Enhancers are crucial cis-regulatory DNA elements that govern gene expression in a spatially and temporally precise manner. These distal-acting regulatory elements play a key role in orchestrating transcriptional programs essential for cellular identity, differentiation, and overall brain development.
Our recently published study highlights the significance of combinatorial transcription factor (TF) binding in defining enhancer activity and specificity, particularly in the forebrain (DOI: 10.1242/bio.061751).
In this track, we present a subset of 2,614 predicted human forebrain enhancers (from our genome-wide catalogue of 25,000 forebrain enhancers available in the UCSC Public Track Hub).
These enhancers exhibit a conserved binding syntax for the transcription factors HES5, FOXP2, and GATA3 (HFG). Notably, FOXP2 binding sites are spaced between HES5 and GATA3, defining a forebrain-specific syntactical organization of TF binding. These three TFs are known regulators of neuronal differentiation, cortical development, and neurodevelopmental processes.
Using an in silico sequence-based predictive model, we identified enhancer sequences containing co-occurring binding motifs for HES5, FOXP2, and GATA3. This computational approach enhances enhancer prediction accuracy by:
The predicted HES5-FOXP2-GATA3 (HFG) enhancers were further analyzed for functional relevance by intersecting them with:
This track hub enables visualization of 2,614 HFG-predicted enhancers in the UCSC Genome Browser (hg19). Users can integrate these enhancer annotations with various genomic datasets to:
To explore these HFG enhancer predictions, load the track hub in the UCSC Genome Browser: UCSC Genome Browser.
Batool, F., Shireen, H., Malik, M. F., Abrar, M., & Abbasi, A. A. (2025). The combinatorial binding syntax of transcription factors in forebrain-specific enhancers. Biology Open, 14, bio.061751R1. DOI: 10.1242/bio.061751
Amir Ali Abbasi
📧 Email: abbasiam@qau.edu.pk