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Gautam P, Sinha SK. The Blueprint of Logical Decisions in a NF-κB Signaling System. ACS OMEGA 2024; 9:22625-22634. [PMID: 38826544 PMCID: PMC11137707 DOI: 10.1021/acsomega.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 06/04/2024]
Abstract
Nearly identical cells can exhibit substantially different responses to the same stimulus that causes phenotype diversity. Such interplay between phenotype diversity and the architecture of regulatory circuits is crucial since it determines the state of a biological cell. Here, we theoretically analyze how the circuit blueprints of NF-κB in cellular environments are formed and their role in determining the cells' metabolic state. The NF-κB is a collective name for a developmental conserved family of five different transcription factors that can form homodimers or heterodimers and often promote DNA looping to reprogram the inflammatory gene response. The NF-κB controls many biological functions, including cellular differentiation, proliferation, migration, and survival. Our model shows that nuclear localization of NF-κB differentially promotes logic operations such as AND, NAND, NOR, and OR in its regulatory network. Through the quantitative thermodynamic model of transcriptional regulation and systematic variation of promoter-enhancer interaction modes, we can account for the origin of various logic gates as formed in the NF-κB system. We further show that the interconversion or switching of logic gates yielded under systematic variations of the stimuli activity and DNA looping parameters. Such computation occurs in regulatory and signaling pathways in individual cells at a molecular scale, which one can exploit to design a biomolecular computer.
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Affiliation(s)
- Pankaj Gautam
- Theoretical and Computational
Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Sudipta Kumar Sinha
- Theoretical and Computational
Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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2
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Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA. Echinobase: a resource to support the echinoderm research community. Genetics 2024; 227:iyae002. [PMID: 38262680 PMCID: PMC11075573 DOI: 10.1093/genetics/iyae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024] Open
Abstract
Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.
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Affiliation(s)
- Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Macie M Chess
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sergei Agalakov
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bradley I Arshinoff
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Dong Zhuo Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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3
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Pickett CJ, Gruner HN, Davidson B. Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling. PLoS Biol 2024; 22:e3002169. [PMID: 38271304 PMCID: PMC10810493 DOI: 10.1371/journal.pbio.3002169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Individual signaling pathways, such as fibroblast growth factors (FGFs), can regulate a plethora of inductive events. According to current paradigms, signal-dependent transcription factors (TFs), such as FGF/MapK-activated Ets family factors, partner with lineage-determining factors to achieve regulatory specificity. However, many aspects of this model have not been rigorously investigated. One key question relates to whether lineage-determining factors dictate lineage-specific responses to inductive signals or facilitate these responses in collaboration with other inputs. We utilize the chordate model Ciona robusta to investigate mechanisms generating lineage-specific induction. Previous studies in C. robusta have shown that cardiopharyngeal progenitor cells are specified through the combined activity of FGF-activated Ets1/2.b and an inferred ATTA-binding transcriptional cofactor. Here, we show that the homeobox TF Lhx3/4 serves as the lineage-determining TF that dictates cardiopharyngeal-specific transcription in response to pleiotropic FGF signaling. Targeted knockdown of Lhx3/4 leads to loss of cardiopharyngeal gene expression. Strikingly, ectopic expression of Lhx3/4 in a neuroectodermal lineage subject to FGF-dependent specification leads to ectopic cardiopharyngeal gene expression in this lineage. Furthermore, ectopic Lhx3/4 expression disrupts neural plate morphogenesis, generating aberrant cell behaviors associated with execution of incompatible morphogenetic programs. Based on these findings, we propose that combinatorial regulation by signal-dependent and lineage-determinant factors represents a generalizable, previously uncategorized regulatory subcircuit we term "cofactor-dependent induction." Integration of this subcircuit into theoretical models will facilitate accurate predictions regarding the impact of gene regulatory network rewiring on evolutionary diversification and disease ontogeny.
