A major goal of regenerative medicine is to instruct formation of multipotent, tissue-specific stem cells from induced pluripotent stem cells (iPSCs) for cell replacement therapies. Generation of hematopoietic stem cells (HSCs) from iPSCs or embryonic stem cells (ESCs) is not currently possible, however, necessitating a better understanding of how HSCs normally arise during embryonic development. We previously showed that hematopoiesis occurs through four distinct waves during zebrafish development, with HSCs arising in the final wave in close association with the dorsal aorta. Recent reports have suggested that murine HSCs derive from hemogenic endothelial cells (ECs) lining the aortic floor1,2. Additional in vitro studies have similarly suggested that the hematopoietic progeny of ESCs arise through intermediates with endothelial potential3,4. In this report, we have utilized the unique strengths of the zebrafish embryo to image directly the birth of HSCs from the ventral wall of the dorsal aorta. Utilizing combinations of fluorescent reporter transgenes, confocal timelapse microscopy and flow cytometry, we have identified and isolated the stepwise intermediates as aortic hemogenic endothelium transitions to nascent HSCs. Finally, using a permanent lineage tracing strategy, we demonstrate that the HSCs generated from hemogenic endothelium are the lineal founders of the adult hematopoietic system.

SUMMARY Epigenetic mechanisms have been proposed to play crucial roles in mammalian development, but their precise functions are only partially understood. To investigate epigenetic regulation of embryonic development, we differentiated human embryonic stem cells into mesendoderm, neural progenitor cells, trophoblast-like cells, and mesenchymal stem cells, and systematically characterized DNA methylation, chromatin modifications, and the transcriptome in each lineage. We found that promoters that are active in early developmental stages tend to be CG rich and mainly engage H3K27me3 upon silencing in non-expressing lineages. By contrast, promoters for genes expressed preferentially at later stages are often CG poor and primarily employ DNA methylation upon repression. Interestingly, the early developmental regulatory genes are often located in large genomic domains that are generally devoid of DNA methylation in most lineages, which we termed DNA methylation valleys (DMVs). Our results suggest that distinct epigenetic mechanisms regulate early and late stages of ES cell differentiation.

Lymphatic vessels have important roles in fluid homeostasis, fat absorption, inflammation and cancer metastasis and develop in a dynamic process (called lymphangiogenesis) involving budding, migration and proliferation of lymphangioblasts. Using a genetic screen in zebrafish we identify ccbe1 (collagen and calcium-binding EGF domain-1) as indispensible for embryonic lymphangiogenesis. Ccbe1 acts at the same stage of development as Vegfc and is required for lymphangioblast budding and angiogenic sprouting from venous endothelium.

Cardiac chamber formation represents an essential evolutionary milestone that allows for the heart to receive (atrium) and pump (ventricle) blood throughout a closed circulatory system. Here, we reveal a novel transcriptional pathway between foxn4 and tbx genes that facilitates this evolutionary event. We show that the zebrafish gene slipjig, which encodes Foxn4, regulates the formation of the atrioventricular (AV) canal to divide the heart. sli/foxn4 is expressed in the AV canal, and its encoded product binds to a highly conserved tbx2 enhancer domain that contains Foxn4-and T-box-binding sites, both necessary to regulate tbx2b expression in the AV canal.Supplemental material is available at http://www.genesdev.org.Received October 30, 2007; revised version accepted January 23, 2008. The evolution of organs and adaptation of specialized structures utilizes the duplication of highly conserved transcription factors and their cis-regulatory elements. Because of its gradual progression from a single-chambered muscular tube with peristaltic contractility (invertebrates) to a complex multichambered structure with diverse specialized cardiomyocytes (vertebrates), the heart is ideal to study the genetic underpinnings of organogenesis as well as the evolutionary basis of morphological complexity. Division of the heart into chambers represents an essential evolutionary milestone that allows for the heart to receive and pump blood throughout a closed circulatory system (for review, see Olson 2006). Initially, the vertebrate heart develops as a linear tube without significant cellular or physiological differences; however, as the heart tube loops, distinct cardiac chambers begin to develop and acquire high gap junction density leading to faster conduction velocities. In contrast, the atrioventricular (AV) canal and inner curvature regions expand more slowly and maintain characteristics of embryonic tubular hearts including slow conduction velocity (for review, see Moorman and Christoffels 2003). Due to its primitive myocardial nature, the AV canal has evolved several specialized functions in heart formation and function including the formation of AV cushions as well as AV cardiac conduction delay. Here we reveal how these evolutionarily specialized AV structures are coupled developmentally through a novel transcriptional circuit to structurally (AV valves) and functionally (AV conduction delay) separate the atrium and ventricle. Results and DiscussionFrom a recent ENU mutagenesis screen ), we identified a unique cardiovascular mutant, slipjig (sli) (Chen et al. 1996), which displays not only structural AV canal malformations but also AV conduction defects (Fig. 1). sli mutants appear indistinguishable from their wild-type siblings up to 30 h post-fertilization (hpf), displaying formation of a cardiac tube that pumps blood throughout the embryo (data not shown). However, by 36-48 hpf, sli mutants exhibit pericardial edema due to dysmorphic hearts that fail to loop and form an AV canal (Fig. 1A, and cf. B,D and C,E). Fur...

