• buttonhead
• cap'n'collar
• caudal
• collier
• crocodile
• empty spiracles
• giant
• hunchback
• huckebein
• Krüppel
• knirps
• orthodenticle
• sloppy paired
• tailless

Pair rule genes

• even-skipped
• fushi tarazu
• hairy
• odd-paired
• odd skipped
• paired
• runt
• sloppy paired
• Tenascin major

• Chip
• C-terminal binding protein
• degringolade
• eyelid
• ftz-F1
• dead ringer
• domeless
• hopscotch
• lilliputian
• marelle (also known as STAT)
• mir-184
• outstretched
• Rpd3
• shuttle craft
• Sir2
• Sox box protein 70D (also known as Dichaete)
• squid

The pair-rule class of segmentation genes was identified in a Nobel award winning genetic screen, performed in the late 1970s by Christiane Nusslein-Volhard, Eric Wieschaus and co-workers. Pair-rule mutants affect homologous parts of the cuticle pattern in alternate segments, resulting in the so-called "double-segment" periodicity of defects. As noted by Nusslein-Volhard and Wieschaus (1980) in their original report, the pair-rule class of segmentation genes was unexpected; the presence of this class suggests that during development, the embryo initially has a repeat unit corresponding to two segments, which are later subdivided into individual segments. Since their discovery, all eight 'classical' pair-rule genes (even-skipped, hairy, runt, fushi-tarazu, odd-skipped, paired, odd-paired, and sloppy-paired) have been studied at the genetic and molecular levels. Each gene encodes a transcription factor (Pankratz, 1993) that is expressed in regions corresponding to each gene's domains of function, as deduced from the gene's mutant phenotype.

A hallmark of the pair-rule genes is their striped pattern of expression at the end of the cellular blastoderm stage. Interestingly, analysis of pair-rule gene expression during early cellularization indicates that, as a class, the pair-rule genes are initially expressed in domains larger than their 'final' pair-rule pattern. In fact, the products of most pair-rule genes initially accumulate throughout the entire metameric region. During cellularization, pair-rule stripes are formed by a combination of events: accumulation of products within the stripes and loss of pair-rule products in the intervening interstripes (Carroll, 1990). Formation of the interstripes must reflect a combination of transcriptional repression coupled with the turnover of gene products, whereas, establishment of stripes must reflect continued (and possibly increased) expression. Since the equivalent sequence of stripe patterns is seen for pair-rule mRNA and protein, neither translational regulation nor differential rates of protein turnover (relative to mRNA) appear likely to have a s ignificant influence on pair-rule pattern. This suggests that as a class, the pair-rule genes share a common mechanism for the rapid turnover of their gene products. Since the pair-rule genes are posited to function in discrete domains of the embryo, determining how the pair-rule gene products are specifically synthesized and degraded (or turned-over) will be important for a thorough understanding of how this class functions during development.

Interestingly, although the pair-rule genes were identified genetically by their pattern defects in alternate segments, this class of segmentation genes is expressed in a wide variety of tissues during embryogenesis. One of the most fascinating examples of unexpected expression subsequent to cellularization is the 'segment-polarity' pattern of expression observed with gene products from the even-skipped, runt, odd-skipped, paired and odd-paired loci. In addition, select pair-rule genes are expressed in the mesoderm, gut and most notably the central nervous system.

During segmentation, the pair-rule genes function as intermediates between the nonperiodic expression of gap genes and the repeated expression patterns of the segment-polarity genes. Understanding how each pair-rule gene functions within the segmentation hierarchy involves addressing at least three questions:

1. What genes are required for the correct expression of a particular pair-rule gene?
2. For a given pair-rule gene, what are its downstream targets?
3. What other pair-rule genes, if any, interact with an individual pair-rule gene in regulating these targets?

