HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs

Kartik Kulkarni, Gabriella Quinn, Jared Rosa, Sean Goetsch, Vrushali Pandit, Lin Wang, Akane Sakaguchi, Sushama Sivakumar and Nikhil V. Munshi ()
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Kartik Kulkarni: University of Texas Southwestern Medical Center
Gabriella Quinn: University of Texas Southwestern Medical Center
Jared Rosa: University of Texas Southwestern Medical Center
Sean Goetsch: University of Texas Southwestern Medical Center
Vrushali Pandit: University of Texas Southwestern Medical Center
Lin Wang: University of Texas Southwestern Medical Center
Akane Sakaguchi: University of Texas Southwestern Medical Center
Sushama Sivakumar: University of Texas Southwestern Medical Center
Nikhil V. Munshi: University of Texas Southwestern Medical Center

Nature Communications, 2025, vol. 16, issue 1, 1-20

Abstract: Abstract Although best known as the site for ribosome assembly, the nucleolus organizes heterochromatin into transcriptionally repressed Nucleolus-Associated Domains (NADs). NADs harbor many genes involved in cell-type specification, yet the mechanisms by which transcription factors (TFs) access this heterochromatin to activate gene expression remain unknown. Using a model of TF-induced cardiac pacemaker reprogramming, we conclusively establish that nucleolar localization of HAND2 is required for successful lineage conversion. Moreover, we perform unbiased transcriptional profiling to demonstrate that pacemaker gene programs are highly compartmentalized within the nucleus. Finally, we show that HAND2 homodimers invade nucleolar condensates and concentrate within the nucleolus to bind palindromic motifs required for activating lineage-specific enhancers buried within NADs. Taken together, our data highlight a key role for the nucleolus in orchestrating pacemaker gene expression by HAND2. More broadly, these results suggest that TF localization to sub-nuclear heterochromatin domains may represent a potent strategy for activating lineage-specific gene programs.

Date: 2025
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DOI: 10.1038/s41467-025-64076-9

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