scholarly journals FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1484 ◽  
Author(s):  
Stefan A. Koestler ◽  
Begum Alaybeyoglu ◽  
Christian X. Weichenberger ◽  
Arzu Celik
Keyword(s):  
Regulatory Networks ◽  
Eye Development ◽  
Expression Patterns ◽  
Model Organism ◽  
High Standard ◽  
Manual Curation ◽  
Dynamic Expression ◽  
Versatile Tool ◽  
Community Curation ◽  
Gene Regulatory

Motivation: Understanding the regulatory mechanisms governing eye development of the model organism Drosophila melanogaster (D. m.) requires structured knowledge of the involved genes and proteins, their interactions, and dynamic expression patterns. Especially the latter information is however to a large extent scattered throughout the literature.Results: FlyOde is an online platform for the systematic assembly of data on D. m. eye development. It consists of data on eye development obtained from the literature, and a web interface for users to interactively display these data as a gene regulatory network. Our manual curation process provides high standard structured data, following a specifically designed ontology. Visualization of gene interactions provides an overview of network topology, and filtering according to user-defined expression patterns makes it a versatile tool for daily tasks, as demonstrated by usage examples. Users are encouraged to submit additional data via a simple online form.

scholarly journals Molecular patterning during the development of Phoronopsis harmeri reveals similarities to rhynchonelliform brachiopods

2019 ◽  
Author(s):  
Carmen Andrikou ◽  
Yale J. Passamaneck ◽  
Chris J. Lowe ◽  
Mark Q. Martindale ◽  
Andreas Hejnol
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Dynamic Expression ◽  
Evolutionarily Conserved ◽  
Oral Ectoderm ◽  
Gene Regulatory ◽  
Phoronopsis Harmeri ◽  
Evolutionary Lineages ◽  
Germ Layer Formation

AbstractBackgroundAnswering the question how conserved patterning systems are across evolutionary lineages requires a broad taxon sampling. Phoronid development has previously been studied using fate mapping and morphogenesis, yet molecular descriptions are missing. Here we report the expression patterns of the evolutionarily conserved anterior (otx, gsc, six3/6, nk2.1), posterior (cdx, bra) and endomesodermal (foxA, gata4/5/6, twist) markers in the phoronid Phoronopsis harmeri.ResultsThe transcription factors foxA, gata4/5/6 and cdx show conserved expression in patterning the development and regionalization of the phoronid embryonic gut, with foxA expressed in the presumptive foregut, gata4/5/6 demarcating the midgut and cdx confined to the hindgut. Surprisingly, brachyury, an evolutionary conserved transcription factor often associated with gastrulation movements and patterning of the mouth and hindgut, seems to be unrelated with gastrulation and mouth patterning in phoronids. Furthermore, six3/6, a well-conserved anterior marker, shows a remarkably dynamic expression, demarcating not only the apical organ and the oral ectoderm, but also clusters of cells of the developing midgut and the anterior mesoderm, similar to what has been reported for brachiopods, bryozoans and some deuterostome Bilateria.ConclusionsOur comparison of gene expression patterns with other studied Bilateria reveals that the timing of axis determination and cell fate distribution of the phoronid shows highest similarities to rhynchonelliform brachiopods. Despite these similarities, the phoronid P. harmeri shows also particularities in its development, which hint to divergences in the arrangement of gene regulatory networks responsible for germ layer formation and axis specification.

scholarly journals Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

2020 ◽  
Author(s):  
Alexander Calderwood ◽  
Jo Hepworth ◽  
Shannon Woodhouse ◽  
Lorelei Bilham ◽  
D. Marc Jones ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Detailed Comparison ◽  
Developmental Time ◽  
Floral Transition ◽  
Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

scholarly journals Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference

Cell Reports ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. 2290-2303 ◽  
Author(s):  
Delphine Potier ◽  
Kristofer Davie ◽  
Gert Hulselmans ◽  
Marina Naval Sanchez ◽  
Lotte Haagen ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Large Scale ◽  
Eye Development ◽  
Drosophila Eye ◽  
Mapping Gene ◽  
Gene Regulatory

scholarly journals Expression pattern determines regulatory logic

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244864
Author(s):  
Carlos Mora-Martinez
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Networks ◽  
Dna Sequences ◽  
In Silico ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Cell Types ◽  
Evolutionary Strategy ◽  
Specific Gene ◽  
Gene Regulatory

Large amounts of effort have been invested in trying to understand how a single genome is able to specify the identity of hundreds of cell types. Inspired by some aspects of Caenorhabditis elegans biology, we implemented an in silico evolutionary strategy to produce gene regulatory networks (GRNs) that drive cell-specific gene expression patterns, mimicking the process of terminal cell differentiation. Dynamics of the gene regulatory networks are governed by a thermodynamic model of gene expression, which uses DNA sequences and transcription factor degenerate position weight matrixes as input. In a version of the model, we included chromatin accessibility. Experimentally, it has been determined that cell-specific and broadly expressed genes are regulated differently. In our in silico evolved GRNs, broadly expressed genes are regulated very redundantly and the architecture of their cis-regulatory modules is different, in accordance to what has been found in C. elegans and also in other systems. Finally, we found differences in topological positions in GRNs between these two classes of genes, which help to explain why broadly expressed genes are so resilient to mutations. Overall, our results offer an explanatory hypothesis on why broadly expressed genes are regulated so redundantly compared to cell-specific genes, which can be extrapolated to phenomena such as ChIP-seq HOT regions.

