Article
Multidisciplinary Sciences
Roberto Feuda, Isabelle S. Peter
Summary: This study reveals that the development of apical organs in sea urchins shares common developmental mechanisms with the more complex nervous systems of other animals. The gene regulatory network controlling the formation of apical organ involves key transcription factors such as FoxQ2, Hbn, Delta/Notch signaling, and SoxC. These findings suggest that the ancestral regulatory program for the formation of nervous systems in bilaterians likely resembles the regulatory program for apical organ development.
Article
Developmental Biology
Abdull J. Massri, Laura Greenstreet, Anton Afanassiev, Alejandro Berrio, Gregory A. Wray, Geoffrey Schiebinger, David R. McClay
Summary: By using scRNA-seq and computational methods, researchers studied the transcriptional changes in cell states of sea urchin embryos from development to larval stage. They found that skeletogenic and primordial germ cell trajectories diverged early, and ectodermal progenitors were distinct from other lineages by the 6th cleavage. Endomesoderm cells originated at the 6th cleavage and diverged into endoderm and mesoderm fates asynchronously.
Article
Fisheries
Lili Xing, Lingyu Wang, Femke Roos, Michelle Lee, Gregory A. Wray
Summary: Sea urchins are important mariculture species and model organisms in developmental biology. Cis-regulatory elements control development and physiology by regulating gene expression. Mutations affecting these sequences contribute to phenotypic diversity. Cis-regulatory targets offer new breeding potential for the future.
Article
Anatomy & Morphology
Kristina Tarsis, Tsvia Gildor, Miri Morgulis, Smadar Ben-Tabou de-Leon
Summary: The study reveals the dynamic expression of skeletogenic regulatory genes that define a specific regulatory state for each pair of skeletal rods in the sea urchin Paracentrotus lividus. Vascular endothelial growth factor (VEGF) signaling is essential for skeleton formation, specifically controlling the migration of cells that form specific skeletal rods. VEGF signaling also regulates the expression of regulatory genes in cells at the tips of certain skeletal rods.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Developmental Biology
Majed Layous, Lama Khalaily, Tsvia Gildor, Smadar Ben-Tabou de-Leon
Summary: The tolerance to hypoxic conditions changes between different developmental stages of sea urchin embryos, possibly due to the structure of gene regulatory networks. Hypoxia applied during early development strongly affects the activity of certain pathways, while pathways are largely unaffected by hypoxia applied after DV-axis formation.
Article
Genetics & Heredity
Damir Baranasic, Matthias Hortenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio M. D'Orazio, Dorde Relic, Mikhail Pachkov, Noelia Diaz, Benjamin Hernandez-Rodriguez, Zelin Chen, Marcus Stoiber, Michael Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn M. Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, Jose Luis Gomez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Muller
Summary: Zebrafish, an important model organism for studying embryonic development and human diseases, lacks a systematic functional annotation program. The international DANIO-CODE consortium addressed this issue by creating a central repository to store and process zebrafish developmental functional genomic data. They improved existing annotations and identified over 140,000 cis-regulatory elements throughout development. They also compared regulatory elements and epigenomic landscapes between zebrafish and mouse, predicting functional relationships between them. This study extends the utility of zebrafish developmental genomics to mammals.
Article
Environmental Sciences
Flora Rendell-Bhatti, Periklis Paganos, Anna Pouch, Christopher Mitchell, Salvatore D'Aniello, Brendan J. Godley, Ksenia Pazdro, Maria Ina Arnone, Eva Jimenez-Guri
Summary: The study found that chemicals leached from plastic particles have severe impacts on the development of marine organisms, leading to developmental abnormalities. These findings suggest that microplastic pollution may have unknown negative effects on ecosystems.
ENVIRONMENTAL POLLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jian Ming Khor, Jennifer Guerrero-Santoro, William Douglas, Charles A. Ettensohn
Summary: In this study, CAGE-seq was used to profile eRNA expression and enhancer activity in the sea urchin model, revealing a large number of enhancers active at different stages of embryogenesis. The majority of sea urchin enhancers were found to be associated with nearby genes and exhibited temporal patterns of expression similar to those genes. Furthermore, enhancers near lineage-specific genes showed signatures of inputs from developmental gene regulatory networks in those lineages. Moreover, a significant portion of identified enhancers were shown to drive tissue-specific gene expression on their own in reporter assays.
