Hox specificity unique roles for cofactors and collaborators

'Organ'ising Floral Organ Development

Flowers are plant structures characteristic of the phylum Angiosperms composed of organs thought to have emerged from homologous structures to leaves in order to specialize in a distinctive function: reproduction. Symmetric shapes, colours, and scents all play important functional roles in flower biology. The evolution of flower symmetry and the morphology of individual flower parts (sepals, petals, stamens, and carpels) has significantly contributed to the diversity of reproductive strategies across flowering plant species. This diversity facilitates attractiveness for pollination, protection of gametes, efficient fertilization, and seed production. Symmetry, the establishment of body axes, and fate determination are tightly linked. The complex genetic networks underlying the establishment of organ, tissue, and cellular identity, as well as the growth regulators acting across the body axes, are steadily being elucidated in the field. In this review, we summarise the wealth of research already at our fingertips to begin weaving together how separate processes involved in specifying organ identity within the flower may interact, providing a functional perspective on how identity determination and axial regulation may be coordinated to inform symmetrical floral organ structures.

Stability and dynamics of extradenticle modulates its function

Extradenticle (EXD) is a partner protein of the HOX transcription factors and plays an important role in the development of Drosophila. It confers increased affinity and specificity of DNA-binding to the HOX proteins. However, the DNA-binding homeodomain of EXD has a significantly weaker affinity to DNA compared to the HOX homeodomains. Here, we show that a glycine residue (G290) in the middle of the EXD DNA-binding helix primarily results in this weaker binding. Glycine destabilizes helices. To probe its role in the stability and function of the protein, G290 was mutated to alanine. The intrinsic stability of the DNA-binding helix increased in the G290A mutant as observed by NMR studies and molecular dynamics (MD) simulation. Also, NMR dynamics and MD simulation show that dynamic motions present in the wild-type protein are quenched in the mutant. This in turn resulted in increased stability of the entire homeodomain (ΔΔGG→A of -2.6 kcal/mol). Increased protein stability resulted in three-fold better DNA-binding affinity of the mutant as compared to the wild-type protein. Molecular mechanics with generalized Born and surface area solvation (MMGBSA) analysis of our MD simulation on DNA-bound models of both wild-type and mutant proteins shows that the contribution to binding is enhanced for most of the interface residues in the mutant compared to the wild-type. Interestingly, the flexible N-terminal arm makes more stable contact with the DNA minor groove in the mutant. We found that the two interaction sites i.e. the DNA-binding helix and the unstructured N-terminal arm influence each other via the bound DNA. These results provide an interesting conundrum: alanine at position 290 enhances both the stability and the DNA-binding affinity of the protein, however, evolution prefers glycine at this position. We have provided several plausible explanations for this apparent conundrum. The function of the EXD as a HOX co-factor requires its ability to discriminate similar DNA sequences, which is most likely comprom.

Overlapping binding sites underlie TF genomic occupancy

Sequence-specific DNA binding by transcription factors (TFs) is a crucial step in gene regulation. However, current high-throughput in vitro approaches cannot reliably detect lower affinity TF-DNA interactions, which play key roles in gene regulation. Here, we developed PADIT-seq ( p rotein a ffinity to D NA by in vitro transcription and RNA seq uencing) to assay TF binding preferences to all 10-bp DNA sequences at far greater sensitivity than prior approaches. The expanded catalogs of low affinity DNA binding sites for the human TFs HOXD13 and EGR1 revealed that nucleotides flanking high affinity DNA binding sites create overlapping lower affinity sites that together modulate TF genomic occupancy in vivo . Formation of such extended recognition sequences stems from an inherent property of TF binding sites to interweave each other and expands the genomic sequence space for identifying noncoding variants that directly alter TF binding.

One-Sentence Summary

Overlapping DNA binding sites underlie TF genomic occupancy through their inherent propensity to interweave each other.

CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development

Loss of Cdx2 in vivo leads to stunted development of the allantois, an extraembryonic mesoderm-derived structure critical for nutrient delivery and waste removal in the early embryo. Here, we investigate how CDX2 dose-dependently influences the gene regulatory network underlying extraembryonic mesoderm development. By engineering human induced pluripotent stem cells (hiPSCs) consisting of wild-type (WT), heterozygous (CDX2-Het), and homozygous null CDX2 (CDX2-KO) genotypes, differentiating these cells in a 2D gastruloid model, and subjecting these cells to single-nucleus RNA and ATAC sequencing, we identify several pathways that are dose-dependently regulated by CDX2 including VEGF and non-canonical WNT. snATAC-seq reveals that CDX2-Het cells retain a WT-like chromatin accessibility profile, suggesting accessibility alone is not sufficient to drive this variability in gene expression. Because the loss of CDX2 or TBXT phenocopy one another in vivo, we compared differentially expressed genes in our CDX2-KO to those from TBXT-KO hiPSCs differentiated in an analogous experiment. This comparison identifies several communally misregulated genes that are critical for cytoskeletal integrity and tissue permeability. Together, these results clarify how CDX2 dose-dependently regulates gene expression in the extraembryonic mesoderm and reveal pathways that may underlie the defects in vascular development and allantoic elongation seen in vivo.

