Showing papers by "Eric H. Davidson published in 2014"

Specific functions of the Wnt signaling system in gene regulatory networks throughout the early sea urchin embryo

Abstract: Wnt signaling affects cell-fate specification processes throughout embryonic development. Here we take advantage of the well-studied gene regulatory networks (GRNs) that control pregastrular sea urchin embryogenesis to reveal the gene regulatory functions of the entire Wnt-signaling system. Five wnt genes, three frizzled genes, two secreted frizzled-related protein 1 genes, and two Dickkopf genes are expressed in dynamic spatial patterns in the pregastrular embryo of Strongylocentrotus purpuratus. We present a comprehensive analysis of these genes in each embryonic domain. Total functions of the Wnt-signaling system in regulatory gene expression throughout the embryo were studied by use of the Porcupine inhibitor C59, which interferes with zygotic Wnt ligand secretion. Morpholino-mediated knockdown of each expressed Wnt ligand demonstrated that individual Wnt ligands are functionally distinct, despite their partially overlapping spatial expression. They target specific embryonic domains and affect particular regulatory genes. The sum of the effects of blocking expression of individual wnt genes is shown to equal C59 effects. Remarkably, zygotic Wnt-signaling inputs are required for only three general aspects of embryonic specification: the broad activation of endodermal GRNs, the regional specification of the immediately adjacent stripe of ectoderm, and the restriction of the apical neurogenic domain. All Wnt signaling in this pregastrular embryo is short range (and/or autocrine). Furthermore, we show that the transcriptional drivers of wnt genes execute important specification functions in the embryonic domains targeted by the ligands, thus connecting the expression and function of wnt genes by encoded cross-regulatory interactions within the specific regional GRNs.

Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo

Abstract: By gastrulation the ectodermal territories of the sea urchin embryo have developed an unexpectedly complex spatial pattern of sharply bounded regulatory states, organized orthogonally with respect to the animal/vegetal and oral/aboral axes of the embryo. Although much is known of the gene regulatory network (GRN) linkages that generate these regulatory states, the principles by which the boundaries between them are positioned and maintained have remained undiscovered. Here we determine the encoded genomic logic responsible for the boundaries of the oral aspect of the embryo that separate endoderm from ectoderm and ectoderm from neurogenic apical plate and that delineate the several further subdivisions into which the oral ectoderm per se is partitioned. Comprehensive regulatory state maps, including all spatially expressed oral ectoderm regulatory genes, were established. The circuitry at each boundary deploys specific repressors of regulatory states across the boundary, identified in this work, plus activation by broadly expressed positive regulators. These network linkages are integrated with previously established interactions on the oral/aboral axis to generate a GRN model encompassing the 2D organization of the regulatory state pattern in the pregastrular oral ectoderm of the embryo.

General approach for in vivo recovery of cell type-specific effector gene sets

Abstract: Differentially expressed, cell type-specific effector gene sets hold the key to multiple important problems in biology, from theoretical aspects of developmental gene regulatory networks (GRNs) to various practical applications. Although individual cell types of interest have been recovered by various methods and analyzed, systematic recovery of multiple cell type-specific gene sets from whole developing organisms has remained problematic. Here we describe a general methodology using the sea urchin embryo, a material of choice because of the large-scale GRNs already solved for this model system. This method utilizes the regulatory states expressed by given cells of the embryo to define cell type and includes a fluorescence activated cell sorting (FACS) procedure that results in no perturbation of transcript representation. We have extensively validated the method by spatial and qualitative analyses of the transcriptome expressed in isolated embryonic skeletogenic cells and as a consequence, generated a prototypical cell type-specific transcriptome database.

The uncommon roles of common gene regulatory factors in the genomes of differentiating cells.

Abstract: Viewed through the lens of comparative regulatory mechanisms in developmental processes, the article of Calero‐Nieto et al (2014, this issue) is of particular interest. This work uncovers the causal combinatorial subtleties of the distinct enhancer occupancy profiles displayed by ten different transcription factors, which are expressed in common in two hematopoietic cell types, a stem cell‐like precursor and primary mast cells.

Brief Notes on the Meaning of a Genomic Control System for Animal Embryogenesis

Abstract: This article presents some reflections on how the recently published Boolean gene regulatory network (GRN) model for sea urchin endomesoderm development affects the problem of what we can expect to know about a developmental process. The Boolean computation demonstrated that, on a system-wide level, a topological GRN model can contain sufficient regulatory information to predict in silico all the spatial and almost all the temporal processes of regulatory gene expression observed in this phase of embryonic development. Conclusions that can be drawn illuminate the general and fundamental characteristics of developmental regulatory systems, such as their innate hierarchy and their reliance on logic-processing functions. The automaton-like performance which the Boolean model displayed reflects the basic quality of genomically controlled developmental process. This quality is of course the underlying requirement for a genetically encoded developmental mechanism. The accessibility of system-wide mechanistic explanation is something new in developmental biology, and turns on their head old truisms that for a century have been implicit in science aimed at small parts of systems.

Use of gene regulatory network logic for transformation of cells

Abstract: Described herein is a gene regulatory network based focused approach to cell transformation. The methods described herein allow for identification of circuit and sub-circuit repertoires for which modification in a starting cell type can result in generation of a transformed cell type in a durable and persistent manner, without requiring potentially deleterious genome modification. The described methods and compositions produced by the methods find widespread application in regenerative medicine applications.