Article
Multidisciplinary Sciences
Ksenia Skvortsova, Stephanie Bertrand, Danila Voronov, Paul E. Duckett, Samuel E. Ross, Marta Silvia Magri, Ignacio Maeso, Robert J. Weatheritt, Jose Luis Gomez Skarmeta, Maria Ina Arnone, Hector Escriva, Ozren Bogdanovic
Summary: The study shows that invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes, indicating a conservation of this major gene-regulatory module in vertebrates.
Article
Multidisciplinary Sciences
Ioannis Sarropoulos, Mari Sepp, Robert Fromel, Kevin Leiss, Nils Trost, Evgeny Leushkin, Konstantin Okonechnikov, Piyush Joshi, Peter Giere, Lena M. Kutscher, Margarida Cardoso-Moreira, Stefan M. Pfister, Henrik Kaessmann
Summary: This study investigated the regulatory basis of mouse cerebellum development from early neurogenesis to adulthood using snATAC-seq profiles. The research revealed spatiotemporal heterogeneity among progenitor cells and gradual divergence in the regulatory programs of cerebellar neurons during differentiation. Comparison to vertebrate genomes showed a shared decrease in CRE conservation during development and differentiation, as well as differences in constraint between cell types. The study provides insights into mammalian organ development dynamics and evolutionary gene regulation in cerebellar cells.
Article
Biochemistry & Molecular Biology
Rutger A. F. Gjaltema, Till Schwaemmle, Pauline Kautz, Michael Robson, Robert Schoepflin, Liat Ravid Lustig, Lennart Brandenburg, Ilona Dunkel, Carolina Vechiatto, Evgenia Ntini, Verena Mutzel, Vera Schmiedel, Annalisa Marsico, Stefan Mundlos, Edda G. Schulz
Summary: Developmental genes like Xist are regulated by complex cis regulatory landscapes, which decode multiple signals to establish specific expression patterns. In this study, functional enhancer elements of Xist were identified during random X inactivation. X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. A previously unannotated enhancer cluster associated with Xist-enhancing regulatory transcript, named Xert, was also discovered. The study helps to understand how multiple regulatory elements interact to generate complex expression patterns in mammals.
Article
Biotechnology & Applied Microbiology
Cesar Arenas-Mena, Sofija Miljovska, Edward J. Rice, Justin Gurges, Tanvi Shashikant, Zihe Wang, Sevinc Ercan, Charles G. Danko
Summary: Chromatin accessibility and transcription have substantial power for predicting enhancer activity in sea urchin embryos, with the distribution of Pol II being the best predictor for enhancer activity, especially for promoter-overlapping cis-regulatory elements. Additionally, the predictive value of ATAC-seq and PRO-seq is stage-dependent in the promoter-overlapping subset.
Article
Multidisciplinary Sciences
Tatiana Lebedeva, Andrew J. Aman, Thomas Graf, Isabell Niedermoser, Bob Zimmermann, Yulia Kraus, Magdalena Schatka, Adrien Demilly, Ulrich Technau, Grigory Genikhovich
Summary: Animals rely on concentration-dependent interpretation of morphogen signals for body axis patterning, while the ancient axis patterning system across animal phyla involves beta-catenin signaling. Differences in patterning logic exist between protostomes and deuterostomes, but a common regulatory logic of beta-catenin-dependent patterning is observed in Nematostella and deuterostomes. This suggests a shared evolutionary origin of these processes and the equivalence of cnidarian oral-aboral and bilaterian posterior-anterior body axes.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
David Gokhman, Rachel M. Agoglia, Maia Kinnebrew, Wei Gordon, Danqiong Sun, Vivek K. Bajpai, Sahin Naqvi, Coral Chen, Anthony Chan, Chider Chen, Dmitri A. Petrov, Nadav Ahituv, Honghao Zhang, Yuji Mishina, Joanna Wysocka, Rajat Rohatgi, Hunter B. Fraser
Summary: The study of human-chimpanzee hybrid induced pluripotent stem cells reveals evidence of lineage-specific selection on the hedgehog signaling pathway, which may have contributed to the unique craniofacial morphology of humans. This approach offers a new perspective on understanding gene expression differences between species.