A poly-histidine motif of HOXA1 is involved in regulatory interactions with cysteine-rich proteins

Homopolymeric amino acid repeats are found in about 24 % of human proteins and are over-represented in transcriptions factors and kinases. Although relatively rare, homopolymeric histidine repeats (polyH) are more significantly found in proteins involved in the regulation of embryonic development. To gain a better understanding of the role of polyH in these proteins, we used a bioinformatic approach to search for shared features in the interactomes of polyH-containing proteins in human. Our analysis revealed that polyH protein interactomes are enriched in cysteine-rich proteins and in proteins containing (a) cysteine repeat(s). Focusing on HOXA1, a HOX transcription factor displaying one long polyH motif, we identified that the polyH motif is required for the HOXA1 interaction with such cysteine-rich proteins. We observed a correlation between the length of the polyH repeat and the strength of the HOXA1 interaction with one Cys-rich protein, MDFI. We also found that metal ion chelators disrupt the HOXA1-MDFI interaction supporting that such metal ions are required for the interaction. Furthermore, we identified three polyH interactors which down-regulate the transcriptional activity of HOXA1. Taken together, our data point towards the involvement of polyH and cysteines in regulatory interactions between proteins, notably transcription factors like HOXA1.

Multimodal Hox5 activity generates motor neuron diversity

Motor neurons (MNs) are the final output of circuits driving fundamental behaviors, such as respiration and locomotion. Hox proteins are essential in generating the MN diversity required for accomplishing these functions, but the transcriptional mechanisms that enable Hox paralogs to assign distinct MN subtype identities despite their promiscuous DNA binding motif are not well understood. Here we show that Hoxa5 controls chromatin accessibility in all mouse spinal cervical MN subtypes and engages TALE co-factors to directly bind and regulate subtype-specific genes. We identify a paralog-specific interaction of Hoxa5 with the phrenic MN-specific transcription factor Scip and show that heterologous expression of Hoxa5 and Scip is sufficient to suppress limb-innervating MN identity. We also demonstrate that phrenic MN identity is stable after Hoxa5 downregulation and identify Klf proteins as potential regulators of phrenic MN maintenance. Our data identify multiple modes of Hoxa5 action that converge to induce and maintain MN identity.

CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development

Proper regulation of gene dosage is critical for the development of the early embryo and the extraembryonic tissues that support it. Specifically, loss of Cdx2 in vivo leads to stunted development of the allantois, an extraembryonic mesoderm-derived structure critical for nutrient delivery and waste removal in the early embryo. In this study, we investigate how CDX2 dose-dependently influences the gene regulatory network underlying extraembryonic mesoderm development. We generate an allelic series for CDX2 in human induced pluripotent stem cells (hiPSCs) consisting of WT, heterozygous, and homozygous null CDX2 genotypes, differentiate these cells in a 2D gastruloid model, and subject these cells to multiomic single nucleus RNA and ATAC sequencing. We identify several genes that CDX2 dose-dependently regulate cytoskeletal integrity and adhesiveness in the extraembryonic mesoderm population, including regulators of the VEGF, canonical WNT, and non-canonical WNT signaling pathways. Despite these dose-dependent gene expression patterns, snATAC-seq reveals that heterozygous CDX2 expression is capable of inducing a WT-like chromatin accessibility profile, suggesting accessibility is not sufficient to drive gene expression when the CDX2 dosage is reduced. Finally, because the loss of CDX2 or TBXT phenocopy one another in vivo, we compare differentially expressed genes in our CDX2 knock-out model to those from TBXT knock-out hiPSCs differentiated in an analogous experiment. This comparison identifies several communally misregulated genes that are critical for cytoskeletal integrity and tissue permeability, including ANK3 and ANGPT1. Together, these results clarify how CDX2 dose-dependently regulates gene expression in the extraembryonic mesoderm and suggest these genes may underlie the defects in vascular development and allantoic elongation seen in the absence or reduction of CDX2 in vivo.

Hox gene functions in the C. elegans nervous system: From early patterning to maintenance of neuronal identity

The nervous system emerges from a series of genetic programs that generate a remarkable array of neuronal cell types. Each cell type must acquire a distinct anatomical position, morphology, and function, enabling the generation of specialized circuits that drive animal behavior. How are these diverse cell types and circuits patterned along the anterior-posterior (A-P) axis of the animal body? Hox genes encode transcription factors that regulate cell fate and patterning events along the A-P axis of the nervous system. While most of our understanding of Hox-mediated control of neuronal development stems from studies in segmented animals like flies, mice, and zebrafish, important new themes are emerging from work in a non-segmented animal: the nematode Caenorhabditis elegans. Studies in C. elegans support the idea that Hox genes are needed continuously and across different life stages in the nervous system; they are not only required in dividing progenitor cells, but also in post-mitotic neurons during development and adult life. In C. elegans embryos and young larvae, Hox genes control progenitor cell specification, cell survival, and neuronal migration, consistent with their neural patterning roles in other animals. In late larvae and adults, C. elegans Hox genes control neuron type-specific identity features critical for neuronal function, thereby extending the Hox functional repertoire beyond early patterning. Here, we provide a comprehensive review of Hox studies in the C. elegans nervous system. To relate to readers outside the C. elegans community, we highlight conserved roles of Hox genes in patterning the nervous system of invertebrate and vertebrate animals. We end by calling attention to new functions in adult post-mitotic neurons for these paradigmatic regulators of cell fate.

TALE transcription factors: Cofactors no more

Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.

Homeodomain complex formation and biomolecular condensates in Hox gene regulation

Hox genes are a family of homeodomain transcription factors that regulate specialized morphological structures along the anterior-posterior axis of metazoans. Over the past few decades, researchers have focused on defining how Hox factors with similar in vitro DNA binding activities achieve sufficient target specificity to regulate distinct cell fates in vivo. In this review, we highlight how protein interactions with other transcription factors, many of which are also homeodomain proteins, result in the formation of transcription factor complexes with enhanced DNA binding specificity. These findings suggest that Hox-regulated enhancers utilize distinct combinations of homeodomain binding sites, many of which are low-affinity, to recruit specific Hox complexes. However, low-affinity sites can only yield reproducible responses with high transcription factor concentrations. To overcome this limitation, recent studies revealed how transcription factors, including Hox factors, use intrinsically disordered domains (IDRs) to form biomolecular condensates that increase protein concentrations. Moreover, Hox factors with altered IDRs have been associated with altered transcriptional activity and human disease states, demonstrating the importance of IDRs in mediating essential Hox output. Collectively, these studies highlight how Hox factors use their DNA binding domains, protein-protein interaction domains, and IDRs to form specific transcription factor complexes that yield accurate gene expression.

