The Drosophila genes disconnected and disco-related are redundant with respect to larval head development and accumulation of mRNAs from deformed target genes

Spalt and disco define the dorsal-ventral neuroepithelial compartments of the developing Drosophila medulla

Spatial patterning of neural stem cell populations is a powerful mechanism by which to generate neuronal diversity. In the developing Drosophila medulla, the symmetrically dividing neuroepithelial cells of the outer proliferation center crescent are spatially patterned by the nonoverlapping expression of 3 transcription factors: Vsx1 in the center, Optix in the adjacent arms, and Rx in the tips. These spatial genes compartmentalize the outer proliferation center and, together with the temporal patterning of neuroblasts, act to diversify medulla neuronal fates. The observation that the dorsal and ventral halves of the outer proliferation center also grow as distinct compartments, together with the fact that a subset of neuronal types is generated from only one half of the crescent, suggests that additional transcription factors spatially pattern the outer proliferation center along the dorsal-ventral axis. Here, we identify the spalt (salm and salr) and disco (disco and disco-r) genes as the dorsal-ventral patterning transcription factors of the outer proliferation center. Spalt and Disco are differentially expressed in the dorsal and ventral outer proliferation center from the embryo through to the third instar larva, where they cross-repress each other to form a sharp dorsal-ventral boundary. We show that hedgehog is necessary for Disco expression in the embryonic optic placode and that disco is subsequently required for the development of the ventral outer proliferation center and its neuronal progeny. We further demonstrate that this dorsal-ventral patterning axis acts independently of Vsx1-Optix-Rx and thus propose that Spalt and Disco represent a third outer proliferation center patterning axis that may act to further diversify medulla fates.

Panarthropod tiptop/teashirt and spalt orthologs and their potential role as "trunk"-selector genes

BACKGROUND

In the vinegar fly Drosophila melanogaster, the homeodomain containing transcription factor Teashirt (Tsh) appears to specify trunk identity in concert with the function of the Hox genes. While in Drosophila there is a second gene closely related to tsh, called tiptop (tio), in other arthropods species only one copy exists (called tio/tsh). The expression of tsh and tio/tsh, respectively, is surprisingly similar among arthropods suggesting that its function as trunk selector gene may be conserved. Other research, for example on the beetle Tribolium castaneum, questions even conservation of Tsh function among insects. The zinc-finger transcription factor Spalt (Sal) is involved in the regulation of Drosophila tsh, but this regulatory interaction does not appear to be conserved in Tribolium either. Whether the function and interaction of tsh and sal as potential trunk-specifiers, however, is conserved is still unclear because comparative studies on sal expression (except for Tribolium) are lacking, and functional data are (if at all existing) restricted to Insecta.

RESULTS

Here, we provide additional data on arthropod tsh expression, show the first data on onychophoran tio/tsh expression, and provide a comprehensive investigation on sal expression patterns in arthropods and an onychophoran.

CONCLUSIONS

Our data support the idea that tio/tsh genes are involved in the development of "trunk" segments by regulating limb development. Our data suggest further that the function of Sal is indeed unlikely to be conserved in trunk vs head development like in Drosophila, but early expression of sal is in line with a potential homeotic function, at least in Arthropoda.

Cell-Autonomous and Non-cell-autonomous Function of Hox Genes Specify Segmental Neuroblast Identity in the Gnathal Region of the Embryonic CNS in Drosophila

During central nervous system (CNS) development neural stem cells (Neuroblasts, NBs) have to acquire an identity appropriate to their location. In thoracic and abdominal segments of Drosophila, the expression pattern of Bithorax-Complex Hox genes is known to specify the segmental identity of NBs prior to their delamination from the neuroectoderm. Compared to the thoracic, ground state segmental units in the head region are derived to different degrees, and the precise mechanism of segmental specification of NBs in this region is still unclear. We identified and characterized a set of serially homologous NB-lineages in the gnathal segments and used one of them (NB6-4 lineage) as a model to investigate the mechanism conferring segment-specific identities to gnathal NBs. We show that NB6-4 is primarily determined by the cell-autonomous function of the Hox gene Deformed (Dfd). Interestingly, however, it also requires a non-cell-autonomous function of labial and Antennapedia that are expressed in adjacent anterior or posterior compartments. We identify the secreted molecule Amalgam (Ama) as a downstream target of the Antennapedia-Complex Hox genes labial, Dfd, Sex combs reduced and Antennapedia. In conjunction with its receptor Neurotactin (Nrt) and the effector kinase Abelson tyrosine kinase (Abl), Ama is necessary in parallel to the cell-autonomous Dfd pathway for the correct specification of the maxillary identity of NB6-4. Both pathways repress CyclinE (CycE) and loss of function of either of these pathways leads to a partial transformation (40%), whereas simultaneous mutation of both pathways leads to a complete transformation (100%) of NB6-4 segmental identity. Finally, we provide genetic evidences, that the Ama-Nrt-Abl-pathway regulates CycE expression by altering the function of the Hippo effector Yorkie in embryonic NBs. The disclosure of a non-cell-autonomous influence of Hox genes on neural stem cells provides new insight into the process of segmental patterning in the developing CNS.

