# Specificity in clustering of gene-specific transcription factors is encoded in the genome

## TL;DR

This study shows that gene-specific transcription factors form clusters in the nucleus, and their clustering specificity is determined by DNA-binding domains rather than disordered regions.

## Contribution

The study reveals that DNA-binding domains, not disordered regions, provide specificity in transcription factor clustering.

## Key findings

- Both DNA-binding domains and intrinsically disordered regions are required for transcription factor cluster formation.
- Intrinsically disordered regions alone are insufficient to join pre-existing clusters.
- DNA-binding domains determine the specificity of transcription factor clustering.

## Abstract

Gene-specific transcription factors (TFs) often form clusters in the nucleus. Such clusters can facilitate transcription, but it remains unclear how they form. It has been suggested that clusters are seeded by the sequence-specific binding of TFs to DNA and grow by interactions between intrinsically disordered regions (IDRs) that bring in more TFs. In this model, specificity in TF clustering must be provided by the IDRs. To investigate this model, we studied TF clustering by quantitative imaging of Nanog, Pou5f3, and Sox19b in zebrafish embryos. Using mutant TFs, we show that the formation of a TF cluster requires the DNA-binding domain (DBD) as well as at least one of its IDRs. Importantly, IDRs are not sufficient to join a pre-existing cluster. Rather, both IDR and DBD are needed. Finally, using chimeric TFs, we show that while IDRs are required to join a cluster, they are quite promiscuous, and it is the DBD that provides specificity to the clustering of a TF. Thus, for any TF to join a cluster, motif recognition is required, which explains the specificity in TF cluster formation. Taken together, our work provides an alternative model for how specificity is achieved in the organization of transcriptional machinery in the nucleus.

Graphical Abstract