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Affiliation(s)
- C. J. Pickett
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Hannah N. Gruner
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
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4
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Zhu J, Chu P, Fu X. Unbalanced response to growth variations reshapes the cell fate decision landscape. Nat Chem Biol 2023; 19:1097-1104. [PMID: 36959461 DOI: 10.1038/s41589-023-01302-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/27/2023] [Indexed: 03/25/2023]
Abstract
The global regulation of cell growth rate on gene expression perturbs the performance of gene networks, which would impose complex variations on the cell-fate decision landscape. Here we use a simple synthetic circuit of mutual repression that allows a bistable landscape to examine how such global regulation would affect the stability of phenotypic landscape and the accompanying dynamics of cell-fate determination. We show that the landscape experiences a growth-rate-induced bifurcation between monostability and bistability. Theoretical and experimental analyses reveal that this bifurcating deformation of landscape arises from the unbalanced response of gene expression to growth variations. The path of growth transition across the bifurcation would reshape cell-fate decisions. These results demonstrate the importance of growth regulation on cell-fate determination processes, regardless of specific molecular signaling or regulation.
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Affiliation(s)
- Jingwen Zhu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pan Chu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiongfei Fu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Bronchain O, Ducos B, Putzer H, Delagrange M, Laalami S, Philippe-Caraty L, Saroul K, Ciapa B. Natural antisense transcription of presenilin in sea urchin reveals a possible role for natural antisense transcription in the general control of gene expression during development. J Cell Sci 2023; 136:jcs261284. [PMID: 37345489 DOI: 10.1242/jcs.261284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
One presenilin gene (PSEN) is expressed in the sea urchin embryo, in the vegetal pole of the gastrula and then mainly in cilia cells located around the digestive system of the pluteus, as we recently have reported. PSEN expression must be accurately regulated for correct execution of these two steps of development. While investigating PSEN expression changes in embryos after expansion of endoderm with LiCl or of ectoderm with Zn2+ by whole-mount in situ hybridization (WISH) and quantitative PCR (qPCR), we detected natural antisense transcription of PSEN. We then found that Endo16 and Wnt5, markers of endo-mesoderm, and of Hnf6 and Gsc, markers of ectoderm, are also sense and antisense transcribed. We discuss that general gene expression could depend on both sense and antisense transcription. This mechanism, together with the PSEN gene, should be included in gene regulatory networks (GRNs) that theorize diverse processes in this species. We suggest that it would also be relevant to investigate natural antisense transcription of PSEN in the field of Alzheimer's disease (AD) where the role of human PSEN1 and PSEN2 is well known.
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Affiliation(s)
- Odile Bronchain
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Harald Putzer
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Marine Delagrange
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Soumaya Laalami
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Laetitia Philippe-Caraty
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Krystel Saroul
- Institut CURIE, Université Paris-Saclay, INSERM U932, Immunité et Cancer, 91400 Orsay, France
| | - Brigitte Ciapa
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
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6
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Silic MR, Zhang G. Bioelectricity in Developmental Patterning and Size Control: Evidence and Genetically Encoded Tools in the Zebrafish Model. Cells 2023; 12:cells12081148. [PMID: 37190057 DOI: 10.3390/cells12081148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens. Evidence from multiple model organisms reveals the roles of bioelectricity in embryonic development, regeneration, and cancers. The Zebrafish model is the second most used vertebrate model, next to the mouse model. The zebrafish model has great potential for elucidating the functions of bioelectricity due to many advantages such as external development, transparent early embryogenesis, and tractable genetics. Here, we review genetic evidence from zebrafish mutants with fin-size and pigment changes related to ion channels and bioelectricity. In addition, we review the cell membrane voltage reporting and chemogenetic tools that have already been used or have great potential to be implemented in zebrafish models. Finally, new perspectives and opportunities for bioelectricity research with zebrafish are discussed.
