Intricate embryonic patterning relies on highly precise regulatory mechanisms that control gene expression in both time and space. Our research aims to elucidate the mechanism by which gene expression is regulated by transcription factors (TFs) and the epigenetic landscape in the development of complex embryonic patterns and structures. We also seek to understand how the disruption of this mechanism leads to human congenital malformations.
The Genome-Wide Regulatory Landscape of Heart Development
While key genetic factors controlling heart development are known, how they interact with each other and with epigenetic regulators across developmental stages remains less understood. Our lab investigates cardiomyocytes and cardiac pacemaker cells to uncover how gene regulatory networks shape heart formation and function.
I. Discovery and Functional Analysis of Heart Enhancers
Using integrated genomics approaches, including RNA-seq and ATAC-seq, we map transcriptional and chromatin accessibility dynamics across key stages of zebrafish heart development. Our analyses revealed regulatory hubs driving crucial developmental transitions (Pawlak et al., Genome Res, 2019).
We combine computational modeling, transcription factor footprinting, and in vivo enhancer assays to identify and validate conserved noncoding elements that regulate heart development. Ultimately, our goal is to define how dynamic regulatory landscapes contribute to normal cardiac morphogenesis and congenital heart disease.
II. Genomic Dissection of Pacemaker Development
Pacemaker cells are specialized cardiomyocytes that drive the rhythmic contractions of the heart. Once specified, they acquire unique low-conductance properties through distinct gap junction proteins. Defects in pacemaker development can lead to severe cardiac arrhythmias, yet the molecular mechanisms that govern their specification and function remain incompletely understood.
The zebrafish possesses heart physiology and genetics that closely resemble those of humans. Using this model organism, we explore how pacemaker cells develop and function. Bulk transcriptome analyses revealed key markers of the sinoatrial and atrioventricular pacemakers (Minhas et al., BMC Genomics, 2021; Abu Nahia et al., Cell Mol Life Sci, 2021). These studies showed that zebrafish pacemaker regions express partially overlapping sets of ion channel and connexin genes, reflecting their distinct yet conserved physiological roles.
Building on this foundation, our recent single-cell transcriptomic atlas of the zebrafish heart provides a comprehensive view of cardiac cell diversity, including the molecular identity and heterogeneity of pacemaker populations (Abu Nahia et al., iScience, 2024). This work offers a valuable resource for dissecting cell-type–specific regulatory programs and linking them to human cardiac disorders. Many pacemaker-enriched genes have human homologs implicated in congenital heart disease, underscoring the translational relevance of our findings. Ultimately, we aim to establish zebrafish as a robust model for pacemaker dysfunction, identify novel genetic elements involved in arrhythmia and congenital heart defects, and generate mutant lines for functional validation.
Modeling Rare Diseases in Zebrafish
Our research encompasses the modeling of rare human diseases that affect transcriptional and developmental control. One of our ongoing projects focuses on MED13 and MED13L, genes encoding core components of the Mediator complex which facilitates communication between gene promoters and enhancers. Mutations in MED13 or MED13L are linked to rare syndromes characterized by craniofacial abnormalities, intellectual disability, muscle hypotonia, and congenital heart defects. Our previous work (Utami et al., Hum Mutat, 2014) showed that morpholino-mediated knockdown of med13b in zebrafish induces neural crest defects reminiscent of those seen in human MED13/13L syndromes. Importantly, these defects could be rescued by introducing human MED13L mRNA, highlighting the conserved function of MED13L and supporting zebrafish as a valuable disease model.
Using CRISPR/Cas9, we have created zebrafish mutants to investigate how loss of med13a or med13b affects embryonic development. Our ongoing project aims to uncover the downstream molecular mechanisms of MED13 and MED13L by combining in vivo zebrafish studies with in vitro human iPSC systems. This multi-model approach is envisaged to provide new insights into the role of MED13/MED13L in embryonic development and uncover disease mechanisms of associated syndromes.
Biological Role of RNA Editing
RNA editing refers to post-transcriptional modifications of RNA sequences, the most prevalent being adenosine-to-inosine (A-to-I) conversion, catalyzed by ADAR enzymes through the deamination of adenosine at the C6 position. Misregulation of A-to-I RNA editing in humans has been linked to neurological and metabolic disorders, autoimmune diseases, and cancer.
We developed bioinformatics tools to identify RNA editing events in transcriptomic data and applied them to characterize A-to-I editing during early zebrafish embryogenesis. Our analyses revealed widespread editing in both maternal and early zygotic transcripts, predominantly within 3′ untranslated regions. Notably, many edited transcripts are involved in gastrulation and embryonic axis patterning, containing multiple editing sites. Functional analyses of Adar, the zebrafish ortholog of mammalian ADAR1, established its maternal role in defining the anteroposterior and dorsoventral axes, and its zygotic role in regulating innate immune responses (Niescierowicz et al., Nat. Commun., 2022). Together, these findings reveal RNA editing as an essential layer of post-transcriptional regulation during early vertebrate development.