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

EvoDevo ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Carmen Andrikou ◽  
Yale J. Passamaneck ◽  
Chris J. Lowe ◽  
Mark Q. Martindale ◽  
Andreas Hejnol
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Embryonic Patterning ◽  
Dynamic Expression ◽  
Oral Ectoderm ◽  
Axis Specification ◽  
Phoronopsis Harmeri ◽  
Mode Of Development

Abstract Background Phoronids, rhynchonelliform and linguliform brachiopods show striking similarities in their embryonic fate maps, in particular in their axis specification and regionalization. However, although brachiopod development has been studied in detail and demonstrated embryonic patterning as a causal factor of the gastrulation mode (protostomy vs deuterostomy), molecular descriptions are still missing in phoronids. To understand whether phoronids display underlying embryonic molecular mechanisms similar to those of brachiopods, here we report the expression patterns of anterior (otx, gsc, six3/6, nk2.1), posterior (cdx, bra) and endomesodermal (foxA, gata4/5/6, twist) markers during the development of the protostomic phoronid Phoronopsis harmeri. Results The 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. Furthermore, six3/6, usually 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. Surprisingly, brachyury, a transcription factor often associated with gastrulation movements and mouth and hindgut development, seems not to be involved with these patterning events in phoronids. Conclusions Our description and 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 similarity to that of rhynchonelliform brachiopods, which is likely related to their shared protostomic mode of development. Despite these similarities, the phoronid Ph. harmeri also shows 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 Strength of interactions in the Notch gene regulatory network determine lateral inhibition patterning

2021 ◽  
Author(s):  
Héctor Sánchez-Iranzo ◽  
Aliaksandr Halavatyi ◽  
Alba Diz-Muñoz
Keyword(s):  
Cell Fate ◽  
Lateral Inhibition ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Experimental System ◽  
Dependent Manner ◽  
Experimental Systems ◽  
Gene Regulatory ◽  
Gene Patterning ◽  
Main Components

Gene regulatory networks (GRNs) regulate the generation of diverse gene expression patterns, which in turn determine cell fate during the development of multicellular organisms. However, how the topology and parameters of GRNs determine this patterning remain largely unknown due to the complexity of most experimental systems. To address this, we use the zebrafish notochord, an organ where coin-shaped precursor cells arranged in a simple unidimensional geometry differentiate into vacuolated and sheath cells in a Notch-dependent manner. We identify jag1a and her6/her9 as the main components of an unconventional GRN that generates a lateral inhibition pattern that controls cell differentiation. Moreover, making use of this experimental system and mathematical modeling we show that such patterning requires that ligand-receptor interactions are stronger within the same cell than in neighboring cells. Altogether, we establish the zebrafish notochord as an experimental system to study Notch patterns, and identify and characterize a GRN that determines gene patterning and drives cell fate.

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 GATA-targeted compounds modulate cardiac subtype cell differentiation in dual reporter stem cell line

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mika J. Välimäki ◽  
Robert S. Leigh ◽  
Sini M. Kinnunen ◽  
Alexander R. March ◽  
Ana Hernández de Sande ◽  
...  
Keyword(s):  
Gene Expression ◽  
Progenitor Cells ◽  
Cell Fate ◽  
Reporter Gene ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Cell Fate Decisions ◽  
Dual Reporter ◽  
Gene Regulatory ◽  
Reporter Gene Assays

AbstractBackgroundPharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. Compounds that target tissue-specific transcription factors could overcome non-specific effects of small molecules and lead to the regeneration of heart muscle following myocardial infarction. Due to cellular heterogeneity in the heart, the activation of gene programs representing specific atrial and ventricular cardiomyocyte subtypes would be highly desirable. Chemical compounds that modulate atrial and ventricular cell fate could be used to improve subtype-specific differentiation of endogenous or exogenously delivered progenitor cells in order to promote cardiac regeneration.MethodsTranscription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. Reporter gene assays were conducted to examine combinatorial effects of GATA-targeted compounds and bromodomain and extraterminal domain (BET) inhibition on chamber-specific gene expression.ResultsGATA4-targeted compounds 3i-1000 and 3i-1103 were identified as differential modulators of atrial and ventricular gene expression. More detailed structure-function analysis revealed a distinct subclass of GATA4/NKX2-5 inhibitory compounds with an acetyl lysine-like domain that contributed to ventricular cells (%Myl2-eGFP+). Additionally, BioID analysis indicated broad interaction between GATA4 and BET family of proteins, such as BRD4. This indicated the involvement of epigenetic modulators in the regulation of GATA-dependent transcription. In this line, reporter gene assays with combinatorial treatment of 3i-1000 and the BET bromodomain inhibitor (+)-JQ1 demonstrated the cooperative role of GATA4 and BRD4 in the modulation of chamber-specific cardiac gene expression.ConclusionsCollectively, these results indicate the potential for therapeutic alteration of cell fate decisions and pathological gene regulatory networks by GATA4-targeted compounds modulating chamber-specific transcriptional programs in multipotent cardiac progenitor cells and cardiomyocytes. The compound scaffolds described within this study could be used to develop regenerative strategies for myocardial regeneration.