The central nervous system (CNS) needs to be subdivided into functionally specified regions. In the developing CNS of Drosophila, each neural stem cell, called neuroblasts (NB), acquires a unique identity according to its anterior-posterior and dorso-ventral position to generate a specific cell lineage. Along the anterior-posterior body axis, Hox genes of the Bithorax-Complex convey segmental identities to NBs in the trunk segments. In the derived gnathal and brain segments, the mechanisms specifying segmental NB identities are largely unknown. We investigated the role of Hox genes of the Antennapedia-Complex in the gnathal CNS. In addition to cell-autonomous Hox gene function, we unexpectedly uncovered a parallel non-cell-autonomous pathway in mediating segmental specification of embryonic NBs in gnathal segments. Both pathways restrict the expression of the cell cycle gene CyclinE, ensuring the proper specification of a glial cell lineage. Whereas the Hox gene Deformed mediates this cell-autonomously, labial and Antennapedia influence the identity via transcriptional regulation of the secreted molecule Amalgam (and its downstream pathway) in a non-cell-autonomous manner. These findings shed new light on the role of the highly conserved Hox genes during segmental patterning of neural stem cells in the CNS.

New components of Drosophila leg development identified through genome wide association studies

The adult Drosophila melanogaster body develops from imaginal discs, groups of cells set-aside during embryogenesis and expanded in number during larval stages. Specification and development of Drosophila imaginal discs have been studied for many years as models of morphogenesis. These studies are often based on mutations with large developmental effects, mutations that are often lethal in embryos when homozygous. Such forward genetic screens can be limited by factors such as early lethality and genetic redundancy. To identify additional genes and genetic pathways involved in leg imaginal disc development, we employed a Genome Wide Association Study utilizing the natural genetic variation in leg proportionality found in the Drosophila Genetic Reference Panel fly lines. In addition to identifying genes already known to be involved in leg development, we identified several genes involved in pathways that had not previously been linked with leg development. Several of the genes appear to be involved in signaling activities, while others have no known roles at this time. Many of these uncharacterized genes are conserved in mammals, so we can now begin to place these genes into developmental contexts. Interestingly, we identified five genes which, when their function is reduced by RNAi, cause an antenna-to-leg transformation. Our results demonstrate the utility of this approach, integrating the tools of quantitative and molecular genetics to study developmental processes, and provide new insights into the pathways and networks involved in Drosophila leg development.

A survey of well conserved families of C2H2 zinc-finger genes in Daphnia

Background

A recent comparative genomic analysis tentatively identified roughly 40 orthologous groups of C2H2 Zinc-finger proteins that are well conserved in "bilaterians" (i.e. worms, flies, and humans). Here we extend that analysis to include a second arthropod genome from the crustacean, Daphnia pulex.

Results

Most of the 40 orthologous groups of C2H2 zinc-finger proteins are represented by just one or two proteins within each of the previously surveyed species. Likewise, Daphnia were found to possess a similar number of orthologs for all of these small orthology groups. In contrast, the number of Sp/KLF homologs tends to be greater and to vary between species. Like the corresponding mammalian Sp/KLF proteins, most of the Drosophila and Daphnia homologs can be placed into one of three sub-groups: Class I-III. Daphnia were found to have three Class I proteins that roughly correspond to their Drosophila counterparts, dSP1, btd, CG5669, and three Class II proteins that roughly correspond to Luna, CG12029, CG9895. However, Daphnia have four additional KLF-Class II proteins that are most similar to the vertebrate KLF1/2/4 proteins, a subset not found in Drosophila. Two of these four proteins are encoded by genes linked in tandem. Daphnia also have three KLF-Class III members, one more than Drosophila. One of these is a likely Bteb2 homolog, while the other two correspond to Cabot and KLF13, a vertebrate homolog of Cabot.