scholarly journals Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Sophie de Vries ◽  
Jan de Vries ◽  
John M Archibald ◽  
Claudio H Slamovits
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Reference Points ◽  
Global Perspective ◽  
Specific Gene ◽  
Gene Regulatory ◽  
Specific Array

ABSTRACT Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.

scholarly journals Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map

2019 ◽  
Author(s):  
Pablo Catalán ◽  
Susanna Manrubia ◽  
José A. Cuesta
Keyword(s):  
Regulatory Networks ◽  
Expression Patterns ◽  
Genetic Circuits ◽  
Target Pattern ◽  
Selective Pressures ◽  
Spatiotemporal Expression ◽  
Genotype Space ◽  
Great Relevance ◽  
Gene Regulatory ◽  
The Relationship

AbstractThe evolution of gene regulatory networks (GRNs) is of great relevance for both evolutionary and synthetic biology. Understanding the relationship between GRN structure and its function can allow us to understand the selective pressures that have shaped a given circuit. This is especially relevant when considering spatiotemporal expression patterns, where GRN models have been shown to be extremely robust and evolvable. However, previous models that studied GRN evolution did not include the evolution of protein and genetic elements that underlie GRN architecture. Here we use toyLIFE, a multilevel genotype-phenotype map, to show that not all GRNs are equally likely in genotype space and that evolution is biased to find the most common GRNs. toyLIFE rules create Boolean GRNs that, embedded in a one-dimensional tissue, develop a variety of spatiotemporal gene expression patterns. Populations of toyLIFE organisms choose the most common GRN out of a set of equally fit alternatives and, most importantly, fail to find a target pattern when it is very rare in genotype space. Indeed, we show that the probability of finding the fittest phenotype increases dramatically with its abundance in genotype space. This phenotypic bias represents a mechanism that can prevent the fixation in the population of the fittest phenotype, one that is inherent to the structure of genotype space and the genotype-phenotype map.

scholarly journals Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene Regulatory Networks

2019 ◽  
Author(s):  
Katherine Exelby ◽  
Edgar Herrera-Delgado ◽  
Lorena Garcia Perez ◽  
Ruben Perez-Carrasco ◽  
Andreas Sagner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Cell Fates ◽  
Gene Circuits ◽  
Stochastic Fluctuations ◽  
Network Properties ◽  
Gene Regulatory

AbstractDuring development, gene regulatory networks allocate cell fates by partitioning tissues into spatially organised domains of gene expression. How the sharp boundaries that delineate these gene expression patterns arise, despite the stochasticity associated with gene regulation, is poorly understood. We show, in the vertebrate neural tube, using perturbations of coding and regulatory regions, that the structure of the regulatory network contributes to boundary precision. This is achieved, not by reducing noise in individual genes, but by the configuration of the network modulating the ability of stochastic fluctuations to initiate gene expression changes. We use a computational screen to identify network properties that influence boundary precision, revealing two dynamical mechanisms by which small gene circuits attenuate the effect of noise in order to increase patterning precision. These results highlight design principles of gene regulatory networks that produce precise patterns of gene expression.

scholarly journals Embryonic expression patterns of panarthropod Teneurin-m/odd Oz genes suggest a possible function in segmentation

2019 ◽  
Author(s):  
Ralf Janssen
Keyword(s):  
Regulatory Networks ◽  
Transmembrane Protein ◽  
Expression Patterns ◽  
Expression Data ◽  
Segmentation Gene ◽  
Protein Encoding ◽  
Related Group ◽  
Gene Regulatory ◽  
Encoding Gene ◽  
Pair Rule

AbstractBackgroundA hallmark of arthropods is their segmented body, and the so-called Drosophila segmentation gene cascade that controls this process serves as one of the best-studied gene regulatory networks. An important group of segmentation genes is represented by the pair-rule genes (PRGs). One of these genes was thought to be the type-II transmembrane protein encoding gene Tenascin-m (Ten-m (aka odd Oz)). Ten-m, however, does not have a pair-rule function in Drosophila, despite its characteristic PRG-like expression pattern. A recent study in the beetle Tribolium castaneum showed that its Ten-m gene is not expressed like a segmentation gene, and hence is very unlikely to have a function in segmentation.ResultsIn this study, I present data from a range of arthropods covering the arthropod tree of life, and an onychophoran, representing a closely related group of segmented animals. At least one ortholog of Ten-m/odz in each of these species is expressed in the form of transverse segmental stripes in the ectoderm of forming and newly formed segments – a characteristic of genes involved in segmentation.ConclusionsThe new expression data support the idea that Ten-m orthologs after all may be involved in panarthropod segmentation.

scholarly journals Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression

2019 ◽  
Author(s):  
Sophie de Vries ◽  
Jan de Vries ◽  
John M Archibald ◽  
Claudio H Slamovits
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Reference Points ◽  
Global Perspective ◽  
Specific Gene ◽  
Gene Regulatory ◽  
Specific Array

Oomycetes include many well-studied, devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis growing on axenic litter as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them to (a) 22 oomycete genomes and (b) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions (three pathogenic lifestyles, six hosts/substrates, and four tissues). From these analyses we obtained a global perspective on the gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use generally similar molecular mechanisms for colonization, but exhibit distinct expression patterns. We identify S. sapeloensis' specific array and expression of carbohydrate-active enzymes and regulatory differences in pathogenicity-associated factors, including the virulence factor EpiC2B. Further, S. sapeloensis was found to express only a small repertoire of effector genes. In conclusion, our analyses reveal lifestyle-specific gene regulatory signatures and suggest that, in addition to variation in gene content, shifts in gene regulatory networks might underpin the evolution of oomycete lifestyles.

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