Temporal Expression of Hox Genes and Phox2b in the Rat Nucleus Ambiguus During Development: Implications on Laryngeal Innervation

OBJECTIVES

Recurrent laryngeal nerve (RLN) injury results in synkinetic reinnervation and vocal fold paralysis. Investigation of cues expressed in the developing brainstem that influence correct selective targeting of intrinsic laryngeal muscles may elucidate post-injury abnormalities contributing to non-functional reinnervation. Primary targets of interest were Hoxb1 and Hoxb2, members of the Hox family that create overlapping gradients in the developing brain, and their target Phox2b, a transcription factor necessary for cranial nerve branchio- and visceromotoneuron survival.

METHODS

Rat embryos at developmental days E14, E16, E18, and E20 (4 animals/age) were sectioned for RNA in situ hybridization to detect Hoxb1, Hoxb2, and Phox2b mRNA within the brainstem. Slides were costained with Islet1 antibody for identification of the nucleus ambiguus. Results were confirmed using immunohistochemistry. Sections were imaged on a confocal microscope. RNA and protein expressions were quantified using QuPath. Statistical analyses were performed using R.

RESULTS

Hoxb1, Hoxb2, and Phox2b expressions varied according to embryologic age. Hoxb1 and Hoxb2 expression peaked at E16, with significant decreases at E18 and E20 (one-way ANOVA p = 0.001 for both). Phox2b expression was highest at E14 and trended downward with increased embryologic age (one-way ANOVA p = 0.005).

CONCLUSION

Peak expression of Hoxb1 and Hoxb2 is observed at time points when the RLN arrives at the larynx and begins to branch toward individual muscles, positioning these gene products to be involved in cueing laryngeal motoneuron identity and target identification. Higher expression of Phox2b earlier in development suggests a role in laryngeal motoneuron formation.

LEVEL OF EVIDENCE

NA Laryngoscope, 133:3462-3471, 2023.

Octopod Hox genes and cephalopod plesiomorphies

Few other invertebrates captivate our attention as cephalopods do. Octopods, cuttlefish, and squids amaze with their behavior and sophisticated body plans that belong to the most intriguing among mollusks. Little is, however, known about their body plan formation and the role of Hox genes. The latter homeobox genes pattern the anterior-posterior body axis and have only been studied in a single decapod species so far. Here, we study developmental Hox and ParaHox gene expression in Octopus vulgaris. Hox genes are expressed in a near-to-staggered fashion, among others in homologous organs of cephalopods such as the stellate ganglia, the arms, or funnel. As in other mollusks Hox1 is expressed in the nascent octopod shell rudiment. While ParaHox genes are expressed in an evolutionarily conserved fashion, Hox genes are also expressed in some body regions that are considered homologous among mollusks such as the cephalopod arms and funnel with the molluscan foot. We argue that cephalopod Hox genes are recruited to a lesser extent into the formation of non-related organ systems than previously thought and emphasize that despite all morphological innovations molecular data still reveal the ancestral molluscan heritage of cephalopods.

A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2

A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.

Role of the Hox Genes, Sex combs reduced, Fushi tarazu and Antennapedia, in Leg Development of the Spider Mite Tetranychus urticae

Mites, the second largest arthropod group, exhibit rich phenotypic diversity in the development of appendages (legs). For example, the fourth pair of legs (L4) does not form until the second postembryonic developmental stage, namely the protonymph stage. These leg developmental diversities drive body plan diversity in mites. However, little is known about the mechanisms of leg development in mites. Hox genes, homeotic genes, can regulate the development of appendages in arthropods. Three Hox genes, Sex combs reduced (Scr), Fushi tarazu (Ftz) and Antennapedia (Antp), have previously been shown to be expressed in the leg segments of mites. Here, the quantitative real-time reverse transcription PCR shows that three Hox genes are significantly increased in the first molt stage. RNA interference results in a set of abnormalities, including L3 curl and L4 loss. These results suggest that these Hox genes are required for normal leg development. Furthermore, the loss of single Hox genes results in downregulating the expression of the appendage marker Distal-less (Dll), suggesting that the three Hox genes can work together with Dll to maintain leg development in Tetranychus urticae. This study will be essential to understanding the diversity of leg development in mites and changes in Hox gene function.

A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest

Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.

Major β cell-specific functions of NKX2.2 are mediated via the NK2-specific domain

The consolidation of unambiguous cell fate commitment relies on the ability of transcription factors (TFs) to exert tissue-specific regulation of complex genetic networks. However, the mechanisms by which TFs establish such precise control over gene expression have remained elusive-especially in instances in which a single TF operates in two or more discrete cellular systems. In this study, we demonstrate that β cell-specific functions of NKX2.2 are driven by the highly conserved NK2-specific domain (SD). Mutation of the endogenous NKX2.2 SD prevents the developmental progression of β cell precursors into mature, insulin-expressing β cells, resulting in overt neonatal diabetes. Within the adult β cell, the SD stimulates β cell performance through the activation and repression of a subset of NKX2.2-regulated transcripts critical for β cell function. These irregularities in β cell gene expression may be mediated via SD-contingent interactions with components of chromatin remodelers and the nuclear pore complex. However, in stark contrast to these pancreatic phenotypes, the SD is entirely dispensable for the development of NKX2.2-dependent cell types within the CNS. Together, these results reveal a previously undetermined mechanism through which NKX2.2 directs disparate transcriptional programs in the pancreas versus neuroepithelium.