Conclusion

Consistent with their likely roles as fundamental determinants of bilaterian form and function, most of the 40 groups of C2H2 zinc-finger proteins are conserved in kind and number in Daphnia. However, the KLF family includes several additional genes that are most similar to genes present in vertebrates but missing in Drosophila.

Expression of the apoptosis gene reaper in homeotic, segmentation and other mutants in Drosophila

Apoptosis is an essential process required for development and morphogenesis in metazoan organisms. The apoptosis pathway and cell death machinery have been extensively studied, but little is known how apoptosis genes are regulated in the course of development . In this study, we analyzed the transcriptional regulation of the pro-apoptotic gene reaper (rpr) by performing whole-mount in situ hybridization in embryos mutant for a number of transcription factor genes in Drosophila melanogaster. In sum, our data show that all factors studied have very specific temporal and spatial effects on rpr transcription . Thus, our results reinforce the concept that apoptosis is an essential process for morphogenesis and that apoptosis related genes very tight developmental factors identified in sculpting the morphology of various embryonic structures by modulating the apoptosis pathway.

Mutual regulation of the Drosophila disconnected (disco) and Distal-less (Dll) genes contributes to proximal-distal patterning of antenna and leg

The Drosophila disconnected (disco) gene encodes a C(2)H(2)-type zinc finger transcription factor required for the development of the central and peripheral nervous systems. We report that disco participates in a positive feedback loop with the Dll gene, a master regulator of ventral appendage development. Dll function is not only required for proper disco expression in antenna and leg discs, but is also sufficient for ectopic expression of disco in the developing retina and wing imaginal discs. Conversely, disco gene function is required for the maintenance of Dll expression. We show that Dll phenotypes are partially rescued by the up-regulation of disco expression in the Dll domain. Reduction in disco gene function disrupts antenna and leg development, and the phenotypes closely resemble that produced by Dll alleles. These observations demonstrate that disco plays a fundamental role in the Dll-dependent patterning of antenna and leg, perhaps as a regulator of Dll gene expression.

Basonuclin 2 has a function in the multiplication of embryonic craniofacial mesenchymal cells and is orthologous to disco proteins

Basonuclin 2 is a recently discovered zinc finger protein of unknown function. Its paralog, basonuclin 1, is associated with the ability of keratinocytes to multiply. The basonuclin zinc fingers are closely related to those of the Drosophila proteins disco and discorelated, but the relation between disco proteins and basonuclins has remained elusive because the function of the disco proteins in larval head development seems to have no relation to that of basonuclin 1 and because the amino acid sequence of disco, apart from the zinc fingers, also has no similarity to that of the basonuclins. We have generated mice lacking basonuclin 2. These mice die within 24 h of birth with a cleft palate and abnormalities of craniofacial bones and tongue. In the embryonic head, expression of the basonuclin 2 gene is restricted to mesenchymal cells in the palate, at the periphery of the tongue, and in the mesenchymal sheaths that surround the brain and the osteocartilagineous structures. In late embryos, the rate of multiplication of these mesenchymal cells is greatly diminished. Therefore, basonuclin 2 is essential for the multiplication of craniofacial mesenchymal cells during embryogenesis. Non-Drosophila insect databases available since 2008 reveal that the basonuclins and the disco proteins share much more extensive sequence and gene structure similarity than noted when only Drosophila sequences were examined. We conclude that basonuclin 2 is both structurally and functionally the vertebrate ortholog of the disco proteins. We also note the possibility that some human craniofacial abnormalities are due to a lack of basonuclin 2.

Multifactorial regulation of a hox target gene

Hox proteins play fundamental roles in controlling morphogenetic diversity along the anterior-posterior body axis of animals by regulating distinct sets of target genes. Within their rather broad expression domains, individual Hox proteins control cell diversification and pattern formation and consequently target gene expression in a highly localized manner, sometimes even only in a single cell. To achieve this high-regulatory specificity, it has been postulated that Hox proteins co-operate with other transcription factors to activate or repress their target genes in a highly context-specific manner in vivo. However, only a few of these factors have been identified. Here, we analyze the regulation of the cell death gene reaper (rpr) by the Hox protein Deformed (Dfd) and suggest that local activation of rpr expression in the anterior part of the maxillary segment is achieved through a combinatorial interaction of Dfd with at least eight functionally diverse transcriptional regulators on a minimal enhancer. It follows that context-dependent combinations of Hox proteins and other transcription factors on small, modular Hox response elements (HREs) could be responsible for the proper spatio-temporal expression of Hox targets. Thus, a large number of transcription factors are likely to be directly involved in Hox target gene regulation in vivo.

