Understanding The Genetic Mechanisms Underlying Body Segmentation

Segmented body plans are a common feature of animals from insects to humans and knowingly regulated through the action of segmentation genes. Normal development requires coordinated spatiotemporal expression of an extensive number of genes, but the fact that gene expression is a stochastic process complicates the coordination. In most animals, often the location of co-expressed genes are in close proximity on the chromosome. Such gene pairs can comprise 10-50% of all genes expressed, however, the advantage of maintaining gene pairs for developmental processes is unclear. A study by Zinani et al. from the Özbudak lab examined the zebrafish segmentation linked clock genes her1 and her7. Counting transcripts in single cells, observing segmentation in real-time, manipulating the genome to separate these genes and applying computational modeling revealed that the gene pairing enhances coordinated transcriptional gene regulation and thereby provides robustness to the development of segments along the zebrafish body axis. When disrupting gene pairing of her1 and her7, their oscillations become unsynchronized and impacted segmentation of the body axis, supporting the notion that linkage of co-expressed genes is essential for zebrafish development. It is likely that gene pairing will be a strategic mechanism not only for body axis development in a wide range of species but also in other processes requiring coordinated expression.

Novel Mechanisms of Transcriptional Control During Organogenesis

Researchers know the establishment of embryonic patterning and cell type specification with exquisite precision through morphogen gradients such as that generated by Hedgehog (Hh). Interestingly, work in the Brugmann lab revealed a gradient-independent mechanism of Hh signal transduction during craniofacial development. Using transgenic mouse models, Elliott, et al. demonstrated that instead of driven by a Hh threshold within a morphogen gradient, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix transcription factor, Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed the enrichment of Gli3 and Hand2 at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidated a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a Hh morphogen gradient. Identifying new mechanisms of Hh signal transduction opens possibilities of engineering Hh-dependent tissues and / or repairing Hh-dependent malformations in patients born with craniofacial anomalies.

A study by the Gebelein and Campbell labs examined the DNA binding and transcriptional activities of the conserved Gsx homeodomain (HD) transcription factors (TFs), which play a critical role in developmental brain patterning from flies to humans. HD TFs bind ATrich DNA sequences, and the study by Salomone, et al., showed that in addition to binding as a monomer, the Gsx factors also bind DNA as homodimers with higher affinity and sequence specificity. Remarkably, when bound as a monomer, the Gsx factor contributed to gene repression while the Gsx homodimers stimulated gene expression. Moreover, transgenic assays demonstrated that the ratio of monomer to homodimer sites in a Gsx-regulated enhancer controls gene repression versus stimulation. Thus, these findings establish, for the first time, that a single HD TF can either repress or activate gene expression depending on the composition of the monomer- versus homodimer-binding sites within the gene regulatory elements.

As discussed in the two studies above, co-binding to DNA, especially as homo and heterodimers, impacts transcriptional outputs. One consequence of dimerization is cooperative DNA binding, a key feature of transcriptional regulation. The Kopan lab examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize and thus lose cooperative binding to paired sites. While most known Notch-dependent phenotypes did not have an affect in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity, but only in the presence of environmental insults such as diet allergens or skin ectoparasites. These tissues include the heart, the gut, and marginal zone B cells which, under chronic fur mite infestation, can lead to lymphoma. Thus, the study by Kobia, et al., highlights the role of the environment and a role for Notch cooperativity in protecting against malignancy and colitis.

Insights From Foregut Development and Function Contribute To The Improvement of Next-generation Organoids for Regenerative Therapies

The Wells lab uncovered an important role for enteroendocrine cells (EECs) of the small intestine in regulating macronutrient absorption. The study by McCauley, et al., used mouse and human models of EEC deficiency to show that peptide YY, produced by these cells, contributes to the absorption of glucose and dipeptides as well as the electrophysiology of the small intestine. Importantly, administration of peptide YY to mice lacking EECs restores physiology of the small intestine suggesting a potential therapeutic approach for children born with malabsorption due to lack of EECs.

Work in the Zorn lab by Han, et al. used single-cell transcriptomics to discover an unexpected diversity of cell types in the developing mouse foregut and computationally inferred the signaling interactions between epithelial and mesenchyme cells during the earliest stages of organ formation. Using this signaling “roadmap” from embryos they established protocols to generate organ-specific mesenchyme from human pluripotent stem cells, opening the door to new next-generation organoids for regenerative medicine.