Modulation of DNA-protein interactions by proximal genetic elements as uncovered by interpretable deep learning

Transcription factors (TF) recognize specific motifs in the genome that are typically 6-12 bp long to regulate various aspects of the cellular machinery. Presence of binding motifs and favorable genome accessibility are key drivers for a consistent TF-DNA interaction. Although these pre-requisites may occur thousands of times in the genome, there seems to be a high degree of selectivity for the sites that are actually bound. Here, we present a deep-learning framework that identifies and characterizes the upstream and downstream genetic elements to the binding motif, for their role in enforcing the mentioned selectivity. The proposed framework is based on an interpretable recurrent neural network architecture that enables for the relative analysis of sequence context features. We apply the framework to model twenty-six transcription factors and score the TF-DNA binding at a base-pair resolution. We find significant differences in activations of DNA context features for bound and unbound sequences. In addition to standardized evaluation protocols, we offer outstanding interpretability that enables us to identify and annotate DNA sequence with possible elements that modulate TF-DNA binding. Also, differences in data processing have a huge influence on the overall model performance. Overall, the proposed framework allows for novel insights on the non-coding genetic elements and their role in facilitating a stable TF-DNA interaction.

Large-scale mapping and mutagenesis of human transcriptional effector domains

Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.

Floral Homeotic Factors: A Question of Specificity

MADS-domain transcription factors are involved in the control of a multitude of processes in eukaryotes, and in plants, they play particularly important roles during reproductive development. Among the members of this large family of regulatory proteins are the floral organ identity factors, which specify the identities of the different types of floral organs in a combinatorial manner. Much has been learned over the past three decades about the function of these master regulators. For example, it has been shown that they have similar DNA-binding activities and that their genome-wide binding patterns exhibit large overlaps. At the same time, it appears that only a minority of binding events lead to changes in gene expression and that the different floral organ identity factors have distinct sets of target genes. Thus, binding of these transcription factors to the promoters of target genes alone may not be sufficient for their regulation. How these master regulators achieve specificity in a developmental context is currently not well understood. Here, we review what is known about their activities and highlight open questions that need to be addressed to gain more detailed insights into the molecular mechanisms underlying their functions. We discuss evidence for the involvement of cofactors as well as the results from studies on transcription factors in animals that may be instructive for a better understanding of how the floral organ identity factors achieve regulatory specificity.

Retinoic acid control of pax8 during renal specification of Xenopus pronephros involves hox and meis3

Development of the Xenopus pronephros relies on renal precursors grouped at neurula stage into a specific region of dorso-lateral mesoderm called the kidney field. Formation of the kidney field at early neurula stage is dependent on retinoic (RA) signaling acting upstream of renal master transcriptional regulators such as pax8 or lhx1. Although lhx1 might be a direct target of RA-mediated transcriptional activation in the kidney field, how RA controls the emergence of the kidney field remains poorly understood. In order to better understand RA control of renal specification of the kidney field, we have performed a transcriptomic profiling of genes affected by RA disruption in lateral mesoderm explants isolated prior to the emergence of the kidney field and cultured at different time points until early neurula stage. Besides genes directly involved in pronephric development (pax8, lhx1, osr2, mecom), hox (hoxa1, a3, b3, b4, c5 and d1) and the hox co-factor meis3 appear as a prominent group of genes encoding transcription factors (TFs) downstream of RA. Supporting the idea of a role of meis3 in the kidney field, we have observed that meis3 depletion results in a severe inhibition of pax8 expression in the kidney field. Meis3 depletion only marginally affects expression of lhx1 and aldh1a2 suggesting that meis3 principally acts upstream of pax8. Further arguing for a role of meis3 and hox in the control of pax8, expression of a combination of meis3, hoxb4 and pbx1 in animal caps induces pax8 expression, but not that of lhx1. The same combination of TFs is also able to transactivate a previously identified pax8 enhancer, Pax8-CNS1. Mutagenesis of potential PBX-Hox binding motifs present in Pax8-CNS1 further allows to identify two of them that are necessary for transactivation. Finally, we have tested deletions of regulatory sequences in reporter assays with a previously characterized transgene encompassing 36.5 ​kb of the X. tropicalis pax8 gene that allows expression of a truncated pax8-GFP fusion protein recapitulating endogenous pax8 expression. This transgene includes three conserved pax8 enhancers, Pax8-CNS1, Pax8-CNS2 and Pax8-CNS3. Deletion of Pax8-CNS1 alone does not affect reporter expression, but deletion of a 3.5 ​kb region encompassing Pax8-CNS1 and Pax8-CNS2 results in a severe inhibition of reporter expression both in the otic placode and kidney field domains.

Hox genes in development and beyond

Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.

The pioneering function of the hox transcription factors

Ever since the discovery that the Hox family of transcription factors establish morphological diversity in the developing embryo, major efforts have been directed towards understanding Hox-dependent patterning. This has led to important discoveries, notably on the mechanisms underlying the collinear expression of Hox genes and Hox binding specificity. More recently, several studies have provided evidence that Hox factors have the capacity to bind their targets in an inaccessible chromatin context and trigger the switch to an accessible, transcriptional permissive, chromatin state. In this review, we provide an overview of the evidences supporting that Hox factors behave as pioneer factors and discuss the potential mechanisms implicated in Hox pioneer activity as well as the significance of this functional property in Hox-dependent patterning.

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.