The Drosophila gap gene giant has an anterior segment identity function mediated through disconnected and teashirt

The C2H2 zinc-finger-containing transcription factors encoded by the disconnected (disco) and teashirt (tsh) genes contribute to the regionalization of the Drosophila embryo by establishing fields in which specific Homeotic complex (Hom-C) proteins can function. In Drosophila embryos, disco and the paralogous disco-related (disco-r) are expressed throughout most of the epidermis of the head segments, but only in small patches in the trunk segments. Conversely, tsh is expressed extensively in the trunk segments, with little or no accumulation in the head segments. Little is known about the regulation of these genes; for example, what limits their expression to these domains? Here, we report the regulatory effects of gap genes on the spatial expression of disco, disco-r, and tsh during Drosophila embryogenesis. The data shed new light on how mutations in giant (gt) affect patterning within the anterior gt domain, demonstrating homeotic function in this domain. However, the homeosis does not occur through altered expression of the Hom-C genes but through changes in the regulation of disco and tsh.

The appendage role of insect disco genes and possible implications on the evolution of the maggot larval form

Though initially identified as necessary for neural migration, Disconnected and its partially redundant paralog, Disco-related, are required for proper head segment identity during Drosophila embryogenesis. Here, we present evidence that these genes are also required for proper ventral appendage development during development of the adult fly, where they specify medial to distal appendage development. Cells lacking the disco genes cannot contribute to the medial and distal portions of ventral appendages. Further, ectopic disco transforms dorsal appendages toward ventral fates; in wing discs, the medial and distal leg development pathways are activated. Interestingly, this appendage role is conserved in the red flour beetle, Tribolium (where legs develop during embryogenesis), yet in the beetle we found no evidence for a head segmentation role. The lack of an embryonic head specification role in Tribolium could be interpreted as a loss of the head segmentation function in Tribolium or gain of this function during evolution of flies. However, we suggest an alternative explanation. We propose that the disco genes always function as appendage factors, but their appendage nature is masked during Drosophila embryogenesis due to the reduction of limb fields in the maggot style Drosophila larva.

Identification of a new type of PBX1 partner that contains zinc finger motifs and inhibits the binding of HOXA9-PBX1 to DNA

PBX1 belongs to the TALE-class of homeodomain protein and has a wide functional diversity during development. Indeed, PBX1 is required for haematopoiesis as well as for multiple developmental processes such as skeletal patterning and organogenesis. It has furthermore been shown that PBX1 functions as a HOX cofactor during development. More recent data suggest that PBX1 may act even more broadly by modulating the activity of non-homeodomain transcription factors. To better understand molecular mechanisms triggered by PBX1 during female genital tract development, we searched for additional PBX1 partners that might be involved in this process. Using a two hybrid screen, we identified a new PBX1 interacting protein containing several zinc finger motifs that we called ZFPIP for Zinc Finger PBX1 Interacting Protein. We demonstrated that ZFPIP is expressed in embryonic female genital tract but also in other PBX1 expression domains such as the developing head and the limb buds. We further showed that ZFPIP is able to bind physically and in vivo to PBX1 and moreover, that it prevents the binding of HOXA9/PBX complexes to their consensus DNA site. We suggest that ZFPIP is a new type of PBX1 partner that could participate in PBX1 function during several developmental pathways.

Modulating Hox gene functions during animal body patterning

With their power to shape animal morphology, few genes have captured the imagination of biologists as the evolutionarily conserved members of the Hox clusters have done. Recent research has provided new insight into how Hox proteins cause morphological diversity at the organismal and evolutionary levels. Furthermore, an expanding collection of sequences that are directly regulated by Hox proteins provides information on the specificity of target-gene activation, which might allow the successful prediction of novel Hox-response genes. Finally, the recent discovery of microRNA genes within the Hox gene clusters indicates yet another level of control by Hox genes in development and evolution.

scylla and charybde, homologues of the human apoptotic gene RTP801, are required for head involution in Drosophila

We employed robotic methods and the whole-genome sequence of Drosophila melanogaster to facilitate a large-scale expression screen for spatially restricted transcripts in Drosophila embryos. In this screen, we identified a pair of genes, scylla (scyl) and charybde (chrb), that code for dorsal transcripts in early Drosophila embryos and are homologous to the human apoptotic gene RTP801. In Drosophila, both gene products are transcriptionally regulated targets of Dpp/Zen-mediated signal transduction and appear more generally to be downstream targets of homeobox regulation. Gene disruption studies revealed the functional redundancy of scyl and chrb, as well as their requirement for embryonic head involution. From the perspective of functional genomics, our studies demonstrate that global surveys of gene expression can complement traditional genetic screening methods for the identification of genes essential for development: beginning from their spatio-temporal expression profiles and extending to their downstream placement relative to dpp and zen, our studies reveal roles for the scyl and chrb gene products as links between patterning and cell death.