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Affiliation(s)
- Martin R Silic
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, 625 Harrison Street, West Lafayette, IN 47907, USA
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7
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Gao F, Li C, Smith SM, Peinado N, Kohbodi G, Tran E, Loh YHE, Li W, Borok Z, Minoo P. Decoding the IGF1 signaling gene regulatory network behind alveologenesis from a mouse model of bronchopulmonary dysplasia. eLife 2022; 11:e77522. [PMID: 36214448 PMCID: PMC9581530 DOI: 10.7554/elife.77522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
Lung development is precisely controlled by underlying gene regulatory networks (GRN). Disruption of genes in the network can interrupt normal development and cause diseases such as bronchopulmonary dysplasia (BPD) - a chronic lung disease in preterm infants with morbid and sometimes lethal consequences characterized by lung immaturity and reduced alveolarization. Here, we generated a transgenic mouse exhibiting a moderate severity BPD phenotype by blocking IGF1 signaling in secondary crest myofibroblasts (SCMF) at the onset of alveologenesis. Using approaches mirroring the construction of the model GRN in sea urchin's development, we constructed the IGF1 signaling network underlying alveologenesis using this mouse model that phenocopies BPD. The constructed GRN, consisting of 43 genes, provides a bird's eye view of how the genes downstream of IGF1 are regulatorily connected. The GRN also reveals a mechanistic interpretation of how the effects of IGF1 signaling are transduced within SCMF from its specification genes to its effector genes and then from SCMF to its neighboring alveolar epithelial cells with WNT5A and FGF10 signaling as the bridge. Consistently, blocking WNT5A signaling in mice phenocopies BPD as inferred by the network. A comparative study on human samples suggests that a GRN of similar components and wiring underlies human BPD. Our network view of alveologenesis is transforming our perspective to understand and treat BPD. This new perspective calls for the construction of the full signaling GRN underlying alveologenesis, upon which targeted therapies for this neonatal chronic lung disease can be viably developed.
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Affiliation(s)
- Feng Gao
- Division of Neonatology, Department of Pediatrics, University of Southern CaliforniaLos AngelesUnited States
| | - Changgong Li
- Division of Neonatology, Department of Pediatrics, University of Southern CaliforniaLos AngelesUnited States
| | - Susan M Smith
- Division of Neonatology, Department of Pediatrics, University of Southern CaliforniaLos AngelesUnited States
| | - Neil Peinado
- Division of Neonatology, Department of Pediatrics, University of Southern CaliforniaLos AngelesUnited States
| | - Golenaz Kohbodi
- Division of Neonatology, Department of Pediatrics, University of Southern CaliforniaLos AngelesUnited States
| | - Evelyn Tran
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Yong-Hwee Eddie Loh
- Norris Medical Library, University of Southern CaliforniaLos AngelesUnited States
| | - Wei Li
- Department of Nephrology, Jiangsu Provincial Hospital of Traditional Chinese MedicineNanjingChina
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San DiegoSan DiegoUnited States
| | - Parviz Minoo
- Division of Neonatology, Department of Pediatrics, University of Southern CaliforniaLos AngelesUnited States
- Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
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8
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Ouyang Y, Zhang P, Willner I. Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures. Bioconjug Chem 2022; 34:51-69. [PMID: 35973134 PMCID: PMC9853509 DOI: 10.1021/acs.bioconjchem.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.