The START domain mediates Arabidopsis GLABRA2 dimerization and turnover independently of homeodomain DNA binding

Class IV homeodomain leucine-zipper transcription factors (HD-Zip IV TFs) are key regulators of epidermal differentiation that are characterized by a DNA-binding HD in conjunction with a lipid-binding domain termed steroidogenic acute regulatory-related lipid transfer (START). Previous work established that the START domain of GLABRA2 (GL2), a HD-Zip IV member from Arabidopsis (Arabidopsis thaliana), is required for TF activity. Here, we addressed the functions and possible interactions of START and the HD in DNA binding, dimerization, and protein turnover. Deletion analysis of the HD and missense mutations of a conserved lysine (K146) resulted in phenotypic defects in leaf trichomes, root hairs, and seed mucilage, similar to those observed for START domain mutants, despite nuclear localization of the respective proteins. In vitro and in vivo experiments demonstrated that while HD mutations impair binding to target DNA, the START domain is dispensable for DNA binding. Vice versa, protein interaction assays revealed impaired GL2 dimerization for multiple alleles of START mutants, but not HD mutants. Using in vivo cycloheximide chase experiments, we provided evidence for the role of START, but not HD, in maintaining protein stability. This work advances our mechanistic understanding of HD-Zip TFs as multidomain regulators of epidermal development in plants.

A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint

The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of nkx3.2 and leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.

HOX genes in stem cells: Maintaining cellular identity and regulation of differentiation

Stem cells display a unique cell type within the body that has the capacity to self-renew and differentiate into specialized cell types. Compared to pluripotent stem cells, adult stem cells (ASC) such as mesenchymal stem cells (MSCs) and hematopoietic stem cells (HSCs) exhibit restricted differentiation capabilities that are limited to cell types typically found in the tissue of origin, which implicates that there must be a certain code or priming determined by the tissue of origin. HOX genes, a subset of homeobox genes encoding transcription factors that are generally repressed in undifferentiated pluripotent stem cells, emerged here as master regulators of cell identity and cell fate during embryogenesis, and in maintaining this positional identity throughout life as well as specifying various regional properties of respective tissues. Concurrently, intricate molecular circuits regulated by diverse stem cell-typical signaling pathways, balance stem cell maintenance, proliferation and differentiation. However, it still needs to be unraveled how stem cell-related signaling pathways establish and regulate ASC-specific HOX expression pattern with different temporal-spatial topography, known as the HOX code. This comprehensive review therefore summarizes the current knowledge of specific ASC-related HOX expression patterns and how these were integrated into stem cell-related signaling pathways. Understanding the mechanism of HOX gene regulation in stem cells may provide new ways to manipulate stem cell fate and function leading to improved and new approaches in the field of regenerative medicine.

The emerging role of non-coding RNAs in the epigenetic regulation of pediatric cancers

Epigenetics is a process that involves the regulation of gene expression without altering the sequence of DNA. Numerous studies have documented that epigenetic mechanisms play a critical role in cell growth, differentiation, and cancer over the past decade. The well-known epigenetic modifications are either on DNA or at the histone proteins. Although several studies have focused on regulating gene expression by non-coding RNAs, the current understanding of their biological functions in various human diseases, particularly in cancers, is inadequate. Only about two percent of DNA is involved in coding the protein-coding genes, and leaving the rest 98 percent is non-coding and the scientific community regarded as junk or noise with no known purpose. Most non-coding RNAs are derived from such junk DNA and are known to be involved in various signaling pathways involving cancer initiation, progression, and the development of therapy resistance in many human cancer types. Recent studies have suggested that non-coding RNAs, especially microRNAs, piwi-interactingRNAs, and long non-coding RNAs, play a significant role in controlling epigenetic mechanism(s), indicating the potential effect of epigenetic modulation of non-coding RNAs on cancer progression. In this review article, we briefly presented epigenetic marks' characteristics, crosstalk between epigenetic modifications and microRNAs, piwi-interactingRNAs, and long non-coding RNAs to uncover the effect on the phenotype of pediatric cancers. Further, current knowledge on understanding the RNA epigenetics will help design novel therapeutics that target epigenetic regulatory networks to benefit cancer patients in the clinic.

Hox genes collaborate with helix-loop-helix factor Grainyhead to promote neuroblast apoptosis along the anterior-posterior axis of the Drosophila larval central nervous system

Hox genes code for a family of a homeodomain (HD) containing transcription factors that use TALE-HD containing factors Pbx/Exd and Meis/Hth to specify the development of the anterior-posterior (AP) axis of an organism. However, the absence of TALE-HD containing factors from specific tissues emphasizes the need to identify and validate new Hox cofactors. In Drosophila central nervous system (CNS), Hox execute segment-specific apoptosis of neural stem cells (neuroblasts-NBs) and neurons. In abdominal segments of larval CNS, Hox gene Abdominal-A (AbdA) mediates NB apoptosis with the help of Exd and bHLH factor Grainyhead (Grh) using a 717 bp apoptotic enhancer. In this study, we show that this enhancer is critical for abdominal NB apoptosis and relies on two separable set of DNA binding motifs responsible for its initiation and maintenance. Our results also show that AbdA and Grh interact through their highly conserved DNA binding domains, and the DNA binding specificity of AbdA-HD is important for it to interact with Grh and essential for it to execute NB apoptosis in CNS. We also establish that Grh is required for Hox-dependent NB apoptosis in Labial and Sex Combs Reduced (Scr) expressing regions of the CNS, and it can physically interact with all the Hox proteins in vitro. Our biochemical and functional data collectively support the idea that Grh can function as a Hox cofactor and help them carry out their in vivo roles during development.

Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity

Background

Hox proteins finely coordinate antero-posterior axis during embryonic development and through their action specific target genes are expressed at the right time and space to determine the embryo body plan. As master transcriptional regulators, Hox proteins recognize DNA through the homeodomain (HD) and interact with a multitude of proteins, including general transcription factors and other cofactors. HD binding specificity increases by protein–protein interactions with a diversity of cofactors that outline the Hox interactome and determine the transcriptional landscape of the selected target genes. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but its precise mechanism remains to be elucidated.

Results

Here we report Antennapedia (Antp) Hox protein–protein interaction with the TATA-binding protein (TBP) and the formation of novel trimeric complexes with TFIIEβ and Extradenticle (Exd), as well as its participation in transcriptional regulation. Using Bimolecular Fluorescence Complementation (BiFC), we detected the interaction of Antp-TBP and, in combination with Förster Resonance Energy Transfer (BiFC-FRET), the formation of the trimeric complex with TFIIEβ and Exd in living cells. Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. The trimeric complexes of Antp-TBP with TFIIEβ and Exd were validated using different Antp mutations to disrupt the trimeric complexes. Interestingly, the trimeric complex Antp-TBP-TFIIEβ significantly increased the transcriptional activity of Antp, whereas Exd diminished its transactivation.

Conclusions

Our findings provide important insights into the Antp interactome with the direct interaction of Antp with TBP and the two new trimeric complexes with TFIIEβ and Exd. These novel interactions open the possibility to analyze promoter function and gene expression to measure transcription factor binding dynamics at target sites throughout the genome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-022-00239-8.

Diversification and Functional Evolution of HOX Proteins

Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.

Hox proteins interact to pattern neuronal subtypes in Caenorhabditis elegans males

Hox transcription factors are conserved regulators of neuronal subtype specification on the anteroposterior axis in animals, with disruption of Hox gene expression leading to homeotic transformations of neuronal identities. We have taken advantage of an unusual mutation in the Caenorhabditis elegans Hox gene lin-39, lin-39(ccc16), which transforms neuronal fates in the C. elegans male ventral nerve cord in a manner that depends on a second Hox gene, mab-5. We have performed a genetic analysis centered around this homeotic allele of lin-39 in conjunction with reporters for neuronal target genes and protein interaction assays to explore how LIN-39 and MAB-5 exert both flexibility and specificity in target regulation. We identify cis-regulatory modules in neuronal reporters that are both region-specific and Hox-responsive. Using these reporters of neuronal subtype, we also find that the lin-39(ccc16) mutation disrupts neuronal fates specifically in the region where lin-39 and mab-5 are coexpressed, and that the protein encoded by lin-39(ccc16) is active only in the absence of mab-5. Moreover, the fates of neurons typical to the region of lin-39-mab-5 coexpression depend on both Hox genes. Our genetic analysis, along with evidence from Bimolecular Fluorescence Complementation protein interaction assays, supports a model in which LIN-39 and MAB-5 act at an array of cis-regulatory modules to cooperatively activate and to individually activate or repress neuronal gene expression, resulting in regionally specific neuronal fates.

Roles of Drosophila Hox Genes in the Assembly of Neuromuscular Networks and Behavior

Hox genes have been known for specifying the anterior-posterior axis (AP) in bilaterian body plans. Studies in vertebrates have shown their importance in developing region-specific neural circuitry and diversifying motor neuron pools. In Drosophila, they are instrumental for segment-specific neurogenesis and myogenesis early in development. Their robust expression in differentiated neurons implied their role in assembling region-specific neuromuscular networks. In the last decade, studies in Drosophila have unequivocally established that Hox genes go beyond their conventional functions of generating cellular diversity along the AP axis of the developing central nervous system. These roles range from establishing and maintaining the neuromuscular networks to controlling their function by regulating the motor neuron morphology and neurophysiology, thereby directly impacting the behavior. Here we summarize the limited knowledge on the role of Drosophila Hox genes in the assembly of region-specific neuromuscular networks and their effect on associated behavior.

Transcriptional Regulation and Implications for Controlling Hox Gene Expression

Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.

An Evolutionary Perspective on Hox Binding Site Preferences in Two Different Tissues

Transcription factor (TF) networks define the precise development of multicellular organisms. While many studies focused on TFs expressed in specific cell types to elucidate their contribution to cell specification and differentiation, it is less understood how broadly expressed TFs perform their precise functions in the different cellular contexts. To uncover differences that could explain tissue-specific functions of such TFs, we analyzed here genomic chromatin interactions of the broadly expressed Drosophila Hox TF Ultrabithorax (Ubx) in the mesodermal and neuronal tissues using bioinformatics. Our investigations showed that Ubx preferentially interacts with multiple yet tissue-specific chromatin sites in putative regulatory regions of genes in both tissues. Importantly, we found the classical Hox/Ubx DNA binding motif to be enriched only among the neuronal Ubx chromatin interactions, whereas a novel Ubx-like motif with rather low predicted Hox affinities was identified among the regions bound by Ubx in the mesoderm. Finally, our analysis revealed that tissues-specific Ubx chromatin sites are also different with regards to the distribution of active and repressive histone marks. Based on our data, we propose that the tissue-related differences in Ubx binding behavior could be a result of the emergence of the mesoderm as a new germ layer in triploblastic animals, which might have required the Hox TFs to relax their binding specificity.