Initially, it was proposed that the gap genes were the sole regulators of pair-rule expression, and in turn, the segment-polarity genes were thought to be the sole targets of pair-rule function. However, studies have shown that some pair-rule genes are regulated by other members of the pair-rule class, suggesting that the pair-rule class contains both regulators and targets of pair-rule genes (Pankratz, 1993). According to this view, only a subset of pair-rule genes (even-skipped, hairy, and runt) respond directly to gap information. These so-called "primary" pair-rule genes regulate the expression of the remaining so-called "secondary" pair-rule genes (fushi-tarazu, odd-skipped, paired, odd-paired, and sloppy-paired), which in turn play a more direct role in the establishment of segment-polarity gene expression. While this probably over-simplifies the nature of these interactions, it is clear that understanding the role of a particular pair-rule gene in the segmentation hierarchy requires not only an analysis of the individual gene's role as a mediator between the gap and segment-polarity classes, but also requires identifying its function within the pair-rule class.

A well-characterized target of pair-rule function is the segment-polarity gene engrailed (en), which is expressed in 14 stripes during gastrulation and at all subsequent stages of embryogenesis. Each engrailed stripe marks the posterior margin of a segment, or the anterior margin of a parasegment. Correct establishment of the 14 engrailed stripes requires the activities of all the pair-rule genes (DiNardo, 1987). However, in general, mutations in individual pair-rule genes affect either odd- or even-numbered engrailed stripes. Thus, the correct establishment of alternate engrailed stripes requires the combined activities of a subset of pair-rule genes.

How do these combinations of pair-rule activities regulate engrailed? At the time when en is initially expressed, the various pair-rule genes are present in distinct stripes that frequently overlap. It is widely held that the resulting overlapping stripes can be translated into vertical rows of cells containing unique combinations of pair-rule gene products capable of interacting with one another to establish the correct pattern of en and other segmentation genes (DiNardo, 1987). According to this model, overlapping stripes of activators (e.g. Fushi-tarazu) and repressors (such as Odd-skipped) define the narrow engrailed stripes.

While this 'combinatorial model' provides a basis for understanding how narrow engrailed stripes are specified by broad pair-rule stripes, it does not define the precise interactions between the individual pair-rule genes. For example, Odd-skipped (Odd), a repressor of en, and Fushi-tarazu (Ftz), an activator of en, are proposed to interact with one another to specify the even-numbered en stripes. Two hypotheses have been proposed to account for the correct positioning of a narrow en stripe within a broad Ftz stripe. In the Hierarchy model, en responds to a critical threshold level of Ftz activity within the Ftz stripe (Lawrence, 1989). In this model, Odd and Ftz are proposed to interact in a hierarchy, with Odd protein functioning to repress ftz, presumably at the transcriptional level (Mullen, 1995). A key feature of this model is that Odd represses en indirectly by reducing Ftz levels. In the alternate view, the Combinatorial model, the presence of a negative regulator of en prevents en expression within portions of the Ftz stripe. According to this model, Odd is proposed to interact in a combinatorial (parallel) manner with Ftz. The distinguishing feature of this model is that Odd does not affect en by altering Ftz levels; rather, Odd acts to prevent en activation within the Ftz stripe. Recent experimental data (see Odd) strongly supports the Combinatorial model of interactions between Odd and Ftz (Ward, 1997 and Ward and Coulter, manuscript in prep.). Thus, in this case, two "secondary" pair-rule genes appear to act independently of one another in order to define precisely the even-numbered en stripes. Interestingly, the primary pair-rule gene even-skipped (eve) appears to directly regulate ftz and odd to define the anterior margins of these two secondary pair-rule genes, thereby allowing en to be activated in a narrow stripe (Ward, 1997, Ward and Coulter, manuscript in prep., Fujioka, 1995 and Manoukian, 1992).

This essay courtesy of and copyright © 1997, Ellen J. Ward

Dynamic maternal gradients control timing and shift-rates for Drosophila gap gene expression

This study simulated dynamic morphogen interpretation by the gap gene network in Drosophila. Gap genes are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. This study used a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, the system was simulate in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. A newly developed method was used for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, this study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory processes in development (Verd, 2017).

