively than some established transcription factor binding sites.
- Regulatory activity of motifs depends on their orientation, position, and copy number.
- STARR-seq experiments confirmed the functional relevance of these motifs in T-cell-specific gene regulation.

## Abstract

Considerable progress has been made towards associating transcription factor binding sites (TFBS) with cell-type-specific gene expression, however, the full repertoire of DNA sequence motifs that regulate transcription remains unknown. Improving our understanding of transcriptional regulation is especially important in T cells, given the enormous potential of genetically engineered T cells as an emerging class of therapeutics. Here, we report results from a comprehensive and unbiased survey investigating whether there are novel motifs enriched in regulatory regions of genes with the highest constitutive and selective expression across diverse T-cell subsets. Using computational and experimental methods, we identified 2,036 novel motifs and 629 previously curated TFBS that are enriched, both individually and in specific combinations, in the regulatory regions of genes exhibiting T-cell-specific gene expression. We then used the self-transcribing active regulatory region sequencing (STARR-seq) assay to evaluate all possible three-way combinations of a subset of 18 candidate motifs to test their ability to modulate transcription in immortalized lymphoblastic cell lines of T-cell origin (Jurkat E6) versus myeloid origin (K562). Our results revealed novel motifs that modulate gene transcription in T cells, with some exhibiting stronger regulatory effects than TFBS for TFs with established roles in T cells. The regulatory activity of these novel motifs was influenced by the motif’s orientation, position, and copy number. Overall, these results highlight our incomplete understanding of the relationship between sequence composition and T-cell gene regulation, and indicate that previously annotated TFBS represent only a subset of motifs capable of modulating gene transcription in T cells.

The online version contains supplementary material available at 10.1186/s12864-025-12425-9.