Mechanisms Underlying Hox-Mediated Transcriptional Outcomes

Metazoans differentially express multiple Hox transcription factors to specify diverse cell fates along the developing anterior-posterior axis. Two challenges arise when trying to understand how the Hox transcription factors regulate the required target genes for morphogenesis: First, how does each Hox factor differ from one another to accurately activate and repress target genes required for the formation of distinct segment and regional identities? Second, how can a Hox factor that is broadly expressed in many tissues within a segment impact the development of specific organs by regulating target genes in a cell type-specific manner? In this review, we highlight how recent genomic, interactome, and cis-regulatory studies are providing new insights into answering these two questions. Collectively, these studies suggest that Hox factors may differentially modify the chromatin of gene targets as well as utilize numerous interactions with additional co-activators, co-repressors, and sequence-specific transcription factors to achieve accurate segment and cell type-specific transcriptional outcomes.

Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube

Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.

Naked (N) mutant mice carry a nonsense mutation in the homeobox of Hoxc13

Loss of function mutations in HOXC13 have been associated with Ectodermal Dysplasia-9, Hair/Nail Type (ECTD9) in consanguineous families, characterized by sparse to complete absence of hair and nail dystrophy. Here we characterize the spontaneous mouse mutation Naked (N) as a terminal truncation in the Hoxc13 (homeobox C13) gene. Similar to previous reports for homozygous Hoxc13 knock-out (KO) mice, homozygous N/N mice exhibit generalized alopecia with abnormal nails and a short lifespan. However, in contrast to Hoxc13 heterozygous KO mice, N/+ mice show generalized or partial alopecia, associated with loss of hair fibres, along with normal lifespan and fertility. Our data point to a lack of nonsense-mediated Hoxc13 transcript decay and the presence of the truncated mutant protein in N/N and N/+ hair follicles, thus suggesting a dominant-negative mutation. To our knowledge, this is the first report of a semi-dominant and potentially dominant-negative mutation affecting Hoxc13/HOXC13. Furthermore, recreating the N mutant allele in mice using CRISPR/Cas9-mediated genome editing resulted in the same spectrum of deficiencies as those associated with the spontaneous Naked mutation, thus confirming that N is indeed a Hoxc13 mutant allele. Considering the low viability of the Hoxc13 KO mice, the Naked mutation provides an attractive new model for studying ECTD9 disease mechanisms.

Cell-type-specific Hox regulatory strategies orchestrate tissue identity

Hox proteins are homeodomain transcription factors that diversify serially homologous segments along the animal body axis, as revealed by the classic bithorax phenotype of Drosophila melanogaster, in which mutations in Ultrabithorax (Ubx) transform the third thoracic segment into the likeness of the second thoracic segment. To specify segment identity, we show that Ubx both increases and decreases chromatin accessibility, coinciding with its dual role as both an activator and repressor of transcription. However, the choice of transcriptional activity executed by Ubx is spatially regulated and depends on the availability of cofactors, with Ubx acting as a repressor in some populations and as an activator in others. Ubx-mediated changes to chromatin accessibility positively and negatively affect the binding of Scalloped (Sd), a transcription factor that is required for appendage development in both segments. These findings illustrate how a single Hox protein can modify complex gene regulatory networks to transform the identity of an entire tissue.

A genome-wide identification and analysis of the homeobox genes in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae)

The homeobox family is a large and diverse superclass of genes, many of which act as transcription factors that play important roles in tissue differentiation and embryogenesis in animals. The brown planthopper (BPH), Nilaparvata lugens, is the most destructive pest of rice in Asia, and high fecundity contributes significantly to its ecological success in natural and agricultural habits. Here, we identified 94 homeobox genes in BPH, which could be divided into 75 gene families and 9 classes. This number is comparable to the number of homeobox genes found in the honeybee Apis mellifera, but is slightly less than in Drosophila or the red flour beetle Tribolium castaneum. A spatio-temporal analysis indicated that most BPH homeobox genes were expressed in a development and tissue-specific manner, of which 21 genes were highly expressed in ovaries. RNA interference (RNAi)-mediated functional assay showed that 22 homeobox genes were important for nymph development and the nymph to adult transition, whereas 67 genes were dispensable during this process. Fecundity assay showed that knockdown of 13 ovary-biased genes (zfh1, schlank, abd-A, Lim3_2, Lmxb, Prop, ap_1, Not, lab, Hmx, vis, Pknox, and C15) led to the reproductive defect. This is the first comprehensive investigation into homeobox genes in a hemipteran insect and thus helps us to understand the functional significance of homeobox genes in insect reproduction.

Scarless engineering of the Drosophila genome near any site-specific integration site

We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as a MiMIC insertion. This two-step method combines phiC31 integrase-mediated site-specific integration and homing nuclease-mediated resolution of local duplications, efficiently converting the original landing site allele to modified alleles that only have the desired change(s). Dominant markers incorporated into this method allow correct individual flies to be efficiently identified at each step. In principle, single attP sites and FRT sites are also valid landing sites. Given the large and increasing number of landing site lines available in the fly community, this method provides an easy and fast way to efficiently edit the majority of the Drosophila genome in a scarless manner. This technique should also be applicable to other species.

A TALE/HOX code unlocks WNT signalling response towards paraxial mesoderm

One fundamental yet unresolved question in biology remains how cells interpret the same signalling cues in a context-dependent manner resulting in lineage specification. A key step for decoding signalling cues is the establishment of a permissive chromatin environment at lineage-specific genes triggering transcriptional responses to inductive signals. For instance, bipotent neuromesodermal progenitors (NMPs) are equipped with a WNT-decoding module, which relies on TCFs/LEF activity to sustain both NMP expansion and paraxial mesoderm differentiation. However, how WNT signalling activates lineage specific genes in a temporal manner remains unclear. Here, we demonstrate that paraxial mesoderm induction relies on the TALE/HOX combinatorial activity that simultaneously represses NMP genes and activates the differentiation program. We identify the BRACHYURY-TALE/HOX code that destabilizes the nucleosomes at WNT-responsive regions and establishes the permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1, unlocking the WNT-mediated transcriptional program that drives NMPs towards the paraxial mesodermal fate.