An enhancer's length and composition are shaped by its regulatory task

Enhancers drive the gene expression patterns required for virtually every process in metazoans. It is proposed that enhancer length and transcription factor (TF) binding site composition-the number and identity of TF binding sites-reflect the complexity of the enhancer's regulatory task. In development, regulatory task complexity is defined as the number of fates specified in a set of cells at once. It is hypothesized that enhancers with more complex regulatory tasks will be longer, with more, but less specific, TF binding sites. Larger numbers of binding sites can be arranged in more ways, allowing enhancers to drive many distinct expression patterns, and therefore cell fates, using a finite number of TF inputs. This study compared ~100 enhancers patterning the more complex anterior-posterior (AP) axis and the simpler dorsal-ventral (DV) axis in Drosophila and found that the AP enhancers are longer with more, but less specific binding sites than the (DV) enhancers. Using a set of ~3,500 enhancers, enhancer length and TF binding site number were found to increase with increasing regulatory task complexity. Therefore, to be broadly applicable, computational tools to study enhancers must account for differences in regulatory task (Li, 2017).

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

Drosophila segmentation is a well-established paradigm for developmental pattern formation. However, the later stages of segment patterning, regulated by the "pair-rule" genes, are still not well understood at the system level. Building on established genetic interactions, a logical model of the Drosophila pair-rule system was constructed that takes into account the demonstrated stage-specific architecture of the pair-rule gene network. Simulation of this model can accurately recapitulate the observed spatiotemporal expression of the pair-rule genes, but only when the system is provided with dynamic "gap" inputs. This result suggests that dynamic shifts of pair-rule stripes are essential for segment patterning in the trunk and provides a functional role for observed posterior-to-anterior gap domain shifts that occur during cellularisation. The model also suggests revised patterning mechanisms for the parasegment boundaries and explains the aetiology of the even-skipped null mutant phenotype. Strikingly, a slightly modified version of the model is able to pattern segments in either simultaneous or sequential modes, depending only on initial conditions. This suggests that fundamentally similar mechanisms may underlie segmentation in short-germ and long-germ arthropods (Clark, 2017).

Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans

Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. Two processes were reviewed that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. To study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), This study elucidates the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms (Diaz-Cuadros, 2021).

A re-inducible gap gene cascade patterns the anterior-posterior axis of insects in a threshold-free fashion

Gap genes mediate the division of the anterior-posterior axis of insects into different fates through regulating downstream hox genes. Decades of tinkering the segmentation gene network of Drosophila melanogaster led to the conclusion that gap genes are regulated (at least initially) through a threshold-based mechanism, guided by both anteriorly- and posteriorly-localized morphogen gradients. This paper shows that the response of the gap gene network in the beetle Tribolium castaneum upon perturbation is consistent with a threshold-free 'Speed Regulation' mechanism, in which the speed of a genetic cascade of gap genes is regulated by a posterior morphogen gradient. This is shown by re-inducing the leading gap gene (namely, hunchback) resulting in the re-induction of the gap gene cascade at arbitrary points in time. This demonstrates that the gap gene network is self-regulatory and is primarily under the control of a posterior regulator in Tribolium and possibly other short/intermediate-germ insects (Boos, 2018).

Shaping the scaling characteristics of gap gene expression patterns in Drosophila

How patterns are formed to scale with tissue size remains an unresolved problem. This study investigated embryonic patterns of gap gene expression along the anterior-posterior (AP) axis in Drosophila. Embryos were used that greatly differed in length and, importantly, possess distinct length-scaling characteristics of the Bicoid (Bcd) gradient. The dynamic movements of gap gene expression boundaries were systematically analyze in relation to both embryo length and Bcd input as a function of time. The process through which such dynamic movements drive both an emergence of a global scaling landscape was shown, and evolution of boundary-specific scaling characteristics was documented. Despite initial differences in pattern scaling characteristics that mimic those of Bcd in the anterior, such characteristics of final patterns converge. This study thus partitions the contributions of Bcd input and regulatory dynamics inherent to the AP patterning network in shaping embryonic pattern's scaling characteristics (Xu, 2023).

Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo

Positional information in development often manifests as stripes of gene expression, but how stripes form remains incompletely understood. This study used optogenetics and live-cell biosensors to investigate the posterior brachyenteron (byn) stripe in early Drosophila embryos. This stripe depends on interpretation of an upstream ERK activity gradient and the expression of two target genes, tailless (tll) and huckebein (hkb), that exert antagonistic control over byn. High or low doses of ERK signaling were found to produce transient or sustained byn expression, respectively. Although tll transcription is always rapidly induced, hkb converts graded ERK inputs into a variable time delay. Nuclei thus interpret ERK amplitude through the relative timing of tll and hkb transcription. Antagonistic regulatory paths acting on different timescales are hallmarks of an incoherent feedforward loop, which is sufficient to explain byn dynamics and adds temporal complexity to the steady-state model of byn stripe formation. It was further shown that 'blurring' of an all-or-none stimulus through intracellular diffusion non-locally produces a byn stripe. Overall, this study provides a blueprint for using optogenetics to dissect developmental signal interpretation in space and time (Ho, 2023).

Optimal decoding of cellular identities in a genetic network

In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. This study used the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network.These results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy (Petkova, 2019).

ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization is not well understood. Chromatin accessibility was profiled with ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) in narrow, genetically tagged domains along the antero-posterior axis in the Drosophila blastoderm. One-quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable intervals, and their accessibility changes correlate with their regulatory activity. In an embryonic domain where an enhancer receives a net activating TF input and promotes transcription, it displays elevated accessibility in comparison to a domain where it receives a net repressive input. It is proposed that differential accessibility is a signature of patterning cis-regulatory elements in the Drosophila blastoderm, and potential mechanisms are discussed by which accessibility of enhancers may be modulated by activator and repressor TFs (Bozek, 2019).

In-silico identification and comparison of transcription factor binding sites cluster in anterior-posterior patterning genes in Drosophila melanogaster and Tribolium castaneum

The cis-regulatory data that help in transcriptional regulation is arranged into modular pieces of a few hundred base pairs called CRMs (cis-regulatory modules) and numerous binding sites for multiple transcription factors are prominent characteristics of these cis-regulatory modules. The present study was designed to localize transcription factor binding site (TFBS) clusters on twelve Anterior-posterior (A-P) genes in Tribolium castaneum and compare them to their orthologous gene enhancers in Drosophila melanogaster. Out of the twelve A-P patterning genes, six were gap genes (Kruppel, Knirps, Tailless, Hunchback, Giant, and Caudal) and six were pair rule genes (Hairy, Runt, Even-skipped, Fushi-tarazu, Paired, and Odd-skipped). The genes along with 20 kb upstream and downstream regions were scanned for TFBS clusters using the Motif Cluster Alignment Search Tool (MCAST), a bioinformatics tool that looks for set of nucleotide sequences for statistically significant clusters of non-overlapping occurrence of a given set of motifs. The motifs used in the current study were Hunchback, Caudal, Giant, Kruppel, Knirps, and Even-skipped. The results of the MCAST analysis revealed the maximum number of TFBS for Hunchback, Knirps, Caudal, and Kruppel in both D. melanogaster and T. castaneum, while Bicoid TFBS clusters were found only in D. melanogaster. The size of all the predicted TFBS clusters was less than 1kb in both insect species. These sequences revealed more transversional sites (Tv) than transitional sites (Ti) and the average Ti/Tv ratio was 0.75 (Moudgil, 2023).

How enhancers regulate wavelike gene expression patterns

A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called 'enhancers.' Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such a view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expression patterns in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle Tribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. This study establish the AP patterning of the short-germ beetle Tribolium as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, an enhancer prediction system was established in Tribolium based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, several Tribolium enhancers of gap and pair-rule genes were discovered, and the spatiotemporal activities of some of them in live embryos was assessed assessed. The data was found to be consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expression patterns (that are called 'dynamic enhancers') and enhancers that stabilize gene expression patterns (that are called 'static enhancers'). However, more data is needed for a strong support for this or any other alternative models (Mau, 2023).