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9
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Schaffter SW, Chen KL, O'Brien J, Noble M, Murugan A, Schulman R. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nat Chem 2022; 14:1224-1232. [PMID: 35927329 DOI: 10.1038/s41557-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network's various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuan-Lin Chen
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jackson O'Brien
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Madeline Noble
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. .,Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
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10
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Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models. Nat Commun 2022; 13:4414. [PMID: 35906232 PMCID: PMC9338015 DOI: 10.1038/s41467-022-32148-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
Dynamic, transient, out-of-equilibrium networks guide cellular genetic, metabolic or signaling processes. Designing synthetic networks emulating natural processes imposes important challenges including the ordered connectivity of transient reaction modules, engineering of the appropriate balance between production and depletion of reaction constituents, and coupling of the reaction modules with emerging chemical functions dictated by the networks. Here we introduce the assembly of three coupled reaction modules executing a cascaded dynamic process leading to the transient formation and depletion of three different Mg2+-ion-dependent DNAzymes. The transient operation of the DNAzyme in one layer triggers the dynamic activation of the DNAzyme in the subsequent layer, leading to a three-layer transient catalytic cascade. The kinetics of the transient cascade is computationally simulated. The cascaded network is coupled to a polymerization/nicking DNA machinery guiding transient synthesis of three coded strands acting as “gene models”, and to the rolling circle polymerization machinery leading to the transient synthesis of fluorescent Zn(II)-PPIX/G-quadruplex chains or hemin/G-quadruplex catalytic wires. A reaction network executing a cascaded transient formation and depletion of three different catalytic strands is introduced. The system is coupled to the secondary temporal synthesis of different coded strands as gene models.
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11
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Gonçalves LO, Pulido AFV, Mathias FAS, Enes AES, Carvalho MGR, de Melo Resende D, Polak ME, Ruiz JC. Expression Profile of Genes Related to the Th17 Pathway in Macrophages Infected by Leishmania major and Leishmania amazonensis: The Use of Gene Regulatory Networks in Modeling This Pathway. Front Cell Infect Microbiol 2022; 12:826523. [PMID: 35774406 PMCID: PMC9239034 DOI: 10.3389/fcimb.2022.826523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Leishmania amazonensis and Leishmania major are the causative agents of cutaneous and mucocutaneous diseases. The infections‘ outcome depends on host–parasite interactions and Th1/Th2 response, and in cutaneous form, regulation of Th17 cytokines has been reported to maintain inflammation in lesions. Despite that, the Th17 regulatory scenario remains unclear. With the aim to gain a better understanding of the transcription factors (TFs) and genes involved in Th17 induction, in this study, the role of inducing factors of the Th17 pathway in Leishmania–macrophage infection was addressed through computational modeling of gene regulatory networks (GRNs). The Th17 GRN modeling integrated experimentally validated data available in the literature and gene expression data from a time-series RNA-seq experiment (4, 24, 48, and 72 h post-infection). The generated model comprises a total of 10 TFs, 22 coding genes, and 16 cytokines related to the Th17 immune modulation. Addressing the Th17 induction in infected and uninfected macrophages, an increase of 2- to 3-fold in 4–24 h was observed in the former. However, there was a decrease in basal levels at 48–72 h for both groups. In order to evaluate the possible outcomes triggered by GRN component modulation in the Th17 pathway. The generated GRN models promoted an integrative and dynamic view of Leishmania–macrophage interaction over time that extends beyond the analysis of single-gene expression.
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Affiliation(s)
- Leilane Oliveira Gonçalves
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| | - Andrés F. Vallejo Pulido
- Systems Immunology Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Alexandre Estevão Silvério Enes
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| | | | - Daniela de Melo Resende
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| | - Marta E. Polak
- Systems Immunology Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- *Correspondence: Jeronimo C. Ruiz, ; Marta E. Polak,
| | - Jeronimo C. Ruiz
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
- *Correspondence: Jeronimo C. Ruiz, ; Marta E. Polak,
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12
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Differential Etv2 threshold requirement for endothelial and erythropoietic development. Cell Rep 2022; 39:110881. [PMID: 35649376 PMCID: PMC9203129 DOI: 10.1016/j.celrep.2022.110881] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/23/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022] Open
Abstract
Endothelial and erythropoietic lineages arise from a common developmental progenitor. Etv2 is a master transcriptional regulator required for the development of both lineages. However, the mechanisms through which Etv2 initiates the gene-regulatory networks (GRNs) for endothelial and erythropoietic specification and how the two GRNs diverge downstream of Etv2 remain incompletely understood. Here, by analyzing a hypomorphic Etv2 mutant, we demonstrate different threshold requirements for initiation of the downstream GRNs for endothelial and erythropoietic development. We show that Etv2 functions directly in a coherent feedforward transcriptional network for vascular endothelial development, and a low level of Etv2 expression is sufficient to induce and sustain the endothelial GRN. In contrast, Etv2 induces the erythropoietic GRN indirectly via activation of Tal1, which requires a significantly higher threshold of Etv2 to initiate and sustain erythropoietic development. These results provide important mechanistic insight into the divergence of the endothelial and erythropoietic lineages.