Assisting Hox proteins in controlling body form: are there new lessons from flies (and mammals)?

Hox proteins regulate specific sets of target genes to give rise to morphological distinctions along the anterior-posterior body axis of metazoans. Though they have high developmental specificity, Hox proteins have low DNA binding specificity, so how they select the appropriate target genes has remained enigmatic. There is general agreement that cofactors provide additional specificity, but a comprehensive model of Hox control of gene expression has not emerged. There is now evidence that a global network of zinc finger transcription factors contributes to patterning of the Drosophila embryo. These zinc finger proteins appear to establish fields in which certain Hox proteins can function. Though the nature of these fields is uncertain at this time, it is possible that these zinc finger proteins are Hox cofactors, providing additional specificity during Hox target-gene selection. Furthermore, these zinc finger proteins are conserved, as are aspects of their anterior-posterior expression, suggesting that their roles might be conserved, as well. Perhaps this layer in the genetic control of body patterning will help bridge some of the chasms that remain in our understanding of the genetic control of pattern formation.

A critical role of teashirt for patterning the ventral epidermis is masked by ectopic expression of tiptop, a paralog of teashirt in Drosophila

The teashirt gene encodes a protein with three widely spaced zinc finger motifs that is crucial for specifying trunk identity in Drosophila embryos. Here, we describe a gene called tiptop, which encodes a protein highly similar to Teashirt. We have analyzed the expression patterns and functions of these two genes in the trunk of the embryo. Initially, teashirt and tiptop expressions are detected in distinct domains; teashirt in the trunk and tiptop in parts of the head and tail. In different mutant situations, we show that, in the trunk and head, they repress each other's expression. Unlike teashirt, we found that deletion of tiptop is homozygous viable and fertile. However, embryos lacking both gene activities display a more severe trunk phenotype than teashirt mutant embryos alone. Ectopic expression of either gene produces an almost identical phenotype, indicating that Teashirt and Tiptop have, on the whole, common activities. We conclude that Teashirt and Tiptop repress each other's expression and that Teashirt has a crucial role for trunk patterning that is in part masked by ectopic expression of Tiptop.

Identification of Basonuclin2, a DNA-binding zinc-finger protein expressed in germ tissues and skin keratinocytes

We used a bioinformatics approach to identify Basonuclin2, the second member of the Basonuclin zinc-finger family of transcription factors. The mouse Basonuclin2 protein consists of 1049 amino acids and contains three pairs of zinc fingers in the C-terminus that show a high level of amino acid sequence similarity with Basonuclin1. In addition, other characteristic domains of Basonuclin1, such as the serine strip and a nuclear localization signal, are also present in Basonuclin2. We used genomic and in silico database analysis to identify the human and rat homologs of basonuclin2. A search of the mouse genome showed that the basonuclin2 gene maps to chromosome 4 and consists of six exons spanning approximately 300 kb. Northern blot analysis revealed multiple transcripts of basonuclin2 in tissues of the reproductive system (ovary and testis) and also in kidney and skin. We demonstrate that, as expected from sequence conservation, recombinant Basonuclin2 can bind to a sequence in the promoter of a rRNA gene previously characterized as a Basonuclin-binding site. Full-length Basonuclin2 exclusively localizes to the nucleus, indicating that it likely plays an important role in nuclear function, probably in gene regulation. Our study establishes Basonuclin2 as a novel member of the Basonuclin family. Moreover, the structural and functional similarities with Basonuclin1 suggest that Basonuclin2 may play an analogous function in germ cells and skin keratinocytes.