Cells in the developing embryo interpret WNT signalling with context-dependence, but the mechanism decoding these cues is unclear. Here, the authors show that combinatorial TALE/HOX activity destabilizes nucleosomes at WNT-responsive regions to activate paraxial mesodermal genes.

Hox genes are essential for the development of eyespots in Bicyclus anynana butterflies

The eyespot patterns found on the wings of nymphalid butterflies are novel traits that originated first in hindwings and subsequently in forewings, suggesting that eyespot development might be dependent on Hox genes. Hindwings differ from forewings in the expression of Ultrabithorax (Ubx), but the function of this Hox gene in eyespot development as well as that of another Hox gene Antennapedia (Antp), expressed specifically in eyespots centers on both wings, are still unclear. We used CRISPR-Cas9 to target both genes in Bicyclus anynana butterflies. We show that Antp is essential for eyespot development on the forewings and for the differentiation of white centers and larger eyespots on hindwings, whereas Ubx is essential not only for the development of at least some hindwing eyespots but also for repressing the size of other eyespots. Additionally, Antp is essential for the development of silver scales in male wings. In summary, Antp and Ubx, in addition to their conserved roles in modifying serially homologous segments along the anterior-posterior axis of insects, have acquired a novel role in promoting the development of a new set of serial homologs, the eyespot patterns, in both forewings (Antp) and hindwings (Antp and Ubx) of B. anynana butterflies. We propose that the peculiar pattern of eyespot origins on hindwings first, followed by forewings, could be due to an initial co-option of Ubx into eyespot development followed by a later, partially redundant, co-option of Antp into the same network.

Developmental Robustness: The Haltere Case in Drosophila

Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a “self-sufficient” molecular model to explain the development of a particular flight organ that is under the control of the Hox gene Ultrabithorax (Ubx) in the fruit fly Drosophila melanogaster. Our model is based on a candidate RNAi screen and additional genetic analyses that all converge to an autonomous and cofactor-independent mode of action for Ubx. We postulate that this self-sufficient molecular mechanism is possible due to an unusually high expression level of the Hox protein. We propose that high dosage could constitute a so far poorly investigated molecular strategy for allowing Hox proteins to both innovate and stabilize new forms during evolution.

Transcription factor control of virulence in phytopathogenic fungi

Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.

The Hox protein conundrum: The "specifics" of DNA binding for Hox proteins and their partners

Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA interactions. It is crucial to study transcription factor binding by incorporating components of more complex, multi-protein interactions in concert with small changes in binding motifs that can significantly impact DNA binding specificity and subsequent alterations in gene expression. To incorporate the multiple elements that can determine HOX protein binding specificity, we propose a more integrative Cooperative Binding model.

Identification of in vivo Hox13-binding sites reveals an essential locus controlling zebrafish brachyury expression

During early embryogenesis, the vertebrate embryo extends from anterior to posterior because of the progressive addition of cells from a posteriorly localized neuromesodermal progenitor (NMp) population. An autoregulatory loop between Wnt and Brachyury/Tbxt is required for NMps to retain mesodermal potential and, hence, normal axis development. We recently showed that Hox13 genes help to support body axis formation and to maintain the autoregulatory loop, although the direct Hox13 target genes were unknown. Here, using a new method for identifying in vivo transcription factor-binding sites, we identified more than 500 potential Hox13 target genes in zebrafish. Importantly, we found two highly conserved Hox13-binding elements far from the tbxta transcription start site that also contain a conserved Tcf7/Lef1 (Wnt response) site. We show that the proximal of the two elements is sufficient to confer somitogenesis-stage expression to a tbxta promoter that, on its own, only drives NMp expression during gastrulation. Importantly, elimination of this proximal element produces shortened embryos due to aberrant formation of the most posterior somites. Our study provides a potential direct connection between Hox13 and regulation of the Wnt/Brachyury loop.

Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation

Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes in T cell acute lymphoblastic leukemia. These results highlight an analogous enhancer repression mechanism at play in normal and cancer conditions, but imposing distinct developmental constraints.

HoxB genes regulate neuronal delamination in the trunk neural tube by controlling the expression of Lzts1

Differential Hox gene expression is central for specification of axial neuronal diversity in the spinal cord. Here, we uncover an additional function of Hox proteins in the developing spinal cord, restricted to B cluster Hox genes. We found that members of the HoxB cluster are expressed in the trunk neural tube of chicken embryo earlier than Hox from the other clusters, with poor antero-posterior axial specificity and with overlapping expression in the intermediate zone (IZ). Gain-of-function experiments of HoxB4, HoxB8 and HoxB9, respectively, representative of anterior, central and posterior HoxB genes, resulted in ectopic progenitor cells in the mantle zone. The search for HoxB8 downstream targets in the early neural tube identified the leucine zipper tumor suppressor 1 gene (Lzts1), the expression of which is also activated by HoxB4 and HoxB9. Gain- and loss-of-function experiments showed that Lzts1, which is expressed endogenously in the IZ, controls neuronal delamination. These data collectively indicate that HoxB genes have a generic function in the developing spinal cord, controlling the expression of Lzts1 and neuronal delamination.

Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression

Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif HB1RE (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel HB1RE motif contributes to HOXB1 function in part through a repressive role in gene expression.

Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification

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The mechanisms by which ISL1 and LHX3 specify neuronal cell identity are unknown.

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EMSA/SPR data show ISL1 and LHX3 have markedly different DNA-binding behaviours.

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SAXS shows ISL1/LHX3:DNA complexes are flexible in nature.

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ISL1 binds DNA poorly but appears to modulate the DNA-binding specificity of LHX3.

The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.