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13
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Palmquist KH, Tiemann SF, Ezzeddine FL, Yang S, Pfeifer CR, Erzberger A, Rodrigues AR, Shyer AE. Reciprocal cell-ECM dynamics generate supracellular fluidity underlying spontaneous follicle patterning. Cell 2022; 185:1960-1973.e11. [DOI: 10.1016/j.cell.2022.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/14/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
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14
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Kremnev SV. Evolutionary and Ontogenetic Plasticity of Conserved Signaling Pathways in Animals’ Development. Russ J Dev Biol 2022. [DOI: 10.1134/s1062360422020114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Levis NA, Ragsdale EJ. Linking Molecular Mechanisms and Evolutionary Consequences of Resource Polyphenism. Front Integr Neurosci 2022; 16:805061. [PMID: 35210995 PMCID: PMC8861301 DOI: 10.3389/fnint.2022.805061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Resource polyphenism—the occurrence of environmentally induced, discrete, and intraspecific morphs showing differential niche use—is taxonomically widespread and fundamental to the evolution of ecological function where it has arisen. Despite longstanding appreciation for the ecological and evolutionary significance of resource polyphenism, only recently have its proximate mechanisms begun to be uncovered. Polyphenism switches, especially those influencing and influenced by trophic interactions, offer a route to integrating proximate and ultimate causation in studies of plasticity, and its potential influence on evolution more generally. Here, we use the major events in generalized polyphenic development as a scaffold for linking the molecular mechanisms of polyphenic switching with potential evolutionary outcomes of polyphenism and for discussing challenges and opportunities at each step in this process. Not only does the study of resource polyphenism uncover interesting details of discrete plasticity, it also illuminates and informs general principles at the intersection of development, ecology, and evolution.
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16
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Chen YS, Racca JD, Weiss MA. Tenuous Transcriptional Threshold of Human Sex Determination. I. SRY and Swyer Syndrome at the Edge of Ambiguity. Front Endocrinol (Lausanne) 2022; 13:945030. [PMID: 35957822 PMCID: PMC9360328 DOI: 10.3389/fendo.2022.945030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Male sex determination in mammals is initiated by SRY, a Y-encoded transcription factor. The protein contains a high-mobility-group (HMG) box mediating sequence-specific DNA bending. Mutations causing XY gonadal dysgenesis (Swyer syndrome) cluster in the box and ordinarily arise de novo. Rare inherited variants lead to male development in one genetic background (the father) but not another (his sterile XY daughter). De novo and inherited mutations occur at an invariant Tyr adjoining the motif's basic tail (box position 72; Y127 in SRY). In SRY-responsive cell lines CH34 and LNCaP, de novo mutations Y127H and Y127C reduced SRY activity (as assessed by transcriptional activation of principal target gene Sox9) by 5- and 8-fold, respectively. Whereas Y127H impaired testis-specific enhancer assembly, Y127C caused accelerated proteasomal proteolysis; activity was in part rescued by proteasome inhibition. Inherited variant Y127F was better tolerated: its expression was unperturbed, and activity was reduced by only twofold, a threshold similar to other inherited variants. Biochemical studies of wild-type (WT) and variant HMG boxes demonstrated similar specific DNA affinities (within a twofold range), with only subtle differences in sharp DNA bending as probed by permutation gel electrophoresis and fluorescence resonance-energy transfer (FRET); thermodynamic stabilities of the free boxes were essentially identical. Such modest perturbations are within the range of species variation. Whereas our cell-based findings rationalize the de novo genotype-phenotype relationships, a molecular understanding of inherited mutation Y127F remains elusive. Our companion study uncovers cryptic biophysical perturbations suggesting that the para-OH group of Y127 anchors a novel water-mediated DNA clamp.