Article
Multidisciplinary Sciences
Jingyi Zhang, Farhan Ibrahim, Emily Najmulski, George Katholos, Doaa Altarawy, Lenwood S. Heath, Sarah L. Tulin
Summary: Gene regulatory network (GRN) prediction for developmental networks using the PEAK network inference algorithm based on gene expression data alone shows high sensitivity, identifying known gene interactions and generating novel predictions. The results suggest that GRN predictions matching known gene interactions can be produced solely from developmental time series experiments using gene expression data.
Article
Developmental Biology
Tsvia Gildor, Assaf Malik, Noa Sher, Smadar Ben-Tabou de-Leon
DEVELOPMENTAL BIOLOGY
(2016)
Article
Genetics & Heredity
Tsvia Gildor, Assaf Malik, Noa Sher, Linor Avraham, Smadar Ben-Tabou de-Leon
Editorial Material
History & Philosophy Of Science
Smadar Ben-Tabou de-Leon
HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES
(2017)
Article
Developmental Biology
Tsvia Gildor, Veronica Hinman, Smadar Ben-Tabou-De-Leon
INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY
(2017)
Article
Genetics & Heredity
Tsvia Gildor, Smadar Ben-Tabou de-Leon
FRONTIERS IN GENETICS
(2018)
Correction
Genetics & Heredity
Tsvia Gildor, Smadar Ben-Tabou de-Leon
FRONTIERS IN GENETICS
(2018)
Article
Multidisciplinary Sciences
Miri Morgulis, Tsvia Gildor, Modi Roopin, Noa Sher, Assaf Malik, Maya Lalzar, Monica Dines, Shlomo Ben-Tabou de-Leon, Lama Khalaily, Smadar Ben-Tabou de-Leon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Tsvia Gildor, Gregory A. Cary, Maya Lalzar, Veronica F. Hinman, Smadar Ben-Tabou De-Leon
SCIENTIFIC REPORTS
(2019)
Article
Biochemical Research Methods
Mark R. Winter, Miri Morgulis, Tsvia Gildor, Andrew R. Cohen, Smadar Ben-Tabou de-Leon
Summary: Biomineralization is the process by which organisms use minerals to harden their tissues. Calcium-bearing vesicles exhibit active diffusion motion in both calcifying and non-calcifying cells of sea urchin embryos. The dynamics of vesicle motion are influenced by mechanical properties of the cells, with vesicle speed and diffusion length inversely correlating with the strength of the actomyosin network.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Developmental Biology
Majed Layous, Lama Khalaily, Tsvia Gildor, Smadar Ben-Tabou de-Leon
Summary: The tolerance to hypoxic conditions changes between different developmental stages of sea urchin embryos, possibly due to the structure of gene regulatory networks. Hypoxia applied during early development strongly affects the activity of certain pathways, while pathways are largely unaffected by hypoxia applied after DV-axis formation.
Article
Developmental Biology
Miri Morgulis, Mark R. Winter, Ligal Shternhell, Tsvia Gildor, Smadar Ben-Tabou de-Leon
Summary: The uptake and mineralization of minerals by organisms are tightly regulated by networks of specialized proteins within biomineralizing cells. In vertebrates, matrix metalloproteases (MMPs) play a role in mineralization of teeth and bones, but much remains unknown about their function in invertebrates. The sea urchin embryo serves as a valuable model for studying genetic and molecular aspects of biomineralization, with membrane type MMPs such as Pl-MmpL7 and Pl-MmpL5 being localized within spicules and playing a crucial role in skeletogenesis.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tsvia Gildor, Mark R. Winter, Majed Layous, Eman Hijaze, Smadar Ben-Tabou de-Leon
Summary: Biomineralization is the process where soft tissues utilize minerals to produce shells, skeletons, and teeth for protection and support. Cells have the remarkable ability to control crystal nucleation, orientation, and stiffness, surpassing current human technologies. Understanding this biological control can advance knowledge of embryo development and offer new approaches to material engineering.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Review
Cell Biology
Smadar Ben-Tabou de-Leon
Summary: Biomineralization is the process by which organisms create hard structures using minerals. It is believed to have independently evolved in different phyla through the co-option of pre-existing developmental programs. A comparison of the gene regulatory networks (GRNs) involved in biomineralization in different species can shed light on its molecular evolution. In this study, the GRNs driving biomineralization and tubulogenesis in echinoderms and vertebrates were compared. The results show that the GRN driving skeletogenesis in sea urchin embryos is different from the GRN driving bone formation in vertebrates, but resembles the GRN driving vascular tubulogenesis in vertebrates. On the other hand, the bone-GRNs in vertebrates are similar to the GRNs operating in the cells that generate cartilage-like tissues in basal chordates and invertebrates that do not produce mineralized tissue. These comparisons suggest that biomineralization in deuterostomes evolved through the phylum-specific co-option of GRNs that control different organic scaffolds for mineralization.
