Specificity of the Hox member Deformed is determined by transcription factor levels and binding site affinities

PBX and Dfd cooperatively regulate stage-specific expression of 30 K protein BmLP1 in Bombyx mori

Nutrient accumulation is essential for insect metamorphosis. As a group of important nutrient-storage proteins, forty-six 30 K proteins (30KPs), including BmLP1-BmLP46, have been identified in the silkworm, Bombyx mori. Most 30KPs are synthesised in the last instar larvae, and the stage-specific expression of 30KPs is believed to be regulated by juvenile hormone (JH)-dependent pathways; however, the specific regulatory mechanism remains unclear. In this study, we found that a 30KP gene Bmlp1 was expressed after Day 3 of the fifth instar, and its expression was down-regulated by JH analogue. We also identified a cis-response element (CRE) on the promoter of Bmlp1. Dfd was determined to bind to this CRE adjacent to another CRE that serves as a binding site for PBX. Dfd is a HOX transcription factor found to exhibit an expression pattern similar to that of PBX. The interaction between PBX and Dfd was confirmed using bimolecular fluorescence complementation and GST pull-down experiments. The expression of Bmlp1 was down-regulated when PBX and Dfd were overexpressed in BmN cells, whereas it was up-regulated when PBX and Dfd were knocked down in BmN cells. Our data show that the transcription factor Dfd, and the cofactor PBX, synergistically regulate the transcription of Bmlp1 in B. mori. This study provides a reference for an in-depth understanding of the regulation of insect development mediated by JH.

Hox gene-specific cellular targeting using split intein Trojan exons

The Trojan exon method, which makes use of intronically inserted T2A-Gal4 cassettes, has been widely used in Drosophila to create thousands of gene-specific Gal4 driver lines. These dual-purpose lines provide genetic access to specific cell types based on their expression of a native gene while simultaneously mutating one allele of the gene to enable loss-of-function analysis in homozygous animals. While this dual use is often an advantage, the truncation mutations produced by Trojan exons are sometimes deleterious in heterozygotes, perhaps by creating translation products with dominant negative effects. Such mutagenic effects can cause developmental lethality as has been observed with genes encoding essential transcription factors. Given the importance of transcription factors in specifying cell type, alternative techniques for generating specific Gal4 lines that target them are required. Here, we introduce a modified Trojan exon method that retains the targeting fidelity and plug-and-play modularity of the original method but mitigates its mutagenic effects by exploiting the self-splicing capabilities of split inteins. "Split Intein Trojan exons" (siTrojans) ensure that the two truncation products generated from the interrupted allele of the native gene are trans-spliced to create a full-length native protein. We demonstrate the efficacy of siTrojans by generating a comprehensive toolkit of Gal4 and Split Gal4 lines for the segmentally expressed Hox transcription factors and illustrate their use in neural circuit mapping by targeting neurons according to their position along the anterior-posterior axis. Both the method and the Hox gene-specific toolkit introduced here should be broadly useful.

Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries

Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.

Deep flanking sequence engineering for efficient promoter design using DeepSEED

Designing promoters with desirable properties is essential in synthetic biology. Human experts are skilled at identifying strong explicit patterns in small samples, while deep learning models excel at detecting implicit weak patterns in large datasets. Biologists have described the sequence patterns of promoters via transcription factor binding sites (TFBSs). However, the flanking sequences of cis-regulatory elements, have long been overlooked and often arbitrarily decided in promoter design. To address this limitation, we introduce DeepSEED, an AI-aided framework that efficiently designs synthetic promoters by combining expert knowledge with deep learning techniques. DeepSEED has demonstrated success in improving the properties of Escherichia coli constitutive, IPTG-inducible, and mammalian cell doxycycline (Dox)-inducible promoters. Furthermore, our results show that DeepSEED captures the implicit features in flanking sequences, such as k-mer frequencies and DNA shape features, which are crucial for determining promoter properties.

Hox dosage and morphological diversification during development and evolution

Hox genes encode for evolutionary conserved transcription factors that have long fascinated biologists since the observation of the first homeotic transformations in flies. Hox genes are developmental architects that instruct the formation of various and precise morphologies along the body axes in cnidarian and bilaterian species. In contrast to these highly specific developmental functions, Hox genes encode for proteins that display poorly selective DNA-binding properties in vitro. This "Hox paradox" has been partially solved with the discovery of the TALE-class cofactors, which interact with all Hox members and form versatile Hox/TALE protein complexes on DNA. Here, we describe the role of the Hox dosage as an additional molecular strategy contributing to further resolve the Hox paradox. We present several cases where the Hox dosage is involved in the formation of different morphologies in invertebrates and vertebrates, with a particular emphasis on flight appendages in insects. We also discuss how the Hox dosage could be interpreted in different types of target enhancers within the nuclear environment in vivo. Altogether our survey underlines the Hox dosage as a key mechanism for shaping Hox molecular function during development and evolution.

Hox function and specificity – A tissue centric view

Since their discovery, the Hox genes, with their incredible power to reprogram the identity of complete body regions, a phenomenon called homeosis, have captured the fascination of many biologists. Recent research has provided new insights into the function of Hox proteins in different germ layers and the mechanisms they employ to control tissue morphogenesis. We focus in this review on the ectoderm and mesoderm to highlight new findings and discuss them with regards to established concepts of Hox target gene regulation. Furthermore, we highlight the molecular mechanisms involved the transcriptional repression of specific groups of Hox target genes, and summarize the role of Hox mediated gene silencing in tissue development. Finally, we reflect on recent findings identifying a large number of tissue-specific Hox interactor partners, which open up new avenues and directions towards a better understanding of Hox function and specificity in different tissues.