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17
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Three topological features of regulatory networks control life-essential and specialized subsystems. Sci Rep 2021; 11:24209. [PMID: 34930908 PMCID: PMC8688434 DOI: 10.1038/s41598-021-03625-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022] Open
Abstract
Gene regulatory networks (GRNs) play key roles in development, phenotype plasticity, and evolution. Although graph theory has been used to explore GRNs, associations amongst topological features, transcription factors (TFs), and systems essentiality are poorly understood. Here we sought the relationship amongst the main GRN topological features that influence the control of essential and specific subsystems. We found that the Knn, page rank, and degree are the most relevant GRN features: the ones are conserved along the evolution and are also relevant in pluripotent cells. Interestingly, life-essential subsystems are governed mainly by TFs with intermediary Knn and high page rank or degree, whereas specialized subsystems are mainly regulated by TFs with low Knn. Hence, we suggest that the high probability of TFs be toured by a random signal, and the high probability of the signal propagation to target genes ensures the life-essential subsystems' robustness. Gene/genome duplication is the main evolutionary process to rise Knn as the most relevant feature. Herein, we shed light on unexplored topological GRN features to assess how they are related to subsystems and how the duplications shaped the regulatory systems along the evolution. The classification model generated can be found here: https://github.com/ivanrwolf/NoC/ .
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18
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Wang C, O'Hagan MP, Willner B, Willner I. Bioinspired Artificial Photosynthetic Systems. Chemistry 2021; 28:e202103595. [PMID: 34854505 DOI: 10.1002/chem.202103595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 12/18/2022]
Abstract
Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael P O'Hagan
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bilha Willner
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Abstract
The temporal coordination of events at cellular and tissue scales is essential for the proper development of organisms, and involves cell-intrinsic processes that can be coupled by local cellular signalling and instructed by global signalling, thereby creating spatial patterns of cellular states that change over time. The timing and structure of these patterns determine how an organism develops. Traditional developmental genetic methods have revealed the complex molecular circuits regulating these processes but are limited in their ability to predict and understand the emergent spatio-temporal dynamics. Increasingly, approaches from physics are now being used to help capture the dynamics of the system by providing simplified, generic descriptions. Combined with advances in imaging and computational power, such approaches aim to provide insight into timing and patterning in developing systems.
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20
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Waymack R, Wunderlich Z. Embryonic development across space and time. NATURE COMPUTATIONAL SCIENCE 2021; 1:507-508. [PMID: 38217246 DOI: 10.1038/s43588-021-00117-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Affiliation(s)
- Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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21
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Herman MA, Aiello BR, DeLong JD, Garcia-Ruiz H, González AL, Hwang W, McBeth C, Stojković EA, Trakselis MA, Yakoby N. A Unifying Framework for Understanding Biological Structures and Functions Across Levels of Biological Organization. Integr Comp Biol 2021; 61:2038-2047. [PMID: 34302339 DOI: 10.1093/icb/icab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between structure and function is a major constituent of the rules of life. Structures and functions occur across all levels of biological organization. Current efforts to integrate conceptual frameworks and approaches to address new and old questions promise to allow a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization. Here, we provide unifying and generalizable definitions of both structure and function that can be applied across all levels of biological organization. However, we find differences in the nature of structures at the organismal level and below as compared to above the level of the organism. We term these intrinsic and emergent structures, respectively. Intrinsic structures are directly under selection, contributing to the overall performance (fitness) of the individual organism. Emergent structures involve interactions among aggregations of organisms and are not directly under selection. Given this distinction, we argue that while the functions of many intrinsic structures remain unknown, functions of emergent structures are the result of the aggregate of processes of individual organisms. We then provide a detailed and unified framework of the structure-function relationship for intrinsic structures to explore how their unknown functions can be defined. We provide examples of how these scalable definitions applied to intrinsic structures provide a framework to address questions on structure-function relationships that can be approached simultaneously from all subdisciplines of biology. We propose that this will produce a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization.