Bayesian model selection for the Drosophila gap gene network

The gap gene system controls the early cascade of the segmentation pathway in Drosophila melanogaster as well as other insects. Owing to its tractability and key role in embryo patterning, this system has been the focus for both computational modelers and experimentalists. The gap gene expression dynamics can be considered strictly as a one-dimensional process and modeled as a system of reaction-diffusion equations. The Bayesian framework offers a means of doing formal model evaluation. This study demonstrates how this framework can be used to compare different models of gene expression. Focus was placed on the Papatsenko-Levine formalism, which exploits a fractional occupancy based approach to incorporate activation of the gap genes by the maternal genes and cross-regulation by the gap genes themselves. The Bayesian approach provides insight about relationship between system parameters. In the regulatory pathway of segmentation, the parameters for number of binding sites and binding affinity have a negative correlation. The model selection analysis supports a stronger binding affinity for Bicoid compared to other regulatory edges, as shown by a larger posterior mean. The procedure doesn't show support for activation of Kruppel by Bicoid. This study provides an efficient solver for the general representation of the Papatsenko-Levine model and demonstrates the utility of Bayes factor for evaluating candidate models for spatial pattering models. In addition, by using the parallel tempering sampler, the convergence of Markov chains can be remarkably improved and robust estimates of Bayes factors obtained (Zubair, 2019).

Conservation and variation in pair-rule gene expression and function in the intermediate-germ beetle, Dermestes maculatus

A set of pair-rule segmentation genes (PRGs) promote the formation of alternate body segments in Drosophila melanogaster While Drosophila embryos are long-germ, with segments specified more-or-less simultaneously, most insects add segments sequentially as the germband elongates. The hide beetle, Dermestes maculatus, represents an intermediate between short- and long-germ development, ideal for comparative study of PRGs. This study shows that eight of nine Drosophila PRG-orthologs are expressed in stripes in Dermestes. Functional results parse these genes into three groups: Dmac-eve, -odd, and -run play roles in both germband elongation and PR-patterning. Dmac-slp and -prd function exclusively as complementary, classic PRGs, supporting functional decoupling of elongation and segment formation. Orthologs of ftz, ftz-f1, h, and opa show more variable function in Dermestes and other species. While extensive cell death generally prefigured Dermestes PRG RNAi cuticle defects, an organized region with high mitotic activity near the margin of the segment addition zone likely contributes to truncation of eve(RNAi) embryos. These results suggest general conservation of clock-like regulation of PR-stripe addition in sequentially-segmenting species while highlighting regulatory re-wiring involving a subset of PRG-orthologs (Xiang, 2017).

Evidence for the temporal regulation of insect segmentation by a conserved sequence of transcription factors

Long-germ insects, such as the fruit fly Drosophila melanogaster, pattern their segments simultaneously, whereas short-germ insects, such as the beetle Tribolium castaneum, pattern their segments sequentially, from anterior to posterior. While the two modes of segmentation at first appear quite distinct, much of this difference might simply reflect developmental heterochrony. This study now shows that, in both Drosophila and Tribolium, segment patterning occurs within a common framework of sequential Caudal, Dichaete, and Odd-paired expression (see Comparison of long-germ and short-germ segmentation). In Drosophila these transcription factors are expressed like simple timers within the blastoderm, while in Tribolium they form wavefronts that sweep from anterior to posterior across the germband. In Drosophila, all three are known to regulate pair-rule gene expression and influence the temporal progression of segmentation. It is proposed that these regulatory roles are conserved in short-germ embryos, and that therefore the changing expression profiles of these genes across insects provide a mechanistic explanation for observed differences in the timing of segmentation. In support of this hypothesis it was demonstrated that Odd-paired is essential for segmentation in Tribolium, contrary to previous reports (Clark, 2018).

This study has found that segment patterning in both Drosophila and Tribolium occurs within a conserved framework of sequential Caudal, Dichaete and Odd-paired expression. In the case of Opa, there is also evidence for conserved function. However, although the sequence itself is conserved between the two insects, its spatiotemporal deployment across the embryo is divergent. In Drosophila, the factors are expressed ubiquitously within the main trunk, and each turns on or off almost simultaneously, correlating with the temporal progression of a near simultaneous segmentation process. In Tribolium, their expression domains are staggered in space, with developmentally more advanced anterior regions always subjected to a 'later' regulatory signature than more-posterior tissue. These expression domains retract over the course of germband extension, correlating with the temporal progression of a sequential segmentation process built around a segmentation clock (Clark, 2018).