Article
Anatomy & Morphology
Kristina Tarsis, Tsvia Gildor, Miri Morgulis, Smadar Ben-Tabou de-Leon
Summary: The study reveals the dynamic expression of skeletogenic regulatory genes that define a specific regulatory state for each pair of skeletal rods in the sea urchin Paracentrotus lividus. Vascular endothelial growth factor (VEGF) signaling is essential for skeleton formation, specifically controlling the migration of cells that form specific skeletal rods. VEGF signaling also regulates the expression of regulatory genes in cells at the tips of certain skeletal rods.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Developmental Biology
Assaf Malik, Tsvia Gildor, Noa Sher, Majed Layous, Smadar Ben-Tabou de-Leon
DEVELOPMENTAL BIOLOGY
(2017)
Review
Developmental Biology
Cheng Shi, Pengfei Jiao, Zhiyi Chen, Lan Ma, Siyue Yao
Summary: This review discusses the molecular etiology of congenital craniofacial abnormalities, with a focus on the role and mechanism of noncoding RNAs in regulating craniofacial development. Aberrant expression of noncoding RNAs has been implicated in the pathogenesis of craniofacial abnormalities, providing potential therapeutic targets.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Hideru Togashi, Steven Ray Davis, Makoto Sato
Summary: Tile patterns, regulated by cell adhesion molecules, are regular arrangements of cells that play important functional roles in multicellular organisms. The physical constraints and cell adhesion regulate both cell shape and tissue morphogenesis.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Armen Khanbabei, Lina Segura, Cynthia Petrossian, Aaron Lemus, Ithan Cano, Courtney Frazier, Armen Halajyan, Donnie Ca, Mariano Loza-Coll
Summary: This article investigates the genetic regulatory mechanisms of Drosophila intestinal stem cells. The study found that most target genes co-regulated by Esg and STAT show a consistent gene expression pattern. However, manipulating these validated targets in vivo rarely replicated the effects of manipulating Esg and STAT, suggesting the presence of complex genetic interactions among the downstream targets of these two master regulator genes.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Bayley J. Waters, Zoe R. Birman, Matthew R. Wagner, Julia Lemanski, Barak Blum
Summary: Researchers found that conditional deletion of Robo2 in adult mice led to a significant loss of islet architecture without affecting beta cell identity or function, suggesting that Robo2 plays a role in actively maintaining adult islet architecture. Understanding the factors required for islet architecture maintenance is crucial for developing future diabetes therapies.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Rhiannon Clements, Tyler Smith, Luke Cowart, Jennifer Zhumi, Alan Sherrod, Aidan Cahill, Ginger L. Hunter
Summary: Cell protrusions play a crucial role in regulating cell activities during development. By studying the regulation mechanism in fruit fly sensory bristle patterning, it was found that Myosin XV is essential for the dynamics of signaling filopodia and promotes long-range Notch signaling.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Margaret Keating, Ryan Hagle, Daniel Osorio-Mendez, Anjelica Rodriguez-Parks, Sarah I. Almutawa, Junsu Kang
Summary: Knock-in reporter (KI) animals are essential for studying gene expression in biomedical research. This study developed a new strategy using minicircle technology and a minimal promoter to enhance knock-in events and establish stable KI transgenic reporter lines. The study also highlighted the importance of selecting the proper KI line due to potential inappropriate influence of genome editing on reporter gene expression.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Christian Altbuerger, Meta Rath, Daniel Armbruster, Wolfgang Driever
Summary: This study reveals that Neurog1 and Olig2 transcription factors have differential requirements for the development of dopaminergic neurons, and they integrate local patterning signals and Notch neurogenic selection signaling to specify the progenitor population and initiate neurogenesis and differentiation.
DEVELOPMENTAL BIOLOGY
(2024)