Laboratory of Zebrafish Developmental Genomics: Winata Laboratory, Max Planck/IIMCB Research Group

The Laboratory of Zebrafish Developmental Genomics, Max Planck/IIMCB Research Group is dedicated to the study of developmental processes by applying genomics methods in combination with experimental embryology, genetics, and biochemistry. The aim is to understand the complex transcriptional regulatory mechanism of embryonic development in vivo. Currently our research focuses on elucidating the downstream regulatory mechanism of heart development by cardiac transcription factors (TFs) and characterization of epigenetic profiles during heart development. A comprehensive understanding of the molecular regulatory networks governing heart development will be a crucial step to a better understanding of the mechanism of congenital heart diseases.

The study of heart development poses a unique challenge due to the importance of the organ for survival. Disruption to factors regulating the early steps of heart formation, cause early embryonic lethality. The zebrafish (Danio rerio) alleviates this problem by allowing access to developing embryos right after fertilization and its ability to survive without a functioning heart up to a comparatively late stage of development. Taking advantage of this model organism, many genes regulating heart development have been identified. However, despite these advances, considerable challenges to understand the mechanism of heart development still exist. Firstly, there is still a lack of knowledge of molecular mechanism and downstream targets of cardiac TFs. Furthermore, the interconnectivity of their mechanisms and functions render it difficult, and possibly of little meaning, to make isolated assessments of individual factors in the characterization of a particular phenotypic outcome. Secondly, the transcription of genes are modulated by cis regulatory elements located in non-coding regions of the genome, which also serve as binding sites for TFs. Thus, mutations in these regulatory elements equally affect developmental outcome as mutations in coding regions. However, there is still a lack of systematic resource for these elements and understanding of their roles in heart development. Thirdly, an additional layer of regulation exists in the form of epigenetics. Cardiac TFs have been shown to interact with chromatin modifying factors, and loss of function of several histone modifying enzymes have been found to affect various aspects of cardiac development.

The high degree of complexity in developmental regulation in vivo necessitates an approach which takes into account both genetic and epigenetic factors. Using a genomics approach and capitalizing on the advantages of zebrafish, we want to uncover genetic and epigenetic factors contributing to the process of heart development and elucidate their regulatory mechanism.


1. Transcriptional regulatory network of heart development

The vertebrate heart undergoes three key stages of morphogenesis: specification and migration of cardiac progenitors, formation of the beating linear heart tube, and looping to form a multi-chambered organ. In each of these stages, TFs play a crucial role in initiating transcription of cardiac genes, leading to a cascade of genetic regulation. At the core of this regulation machinery is the interaction between cardiac TFs Nkx2.5, Gata5, Tbx5, and Hand2 which is necessary for the establishment of cardiac identity in cells of the embryonic mesoderm, their subsequent diversification into atrial and ventricular progenitors, and their migration to the midline to form the linear heart tube.

In our previous work, we have used ChIP-seq on zebrafish whole embryos and FACS-sorted cells to study Zic3, a TF implicated in left-right patterning and neural development. We identified novel target genes of Zic3 and uncovered links to several developmental pathways during gastrulation and neural patterning. Building upon the experience and knowledge gained from this study, we want to characterize the downstream regulatory network of cardiac TFs during key phases of heart development.



Winata et al., 2013 


2. Epigenome profile of heart development

Epigenetic marks in the form of modified histones have been commonly used to identify chromatin states, indicating the transcriptional status or activity of particular genetic elements, such as enhancers and promoter. A systematic catalogue of these marks, combined with the information on TF binding sites in the genome, would provide a comprehensive and unbiased view of transcriptional regulatory landscape during heart development in vivo. Together with functional analysis in zebrafish mutants, we aim to identify genome-wide elements associated with heart defects, and to characterize epigenetic contributions to heart development.