Pair-rule patterning involves several distinct phases of gene expression, each requiring specific regulatory logic. It is proposed that, in both long-germ and short-germ species, the whole process is orchestrated by a series of key regulators, expressed sequentially over time, three of which are the focus of this paper. By rewiring the regulatory connections between other genes, factors such as Dichaete and Opa allow a small set of pair-rule factors to carry out multiple different roles, each specific to a particular spatiotemporal regulatory context. This kind of control logic makes for a flexible, modular regulatory network, and may therefore turn out to be a hallmark of other complex patterning systems (Clark, 2018).

Having highlighted the significance of these 'timing factors' in this paper, the next steps will be to investigate their precise regulatory roles and modes of action. It will be interesting to dissect how genetic interactions with pair-rule factors are implemented at the molecular level. Dichaete is known to act both as a repressive co-factor and as a transcriptional activator; therefore, a number of different mechanisms are plausible. The Odd-paired protein is also likely to possess both these kinds of regulatory activities (Clark, 2018).

Given the phylogenetic distance between beetles and flies (separated by at least 300 million years), it is expected that the similarities seen between Drosophila and Tribolium segmentation are likely to hold true for other insects, and perhaps for many non-insect arthropods as well. It is proposed that these similarities, which argue for the homology of long-germ and short-germ segmentation processes, result from conserved roles of Cad, Dichaete and Opa in the temporal regulation of pair-rule and segment-polarity gene expression during segment patterning. This hypothesis can be tested by detailed comparative studies in various arthropod model organisms (Clark, 2018).

This study provides evidence that a segmentation role for Opa is conserved between Drosophila and Tribolium; clear segmentation phenotypes have also been found for Cad in Nasonia, and for Dichaete in Bombyx. However, as the Tc-opa experiments reveal, functional manipulations in short-germ insects will need to be designed carefully in order to bypass the early roles of these pleiotropic genes. For example, cad knockdowns cause severe axis truncations in many arthropods, whereas Dichaete knockdown in Tribolium yields mainly empty eggs (Clark, 2018).

It was previously thought that Tc-opa was not required for segmentation, and that the segmentation role of Opa may have been recently acquired, in the lineage leading to Drosophila. However, the current analysis reveals that Tc-opa is indeed a segmentation gene, and also has other important roles, including head patterning and blastoderm formation. Given that a similar developmental profile of opa expression is seen in the millipede Glomeris, and even in the onychophoran Euperipatoides, the segmentation role of Opa may actually be ancient (Clark, 2018).

Head phenotypes following Tc-opa RNAi were unexpected, but both the blastoderm expression pattern and cuticle phenotypes that were observed are strikingly similar to those reported for Tc-otd and Tc-ems (Tribolium orthologues of the Drosophila head 'gap' genes orthodenticle and empty spiracles), suggesting that the three genes function together in a gene network that controls early head patterning. This function of Tc-opa might be homologous to the head patterning role for Opa discovered in the spider Parasteatoda, where it interacts with both Otd and Hedgehog (Hh) expression. Opa/Zic is known to modulate Hh signalling, and a role for Hh in head patterning appears to be conserved across arthropods, including Tribolium (Clark, 2018).

Finally, Opa/Zic is also known to modulate Wnt signalling. In chordates, Zic expression tends to overlap with sites of Hh and/or Wnt signalling, suggesting that one of its key roles in development is to ensure cells respond appropriately to these signals. The expression domains of Tc-opa that were observed in Tribolium (e.g. in the head, in the SAZ and between parasegment boundaries) accord well with this idea (Clark, 2018).

