A comparison of midline and tracheal gene regulation during Drosophila development

Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression

Transcriptional cis-regulatory modules, e.g., enhancers, control the time and location of metazoan gene expression. While changes in enhancers can provide a powerful force for evolution, there is also significant deep conservation of enhancers for developmentally important genes, with function and sequence characteristics maintained over hundreds of millions of years of divergence. Not well understood, however, is how the overall regulatory composition of a locus evolves, with important outstanding questions such as how many enhancers are conserved vs. novel, and to what extent are the locations of conserved enhancers within a locus maintained? We begin here to address these questions with a comparison of the respective single-minded (sim) loci in the two dipteran species Drosophila melanogaster (fruit fly) and Aedes aegypti (mosquito). sim encodes a highly conserved transcription factor that mediates development of the arthropod embryonic ventral midline. We identify two enhancers in the A. aegypti sim locus and demonstrate that they function equivalently in both transgenic flies and transgenic mosquitoes. One A. aegypti enhancer is highly similar to known Drosophila counterparts in its activity, location, and autoregulatory capability. The other differs from any known Drosophila sim enhancers with a novel location, failure to autoregulate, and regulation of expression in a unique subset of midline cells. Our results suggest that the conserved pattern of sim expression in the two species is the result of both conserved and novel regulatory sequences. Further examination of this locus will help to illuminate how the overall regulatory landscape of a conserved developmental gene evolves.

Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records

BACKGROUND

Conflicting results regarding alterations to sperm DNA methylation in cases of spermatogenesis defects, male infertility and poor developmental outcomes have been reported in humans. Bulls used for artificial insemination represent a relevant model in this field, as the broad dissemination of bull semen considerably alleviates confounding factors and enables the precise assessment of male fertility. This study was therefore designed to assess the potential for sperm DNA methylation to predict bull fertility.

RESULTS

A unique collection of 100 sperm samples was constituted by pooling 2-5 ejaculates per bull from 100 Montbéliarde bulls of comparable ages, assessed as fertile (n = 57) or subfertile (n = 43) based on non-return rates 56 days after insemination. The DNA methylation profiles of these samples were obtained using reduced representation bisulfite sequencing. After excluding putative sequence polymorphisms, 490 fertility-related differentially methylated cytosines (DMCs) were identified, most of which were hypermethylated in subfertile bulls. Interestingly, 46 genes targeted by DMCs are involved in embryonic and fetal development, sperm function and maturation, or have been related to fertility in genome-wide association studies; five of these were further analyzed by pyrosequencing. In order to evaluate the prognostic value of fertility-related DMCs, the sperm samples were split between training (n = 67) and testing (n = 33) sets. Using a Random Forest approach, a predictive model was built from the methylation values obtained on the training set. The predictive accuracy of this model was 72% on the testing set and 72% on individual ejaculates collected from an independent cohort of 20 bulls.

CONCLUSION

This study, conducted on the largest set of bull sperm samples so far examined in epigenetic analyses, demonstrated that the sperm methylome is a valuable source of male fertility biomarkers. The next challenge is to combine these results with other data on the same sperm samples in order to improve the quality of the model and better understand the interplay between DNA methylation and other molecular features in the regulation of fertility. This research may have potential applications in human medicine, where infertility affects the interaction between a male and a female, thus making it difficult to isolate the male factor.

The tracheal system in post-embryonic development of holometabolous insects: a case study using the mealworm beetle