An interactive network of zinc-finger proteins contributes to regionalization of the Drosophila embryo and establishes the domains of HOM-C protein function

During animal development, the HOM-C/HOX proteins direct axial patterning by regulating region-specific expression of downstream target genes. Though much is known about these pathways, significant questions remain regarding the mechanisms of specific target gene recognition and regulation, and the role of co-factors. From our studies of the gnathal and trunk-specification proteins Disconnected (DISCO) and Teashirt (TSH), respectively, we present evidence for a network of zinc-finger transcription factors that regionalize the Drosophila embryo. Not only do these proteins establish specific regions within the embryo, but their distribution also establishes where specific HOM-C proteins can function. In this manner, these factors function in parallel to the HOM-C proteins during axial specification. We also show that in tsh mutants, disco is expressed in the trunk segments, probably explaining the partial trunk to head transformation reported in these mutants, but more importantly demonstrating interactions between members of this regionalization network. We conclude that a combination of regionalizing factors, in concert with the HOM-C proteins,promotes the specification of individual segment identity.

Genetics and molecular biology of rhythms in Drosophila and other insects

Application of generic variants (Sections II-IV, VI, and IX) and molecular manipulations of rhythm-related genes (Sections V-X) have been used extensively to investigate features of insect chronobiology that might not have been experimentally accessible otherwise. Most such tests of mutants and molecular-genetic xperiments have been performed in Drosophila melanogaster. Results from applying visual-system variants have revealed that environmental inputs to the circadian clock in adult flies are mediated by external photoreceptive structures (Section II) and also by direct light reception chat occurs in certain brain neurons (Section IX). The relevant light-absorbing molecuLes are rhodopsins and "blue-receptive" cryptochrome (Sections II and IX). Variations in temperature are another clock input (Section IV), as has been analyzed in part by use of molecular techniques and transgenes involving factors functioning near the heart of the circadian clock (Section VIII). At that location within the fly's chronobiological system, approximately a half-dozen-perhaps up to as many as 10-clock genes encode functions that act and interact to form the circadian pacemaker (Sections III and V). This entity functions in part by transcriptional control of certain clock genes' expressions, which result in the production of key proteins that feed back negatively to regulate their own mRNA production. This occurs in part by interactions of such proteins with others that function as transcriptional activators (Section V). The implied feedback loop operates such that there are daily variations in the abundances of products put out by about one-half of the core clock genes. Thus, the normal expression of these genes defines circadian rhythms of their own, paralleling the effects of mutations at the corresponding genetic loci (Section III), which are to disrupt or apparently eliminate clock functioning. The fluctuations in the abundance of gene products are controlled transciptionally and posttranscriptionally. These clock mechanisms are being analyzed in ways that are increasingly complex and occasionally obscure; not all panels of this picture are comprehensive or clear, including problems revolving round the biological meaning or a given features of all this molecular cycling (Section V). Among the complexities and puzzles that have recently arisen, phenomena that stand out are posttranslational modifications of certain proteins that are circadianly regulated and regulating; these biochemical events form an ancillary component of the clock mechanism, as revealed in part by genetic identification of Factors (Section III) that turned out to encode protein kinases whose substrates include other pacemaking polypeptides (Section V). Outputs from insect circadian clocks have been long defined on formalistic and in some cases concrete criteria, related to revealed rhythms such as periodic eclosion and daily fluctuations of locomotion (Sections II and III). Based on the reasoning that if clock genes can regulate circadian cyclings of their own products, they can do the same for genes that function along output pathways; thus clock-regulated genes have been identified in part by virtue of their products' oscillations (Section X). Those studied most intensively have their expression influenced by circadian-pacemaker mutations. The clock-regulated genes discovered on molecular criteria have in some instances been analyzed further in their mutant forms and found to affect certain features of overt whole-organismal rhythmicity (Sections IV and X). Insect chronogenetics touches in part on naturally occurring gene variations that affect biological rhythmicity or (in some cases) have otherwise informed investigators about certain features of the organism's rhythm system (Section VII). Such animals include at least a dozen insect species other than D. melanogaster in which rhythm variants have been encountered (although usually not looked for systematically). The chronobiological "system" in the fruit fly might better be graced with a plural appellation because there is a myriad of temporally related phenomena that have come under the sway of one kind of putative rhythm variant or the other (Section IV). These phenotypes, which range well beyond the bedrock eclosion and locomotor circadian rhythms, unfortunately lead to the creation of a laundry list of underanalyzed or occult phenomena that may or may not be inherently real, whether or not they might be meaningfully defective under the influence of a given chronogenetic variant. However, such mutants seem to lend themselves to the interrogation of a wide variety of time-based attributes-those that fall within the experimental confines of conventionally appreciated circadian rhythms (Sections II, III, VI, and X); and others that consist of 24-hr or nondaily cycles defined by many kinds of biological, physiological, or biochemical parameters (Section IV).