scholarly journals Joint profiling of gene expression and chromatin accessibility of amphioxus development at single cell resolution

2021 ◽  
Author(s):  
Pengcheng Ma ◽  
Xingyan Liu ◽  
Huimin Liu ◽  
Zaoxu Xu ◽  
Xiangning Ding ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Genetic Regulatory Networks ◽  
Public Access ◽  
Origin And Evolution ◽  
Key Species

Abstract Vertebrate evolution was accompanied with two rounds of whole genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single cell sequencing has been widely employed to construct the developmental cell atlas of several key species of vertebrates (human, mouse, zebrafish and frog) and tunicate (sea squirts). Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated we constructed the developmental tree for amphioxus cell fate commitment and lineage specification, and revealed the underlying key regulators and genetic regulatory networks. The generated data were integrated into an online platform, AmphioxusAtlas, for public access at http://120.79.46.200:81/AmphioxusAtlas.

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 Novel generic models for differentiating stem cells reveal oscillatory mechanisms

2021 ◽  
Vol 18 (183) ◽  
Author(s):  
Saeed Farjami ◽  
Karen Camargo Sosa ◽  
Jonathan H. P. Dawes ◽  
Robert N. Kelsh ◽  
Andrea Rocco
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Oscillatory Process ◽  
Oscillatory Regime ◽  
Epigenetic Landscape ◽  
Generic Models ◽  
Gene Regulatory ◽  
Oscillatory Mechanisms ◽  
Gradual Variation ◽  
Standard Framework

Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically motivated mathematical models for cell differentiation that generically generate oscillations and hence suggest alternatives to the standard framework based on Waddington’s epigenetic landscape. The models allow us to suggest two generic dynamical scenarios that describe the differentiation process. In the first scenario, gradual variation of a single control parameter is responsible for both entering and exiting the oscillatory regime. In the second scenario, two control parameters vary: one responsible for entering, and the other for exiting the oscillatory regime. We analyse the standard repressilator and four variants of it and show the dynamical behaviours associated with each scenario. We present a thorough analysis of the associated bifurcations and argue that gene regulatory networks with these repressilator-like characteristics are promising candidates to describe cell fate selection through an oscillatory process.

scholarly journals Distinct and overlapping gene regulatory networks in BMP- and HDAC-controlled cell fate determination in the embryonic forebrain

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 298 ◽  
Author(s):  
Catharina Scholl ◽  
Kathrin Weiβmüller ◽  
Pavlo Holenya ◽  
Maya Shaked-Rabi ◽  
Kerry L Tucker ◽  
...  
Keyword(s):  
Cell Fate ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Cell Fate Determination ◽  
Fate Determination ◽  
Overlapping Gene ◽  
Gene Regulatory

scholarly journals Multiple morphogens and rapid elongation promote segmental patterning during development

2021 ◽  
Vol 17 (6) ◽  
pp. e1009077
Author(s):  
Yuchi Qiu ◽  
Lianna Fung ◽  
Thomas F. Schilling ◽  
Qing Nie
Keyword(s):  
Cell Fate ◽  
Gene Regulatory Networks ◽  
Cell Sorting ◽  
Short Range ◽  
Regulatory Networks ◽  
Neural Plate ◽  
Convergent Extension ◽  
Simultaneous Formation ◽  
Gene Regulatory ◽  
Rapid Elongation

The vertebrate hindbrain is segmented into rhombomeres (r) initially defined by distinct domains of gene expression. Previous studies have shown that noise-induced gene regulation and cell sorting are critical for the sharpening of rhombomere boundaries, which start out rough in the forming neural plate (NP) and sharpen over time. However, the mechanisms controlling simultaneous formation of multiple rhombomeres and accuracy in their sizes are unclear. We have developed a stochastic multiscale cell-based model that explicitly incorporates dynamic morphogenetic changes (i.e. convergent-extension of the NP), multiple morphogens, and gene regulatory networks to investigate the formation of rhombomeres and their corresponding boundaries in the zebrafish hindbrain. During pattern initiation, the short-range signal, fibroblast growth factor (FGF), works together with the longer-range morphogen, retinoic acid (RA), to specify all of these boundaries and maintain accurately sized segments with sharp boundaries. At later stages of patterning, we show a nonlinear change in the shape of rhombomeres with rapid left-right narrowing of the NP followed by slower dynamics. Rapid initial convergence improves boundary sharpness and segment size by regulating cell sorting and cell fate both independently and coordinately. Overall, multiple morphogens and tissue dynamics synergize to regulate the sizes and boundaries of multiple segments during development.

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