The tracheal (respiratory) system is regarded as one of the key elements which enabled insects to conquer terrestrial habitats and, as a result, achieve extreme species diversity. Despite this fact, anatomical data concerning this biological system is relatively scarce, especially in an ontogenetic context. The purpose of this study is to provide novel and reliable information on the post-embryonic development of the tracheal system of holometabolous insects using micro-computed tomography methods. Data concerning the structure of the respiratory system acquired from different developmental stages (larvae, pupae and adults) of a single insect species (Tenebrio molitor) are co-analysed in detail. Anatomy of the tracheal system is presented. Sample sizes used (29 individuals) enabled statistical analysis of the results obtained. The following aspects have been investigated (among others): the spiracle arrangement, the number of tracheal ramifications originating from particular spiracles, the diameter of longitudinal trunks, tracheal system volumes, tracheae diameter distribution and fractal dimension analysis. Based on the data acquired, the modularity of the tracheal system is postulated. Using anatomical and functional factors, the following respiratory module types have been distinguished: cephalo-prothoracic, metathoracic and abdominal. These modules can be unambiguously identified in all of the studied developmental stages. A cephalo-prothoracic module aerates organs located in the head capsule, prothorax and additionally prolegs. It is characterised by relatively thick longitudinal trunks and originates in the first thoracic spiracle pair. Thoracic modules support the flight muscles, wings, elytra, meso- and metalegs. The unique feature of this module is the presence of additional longitudinal connections between the neighbouring spiracles. These modules are concentrated around the second prothoracic and the first abdominal spiracle pairs. An abdominal module is characterised by relatively thin ventral longitudinal trunks. Its main role is to support systems located in the abdomen; however, its long visceral tracheae aerate organs situated medially from the flight muscles. Analysis of changes of the tracheal system volume enabled the calculation of growth scaling among body tissues and the volume of the tracheal system. The data presented show that the development of the body volume and tracheal system is not linear in holometabola due to the occurrence of the pupal stage causing a decrease in body volume in the imago and at the same time influencing high growth rates of the tracheal system during metamorphosis, exceeding that ones observed for hemimetabola.

Reduced Neuronal Transcription of Escargot, the Drosophila Gene Encoding a Snail-Type Transcription Factor, Promotes Longevity

In recent years, several genes involved in complex neuron specification networks have been shown to control life span. However, information on these genes is scattered, and studies to discover new neuronal genes and gene cascades contributing to life span control are needed, especially because of the recognized role of the nervous system in governing homeostasis, aging, and longevity. Previously, we demonstrated that several genes that encode RNA polymerase II transcription factors and that are involved in the development of the nervous system affect life span in Drosophila melanogaster. Among other genes, escargot (esg) was demonstrated to be causally associated with an increase in the life span of male flies. Here, we present new data on the role of esg in life span control. We show that esg affects the life spans of both mated and unmated males and females to varying degrees. By analyzing the survival and locomotion of the esg mutants, we demonstrate that esg is involved in the control of aging. We show that increased longevity is caused by decreased esg transcription. In particular, we demonstrate that esg knockdown in the nervous system increased life span, directly establishing the involvement of the neuronal esg function in life span control. Our data invite attention to the mechanisms regulating the esg transcription rate, which is changed by insertions of DNA fragments of different sizes downstream of the structural part of the gene, indicating the direction of further research. Our data agree with the previously made suggestion that alterations in gene expression during development might affect adult lifespan, due to epigenetic patterns inherited in cell lineages or predetermined during the development of the structural and functional properties of the nervous system.

A Genome-Wide Identification and Analysis of the Basic Helix-Loop-Helix Transcription Factors in Brown Planthopper, Nilaparvata lugens

The basic helix-loop-helix (bHLH) transcription factors in insects play essential roles in multiple developmental processes including neurogenesis, sterol metabolism, circadian rhythms, organogenesis and formation of olfactory sensory neurons. The identification and function analysis of bHLH family members of the most destructive insect pest of rice, Nilaparvata lugens, may provide novel tools for pest management. Here, a genome-wide survey for bHLH sequences identified 60 bHLH sequences (NlbHLHs) encoded in the draft genome of N. lugens. Phylogenetic analysis of the bHLH domains successfully classified these genes into 40 bHLH families in group A (25), B (14), C (10), D (1), E (8) and F (2). The number of NlbHLHs with introns is higher than many other insect species, and the average intron length is shorter than those of Acyrthosiphon pisum. High number of ortholog families of NlbHLHs was found suggesting functional conversation for these proteins. Compared to other insect species studied, N. lugens has the highest number of bHLH members. Furthermore, gene duplication events of SREBP, Kn(col), Tap, Delilah, Sim, Ato and Crp were found in N. lugens. In addition, a putative full set of NlbHLH genes is defined and compared with another insect species. Thus, our classification of these NlbHLH members provides a platform for further investigations of bHLH protein functions in the regulation of N. lugens, and of insects in general.