Similar embryonic expression patterns of Cad, Dichaete and Opa orthologues are observed in other bilaterian clades, including vertebrates. Cdx genes are expressed in the posterior of vertebrate embryos, where they play crucial roles in axial extension and Hox gene regulation. Sox2 (a Dichaete orthologue) has conserved expression in the nervous system, but is also expressed in a posterior domain, where it is a key determinant of neuromesodermal progenitor (posterior stem cell) fate. Finally, Zic2 and Zic3 (Opa orthologues) are expressed in presomitic mesoderm and nascent somites, and have been functionally implicated in somitogenesis and convergent extension. All three factors thus have important functions in posterior elongation, roles that may well be conserved across Bilateria (Clark, 2018).

In Tribolium, all three factors may be integrated into an ancient gene regulatory network downstream of posterior Wnt signalling, which generates their sequential expression and helps regulate posterior proliferation and/or differentiation. The mutually exclusive patterns of Tc-wg and Tc-Dichaete in the posterior germband are particularly suggestive: Wnt signalling and Sox gene expression are known to interact in many developmental contexts and these interactions may form parts of temporal cascades) (Clark, 2018).

The following outline is suggested as a plausible scenario for the evolution of arthropod segmentation; In non-segmented bilaterian ancestors of the arthropods, Cad, Dichaete and Opa were expressed broadly similarly to how they are expressed in Tribolium today, mediating conserved roles in posterior elongation, while gap and pair-rule genes may have had functions in the nervous system. At some point, segmentation genes came under the regulatory control of these factors, which provided a pre-existing source of spatiotemporal information in the developing embryo. Pair-rule genes began oscillating in the posterior, perhaps under the control of Cad and/or Dichaete, while the posteriorly retracting expression boundaries of the timing factors provided smooth wavefronts that effectively translated these oscillations into periodic patterning of the AP axis, analogous to the roles of the opposing retinoic acid and FGF gradients in vertebrate somitogenesis. Much later, in certain lineages of holometabolous insects, the transition to long-germ segmentation occurred. This would have involved two main modifications of the short-germ segmentation process: (1) changes to the expression of the timing factors, away from the situation seen in Tribolium, and towards the situation seen in Drosophila, causing a heterochronic shift in the deployment of the segmentation machinery from SAZ to blastoderm; and (2) recruitment of gap genes to pattern pair-rule stripes, via the ad hoc evolution of stripe-specific elements (Clark, 2018).

The appeal of this model is that the co-option of existing developmental features at each stage reduces the number of regulatory changes required to evolve de novo, facilitating the evolutionary process. In this scenario, arthropod segmentation would not be homologous to segmentation in other phyla, but would probably have been fashioned from common parts (Clark, 2018).

Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans

Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. Two processes were reviewed that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. To study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), This study elucidates the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms (Diaz-Cuadros, 2021).

Shifting roles of Drosophila pair-rule gene orthologs: segmental expression and function in the milkweed bug Oncopeltus fasciatus

The discovery of pair-rule genes (PRGs) in Drosophila revealed the existence of an underlying two-segment-wide prepattern directing embryogenesis. The milkweed bug Oncopeltus fasciatus, a hemimetabolous insect, is a more representative arthropod: most of its segments form sequentially after gastrulation. This study reports the expression and function of orthologs of the complete set of nine Drosophila PRGs in Oncopeltus Seven Of-PRG-orthologs are expressed in stripes in the primordia of every segment, rather than every other segment; Of-runt is PR-like and several orthologs are also expressed in the segment addition zone. RNAi-mediated knockdown of Of-odd-skipped, paired and sloppy-paired impacted all segments, with no indication of PR-like register. Of-E75A is expressed in PR-like stripes, although it is not expressed in this way in Drosophila, demonstrating the existence of an underlying PR-like prepattern in Oncopeltus These findings reveal that a switch occurred in regulatory circuits, leading to segment formation: while several holometabolous insects are 'Drosophila-like', using PRG orthologs for PR patterning, most Of-PRGs are expressed segmentally in Oncopeltus, a more basally branching insect. Thus, an evolutionarily stable phenotype - segment formation - is directed by alternate regulatory pathways in diverse species (Reding, 2019).

