Strength of interactions in the Notch gene regulatory network determine lateral inhibition patterning

Gene regulatory networks (GRNs) regulate the generation of diverse gene expression patterns, which in turn determine cell fate during the development of multicellular organisms. However, how the topology and parameters of GRNs determine this patterning remain largely unknown due to the complexity of most experimental systems. To address this, we use the zebrafish notochord, an organ where coin-shaped precursor cells arranged in a simple unidimensional geometry differentiate into vacuolated and sheath cells in a Notch-dependent manner. We identify jag1a and her6/her9 as the main components of an unconventional GRN that generates a lateral inhibition pattern that controls cell differentiation. Moreover, making use of this experimental system and mathematical modeling we show that such patterning requires that ligand-receptor interactions are stronger within the same cell than in neighboring cells. Altogether, we establish the zebrafish notochord as an experimental system to study Notch patterns, and identify and characterize a GRN that determines gene patterning and drives cell fate.

Thermofluidic heat exchangers for actuation of transcription in artificial tissues

Spatial patterns of gene expression in living organisms orchestrate cell decisions in development, homeostasis, and disease. However, most methods for reconstructing gene patterning in 3D cell culture and artificial tissues are restricted by patterning depth and scale. We introduce a depth- and scale-flexible method to direct volumetric gene expression patterning in 3D artificial tissues, which we call “heat exchangers for actuation of transcription” (HEAT). This approach leverages fluid-based heat transfer from printed networks in the tissues to activate heat-inducible transgenes expressed by embedded cells. We show that gene expression patterning can be tuned both spatially and dynamically by varying channel network architecture, fluid temperature, fluid flow direction, and stimulation timing in a user-defined manner and maintained in vivo. We apply this approach to activate the 3D positional expression of Wnt ligands and Wnt/β-catenin pathway regulators, which are major regulators of development, homeostasis, regeneration, and cancer throughout the animal kingdom.

Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication

We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.

Self-organized patterning and morphogenesis in embryonic epithelia from antagonistic signals and fiber networks

A number of universals can be observed in the developing embryos of all phyla. An attempt is made here to describe some of these with a simple model, one consisting of two mutually repelling regions of gene patterning produced by signaling pathways, two acting at each growth phase. The diffusion of ligands is short range, nearest or near neighbors, but the transcription patterns extend over many cellular diameters. The universals discussed are: gastrulation, formation of a blastopore, patterning of stem cells as surrounding compartments (propagating anew with each growth phase, to the adult), the origin of bilaterality, the prevalence of segmentation, and the general ability to regenerate and duplicate. The origin of organ sizes are determined by the parameters of the signaling pathways involved, independent of cell sizes or numbers. The important fiber mesh, or fiber network that can also extend over many cell diameters is also briefly discussed, and is seen as a partner with the signaling pathways in the overall patterning.

In vivo functional analysis of the Hoxa-1 3′ retinoic acid response element (3′RARE)

Retinoids are essential for normal development and both deficiency and excess of retinoic acid (RA) are teratogenic. Retinoic acid response elements (RAREs) have been identified in Hox gene promoters suggesting that endogenous retinoids may be involved in the direct control of Hox gene patterning functions. In order to test this hypothesis, we have mutated the Hoxa-1 3′RARE using the Cre-loxP targeting strategy, and studied its functional role during mouse development. We find that this enhancer plays an important role in the early establishment of the Hoxa-1 anterior expression boundary in the neural plate. This early disturbance in Hoxa-1 activation results in rhombomere and cranial nerve abnormalities reminiscent of those obtained in the Hoxa-1 total knockout, although their severity and penetrance are lower, thus providing strong evidence for direct control of Hox gene function by retinoids during normal development. Interestingly, we also find that the Hoxa-1 expression response to RA treatment is not entirely controlled by the RARE, suggesting the existence of other retinoid-induced factors mediating the Hoxa-1 response to RA and/or the presence of additional RAREs. Interestingly, although the RARE is not required for the spatiotemporal control of colinear expression of the Hoxa genes, it is absolutely required for correct Hoxa-2 expression in rhombomere 5.