Biology subjects

Winata, C.

Publications and source records attributed to Winata, C..

6 recordsLinked to original sources

bioRxiv2026

Enhancer-mediated metabolic pre-patterning defines trabecular cardiomyocyte identity prior to morphogenesis

Cardiac trabeculae are essential structures of the vertebrate heart critical for ventricular wall integrity and contractility. Despite their importance, the transcriptional regulatory program defining trabecular cardiomyocyte identity and driving their development remains poorly understood. We identify a novel enhancer, -6.8got2b, that drives gene expression specifically in the trabecular myocardium of the zebrafish heart. Functional analyses revealed that - 6.8got2b is required for trabeculae formation, likely acting through its target gene, got2b, which encodes a mitochondrial enzyme. We delineated a 166bp core region responsible for restricting gene expression to trabecular cardiomyocytes, harboring binding motifs for multiple transcription factors (TFs), including Tbx20, whose motif deletion abolished trabeculae-specific expression. A human genomic region sharing partial sequence similarity and TF motifs with -6.8got2b was found near GOT2P4 - a pseudogene related to the human GOT2 gene. Strikingly, the human sequence drove expression in the zebrafish trabeculae and ventricular myocardium, indicating partial but functionally relevant conservation. Using - 6.8got2b as a molecular marker, we transcriptionally profiled trabecular cardiomyocytes and show that, compared to compact layer cardiomyocytes, they exhibit distinct gene signatures indicative of transcriptional priming for elevated energy metabolism prior to the formation of overt trabecular structure. Our findings reveal a conserved -6.8got2b-got2b regulatory axis driving trabecular cardiomyocyte development downstream of Tbx20, establishing a new layer of transcriptional regulation in heart morphogenesis.

developmental biology↗

bioRxiv2023

scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular building blocks of the primary pacemaker

The heart is comprised of a variety of specialized cell types that work in unison to maintain blood flow. Here we utilized scRNA-seq analysis to delineate the diversity of cardiac cell types in the zebrafish. With the growing use of the zebrafish to model human heart biology, a deeper insight into its complex cellular composition is critical for a better understanding of heart function, development, and associated malformations. We present a high resolution atlas of zebrafish heart single cells transcriptomics, consisting of over 50 000 cells representing the building blocks of the zebrafish heart at 48 and 72 hpf. We defined 18 discrete cell populations comprising major cell lineages and sublineages of the developing heart. We pinpointed a population of cells likely to be the primary pacemaker and identified the transcriptome profile defining this critical cell type. Our analyses identified two genes, atp1b3b and colec10, which were enriched in the sinoatrial pacemaker cells. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate which is accompanied by arrhythmia or morphological defects, suggesting their novel function in cardiac development and conduction. Additionally, we describe other subpopulations of cardiac cell lineages, including the endothelial and neural cells, whose expression profiles we provide as a resource for further investigations into the cellular and molecular mechanisms of this organ.

developmental biology↗

bioRxiv2021

Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals, and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery revealed pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning were found to contain multiple editing sites. Adar knockdown or overexpression affected gene expression and global editing patterns at 12 hpf, but not earlier. Our study established that RNA editing by Adar is necessary for the earliest steps of embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes.

developmental biology↗

bioRxiv2021

Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish

Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.

developmental biology↗

bioRxiv2021

Transcriptome profile of the zebrafish atrioventricular canal reveals molecular signatures of pacemaker and valve mesenchyme

The atrioventricular canal (AVC) is an essential feature of the heart, which separates the atrium from the ventricle. During heart morphogenesis, it is a hub of molecular processes necessary for distinguishing heart regions; most importantly, for the formation of the AV conduction system and cardiac valves. To better understand the molecular processes underlying AVC development and function, we utilized the transgenic zebrafish line sqet31Et with EGFP expression in the AVC region to isolate this cell population by FACS and profiled its transcriptome by RNA-seq at 48 and 72 hours post fertilization (hpf). Compared to the rest of the heart, the AVC is enriched for the expression of molecular markers associated with mammalian AVC and AV node, including cx36.7 and cx45 which encode connexins forming low conductance gap junctions. Using the transgenic line Tg(myl7:mermaid) encoding the voltage-sensitive fluorescent protein, we showed that loss of function of Isl1 abolished the pacemaker-containing sinoatrial ring (SAR) and resulted in an erratic spread of excitation pattern from the SAR to AVC, indicating the dysfunction of the primary pacemaker. Concurrently, ectopic excitation in the AVC region was observed, suggesting that the zebrafish AVC possesses inherent automaticity although insufficient to replace the primary pacemaking activity of the SAR. Comparisons between the SAR and AVC transcriptomes revealed partially overlapping expression profiles of various ion channels and gap junction proteins which reflects their diversified functions. Lastly, we observed dynamic expression of epithelial-to-mesenchymal transition markers, as well as components of TGF-{beta}, Notch, and Wnt signaling pathways, which have been implicated in the formation of AVC conduction and cardiac valves. Our results uncovered the molecular hallmarks of the developing AVC region and demonstrated its role in the structural and electrophysiological separation between the atrium and ventricle. Author summaryThe atrioventricular canal is a structure in the embryonic heart which separates the atrium from the ventricle. It gives rise to the AV node and cardiac valves - two important structures which ensure unidirectional blood flow between heart chambers. The AV node serves to regulate the propagation of electrical impulses between the two chambers, such that they contract consecutively. Using the zebrafish as model organism, we performed gene expression profiling and characterized electrical conduction patterns between the sinoatrial primary pacemaker and AVC. We discovered that the zebrafish AVC possesses similar features to the mammalian AV node, including slow conduction, inherent pacemaking activity, and the expression of conserved developmental genes. The molecular profile of the AVC is distinct from that of the sinoatrial pacemaker, which reflects their distinct roles. In addition, we found that genes regulating cardiac valve development were also expressed in the AVC, illustrating the importance of this region for establishing both electrophysiological and structural separation between the heart chambers. Besides establishing conserved aspects between zebrafish and mammalian conduction system, the data generated in this study constitutes a valuable resource for studying AVC development and discovery of novel candidate genes implicated in regulating cardiac rhythm and cardiac valve formation.

developmental biology↗

bioRxiv2019

N6-methyladenosine dynamics during early vertebrate embryogenesis

Early vertebrate embryogenesis is characterized by extensive post-transcriptional regulation during the maternal-to-zygotic transition. The N6-methyladenosine (m6A) modifications on mRNA have been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with polyadenylated mRNA levels. The majority (>70%) of maternal transcripts harbor m6A, and there is a substantial increase of m6A in the polyadenylated mRNA fraction between 0 and 2 hours post fertilization. Notably, we find strong associations between m6A, cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation (ZGA). Interestingly, the relationship between m6A and translation is strongest for peaks located in the 3UTR, but not overlapping stop codons. Sequence analyses revealed enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. After ZGA, m6A seem to diminish the effect of miR-430 mediated degradation. The reported results improve our understanding of the combinatorial code behind post-transcriptional mRNA regulation during embryonic reprogramming and early differentiation.

developmental biology↗