Classification-Based Inference of Dynamical Models of Gene Regulatory Networks

Cell-fate decisions during development are controlled by densely interconnected gene regulatory networks (GRNs) consisting of many genes. The switch-like nature of gene regulation can be exploited to break the gene circuit inference problem into two simpler optimization problems that are amenable to computationally efficient supervised learning techniques. This study presents FIGR (Fast Inference of Gene Regulation), a novel classification-based inference approach to determining gene circuit parameters. FIGR's effectiveness was demonstrated on synthetic data generated from random gene circuits of up to 50 genes as well as experimental data from the gap gene system of Drosophila melanogaster, a benchmark for inferring dynamical GRN models. FIGR is faster than global non-linear optimization by a factor of 600 and its computational complexity scales much better with GRN size. On a practical level, FIGR can accurately infer the biologically realistic gap gene network in under a minute on desktop-class hardware instead of requiring hours of parallel computing. It is anticipated that FIGR would enable the inference of much larger biologically realistic GRNs than was possible before (Fehr, 2019).

Anterior-posterior patterning of segments in Anopheles stephensi offers insights into the transition from sequential to simultaneous segmentation in holometabolous insects

The gene regulatory network for segmentation in arthropods offers valuable insights into how networks evolve owing to the breadth of species examined and the extremely detailed knowledge gained in the model organism Drosophila melanogaster. These studies have shown that Drosophila's network represents a derived state that acquired changes to accelerate segment patterning, whereas most insects specify segments gradually as the embryo elongates. Such heterochronic shifts in segmentation have potentially emerged multiple times within holometabolous insects, resulting in many mechanistic variants and difficulties in isolating underlying commonalities that permit such shifts. Recent studies identified regulatory genes that work as timing factors, coordinating gene expression transitions during segmentation. These studies predict that changes in timing factor deployment explain shifts in segment patterning relative to other developmental events. This study tested this hypothesis by characterizing the temporal and spatial expression of the pair-rule patterning genes in the malaria vector mosquito, Anopheles stephensi. This insect is a Dipteran (fly), like Drosophila, but represents an ancient divergence within this clade, offering a useful counterpart for evo-devo studies. In mosquito embryos, this study observed anterior to posterior sequential addition of stripes for many pair-rule genes and a wave of broad timer gene expression across this axis. Segment polarity gene stripes are added sequentially in the wake of the timer gene wave and the full pattern is not complete until the embryo is fully elongated. This "progressive segmentation" mode in Anopheles displays commonalities with both Drosophila's rapid segmentation mechanism and sequential modes used by more distantly related insects (Jarvela, 2021).

An additive repression mechanism sets the anterior limits of anterior pair-rule stripes 1

Segments are repeated anatomical units forming the body of insects. In Drosophila, the specification of the body takes place during the blastoderm through the segmentation cascade. Pair-rule genes such as hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz) are of the intermediate level of the cascade and each pair-rule gene is expressed in seven transversal stripes along the antero-posterior axis of the embryo. Stripes are formed by independent cis-regulatory modules (CRMs) under the regulation of transcription factors of maternal source and of gap proteins of the first level of the cascade. The initial blastoderm of Drosophila is a syncytium and it also coincides with the mid-blastula transition when thousands of zygotic genes are transcribed and their products are able to diffuse in the cytoplasm. Thus, a complex regulation of the CRMs of the pair-rule stripes is anticipated. The CRMs of h 1, eve 1, run 1, ftz 1 are able to be activated by bicoid (bcd) throughout the anterior blastoderm and several lines of evidence indicate that they are repressed by the anterior gap genes slp1 (sloppy-paired 1), tll (tailless) and hkb (huckebein). The modest activity of these repressors led to the premise of a combinatorial mechanism regulating the expression of the CRMs of h 1, eve 1, run 1, ftz 1 in more anterior regions of the embryo. This possibility was tested by progressively removing the repression activities of slp1, tll and hkb. In doing so, it was possible to expose a mechanism of additive repression limiting the anterior borders of stripes 1. Stripes 1 respond depending on their distance from the anterior end and repressors operating at different levels (Baltruk, 2022).