The Last Breath: A μCT-based method for investigating the tracheal system in Hexapoda

In recent years, μCT-based studies of the insect tracheal system have become an increasingly important area of research. Nevertheless, the methods proposed in previous research for investigating the respiratory system in the three-dimensional space were described and tested based on a relatively small number of specimens. Additionally, the individuals studied in all these cases represented only a single post-embryonic stadium - pupa or imago - of a particular insect species. Therefore, in the current situation it is difficult to predict the reliability and possible limitations of these methods. To address this problem we conducted a methodological study, during which we used 65 individuals representing larvae, pupae and imagines of the mealworm beetle (Tenebrio molitor). In addition to the protocol previously described, which implicated freezing as a killing technique, we also tested a novel one, which was based on ethyl acetate fumigation of the specimens studied. We included step-by-step guides for the manual and semiautomatic approaches in order to facilitate the digital visualization of the tracheal system. Our investigations enabled us to generate multiple models of the tracheal system of all post-embryonic stages of the mealworm beetle. The methods used proved to be minimally invasive, thus allowing for the application of post-scanning manipulations, such as drying with critical point dryer (CPD). This approach enabled us to merge different three-dimensional models into a single picture and analyse the relationship of the tracheal system with other tissues (e.g., muscles, nervous system). We comprehensively discuss the advantages and possible limitations of the tested methods and provide practical suggestions for conducting the analyses on a wider scale. The visualizations presented in this publication are the first three-dimensional models of the respiratory system using a representative of the extremely diverse order Coleoptera.

Enhancer diversity and the control of a simple pattern of Drosophila CNS midline cell expression

Transcriptional enhancers integrate information derived from transcription factor binding to control gene expression. One key question concerns the extent of trans- and cis-regulatory variation in how co-expressed genes are controlled. The Drosophila CNS midline cells constitute a group of neurons and glia in which expression changes can be readily characterized during specification and differentiation. Using a transgenic approach, we compare the cis-regulation of multiple genes expressed in the Drosophila CNS midline primordium cells, and show that while the expression patterns may appear alike, the target genes are not equivalent in how these common expression patterns are achieved. Some genes utilize a single enhancer that promotes expression in all midline cells, while others utilize multiple enhancers with distinct spatial, temporal, and quantitative contributions. Two regulators, Single-minded and Notch, play key roles in controlling early midline gene expression. While Single-minded is expected to control expression of most, if not all, midline primordium-expressed genes, the role of Notch in directly controlling midline transcription is unknown. Midline primordium expression of the rhomboid gene is dependent on cell signaling by the Notch signaling pathway. Mutational analysis of a rhomboid enhancer reveals at least 5 distinct types of functional cis-control elements, including a binding site for the Notch effector, Suppressor of Hairless. The results suggest a model in which Notch/Suppressor of Hairless levels are insufficient to activate rhomboid expression by itself, but does so in conjunction with additional factors, some of which, including Single-minded, provide midline specificity to Notch activation. Similarly, a midline glial enhancer from the argos gene, which is dependent on EGF/Spitz signaling, is directly regulated by contributions from both Pointed, the EGF transcriptional effector, and Single-minded. In contrast, midline primordium expression of other genes shows a strong dependence on Single-minded and varying combinations of additional transcription factors. Thus, Single-minded directly regulates midline primordium-expressed genes, but in some cases plays a primary role in directing target gene midline expression, and in others provides midline specificity to cell signaling inputs.