We present a pilot enhancer trap screen using GAL4 to drive expression of upstream activator sequence (UAS)-linked transgenes in expression patterns dictated by endogenous enhancers in zebrafish. The patterns presented include expression in small subsets of neurons throughout the larval brain, which in some cases persist into adult. Through targeted photoconversion of UAS-driven Kaede and variegated expression of UAS-driven GFP in single cells, we begin to characterize the cellular components of labeled circuits.

Summary The vascular system is essential for embryonic development and adult life. Aberrant vascularization is associated with numerous diseases, including cancer, atherosclerosis, retinopathy, and stroke. Vascular development begins when mesodermal cells differentiate into endothelial cells, which then form primitive vessels. It has been hypothesized that endothelial-specific gene expression may be regulated combinatorially, but the transcriptional mechanisms governing vascular gene expression remain incompletely understood. Here, we identify a transcriptional code, consisting of Forkhead and Ets factors, which is required and sufficient for vascular development and endothelial gene expression through combinatorial activation of a composite cis-acting element. We show that the presence of this FOX:ETS motif is an effective predictor of endothelial-specific enhancers. These studies establish a paradigm in which two broadly expressed classes of transcription factors regulate tissue specific expression combinatorially through a single composite cis-acting element. This mechanism has broad implications for understanding differentiation and gene expression in many tissues.

Chromatin architecture has been implicated in cell-type-specific gene regulatory programs; yet, how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (PSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon HERV-H in creating topologically associating domains (TAD) in human PSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces transcription of upstream genes, while de novo insertion of HERV-Hs can introduce new TAD boundaries. HERV-H’s ability to create these TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents formation of these boundaries. This ability is not limited to human PSCs, as these actively transcribed HERV-Hs and their corresponding TAD boundaries also appear in PSCs from other hominids but not in more distantly related species lacking HERV-Hs. Overall, our results provide direct evidence for retrotransposons in actively shaping cell-type- and species-specific chromatin architecture.

Vertebrate hearts depend on highly specialized cardiomyocytes that form the cardiac conduction system (CCS) to coordinate chamber contraction and drive blood efficiently and unidirectionally throughout the organism. Defects in this specialized wiring system can lead to syncope and sudden cardiac death. Thus, a greater understanding of cardiac conduction development may help to prevent these devastating clinical outcomes. Utilizing a cardiac-specific fluorescent calcium indicator zebrafish transgenic line, Tg(cmlc2:gCaMP)s878, that allows for in vivo optical mapping analysis in intact animals, we identified and analyzed four distinct stages of cardiac conduction development that correspond to cellular and anatomical changes of the developing heart. Additionally, we observed that epigenetic factors, such as hemodynamic flow and contraction, regulate the fast conduction network of this specialized electrical system. To identify novel regulators of the CCS, we designed and performed a new, physiology-based, forward genetic screen and identified for the first time, to our knowledge, 17 conduction-specific mutations. Positional cloning of hobgoblins634 revealed that tcf2, a homeobox transcription factor gene involved in mature onset diabetes of the young and familial glomerulocystic kidney disease, also regulates conduction between the atrium and the ventricle. The combination of the Tg(cmlc2:gCaMP)s878 line/in vivo optical mapping technique and characterization of cardiac conduction mutants provides a novel multidisciplinary approach to further understand the molecular determinants of the vertebrate CCS.