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Affiliation(s)
- M A Herman
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118
| | - B R Aiello
- Schools of Physics and Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - J D DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118
| | - H Garcia-Ruiz
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68503
| | - A L González
- Department of Biology & Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
| | - W Hwang
- Departments of Biomedical Engineering, Materials Science & Engineering, and Physics & Astronomy, Texas A&M University, College Station, TX 77843-3127
| | - C McBeth
- Fraunhofer USA CMI and Boston University, Boston, MA
| | - E A Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL 60641, USA
| | - M A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798
| | - N Yakoby
- Department of Biology & Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
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22
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Integration of photocatalytic and dark-operating catalytic biomimetic transformations through DNA-based constitutional dynamic networks. Nat Commun 2021; 12:4224. [PMID: 34244502 PMCID: PMC8270929 DOI: 10.1038/s41467-021-24512-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023] Open
Abstract
Nucleic acid-based constitutional dynamic networks (CDNs) have recently emerged as versatile tools to control a variety of catalytic processes. A key challenge in the application of these systems is achieving intercommunication between different CDNs to mimic the complex interlinked networks found in cellular biology. In particular, the possibility to interface photochemical ‘energy-harvesting’ processes with dark-operating ‘metabolic’ processes, in a similar way to plants, represents an up to now unexplored yet enticing research direction. The present study introduces two CDNs that allow the intercommunication of photocatalytic and dark-operating catalytic functions mediated by environmental components that facilitate the dynamic coupling of the networks. The dynamic feedback-driven intercommunication of the networks is accomplished via information transfer between the two CDNs effected by hairpin fuel strands in the environment of the system, leading to the coupling of the photochemical and dark-operating modules. Nucleic acid-based constitutional dynamic networks (CDNs) enable control of various catalytic processes, but it is challenging to achieve intercommunication between different CDNs and by that mimic complex cell biology networks. Here, the authors report two CDNs that control the integration of photochemical and dark-operating processes, and show their intercommunication afforded by environmental components.
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23
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Jaeger J, Monk N. Dynamical modules in metabolism, cell and developmental biology. Interface Focus 2021; 11:20210011. [PMID: 34055307 PMCID: PMC8086940 DOI: 10.1098/rsfs.2021.0011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 02/06/2023] Open
Abstract
Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative processes that constitute the genotype-phenotype map must also be functionally modular. Traditionally, modular processes have been identified as structural modules in regulatory networks. However, structure only constrains, but does not determine, the dynamics of a process. Here, we propose an alternative approach that decomposes the behaviour of a complex regulatory system into elementary activity-functions. Modular activities can occur in networks that show no structural modularity, making dynamical modularity more widely applicable than structural decomposition. Furthermore, the behaviour of a regulatory system closely mirrors its functional contribution to the outcome of a process, which makes dynamical modularity particularly suited for functional decomposition. We illustrate our approach with numerous examples from the study of metabolism, cellular processes, as well as development and pattern formation. We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and serve as the foundation for a new account of process homology, which is presented in a separate contribution by DiFrisco and Jaeger to this focus issue.
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Affiliation(s)
- Johannes Jaeger
- Complexity Science Hub (CSH) Vienna, Josefstädter Strasse 39, 1080 Vienna, Austria
| | - Nick Monk
- School of Mathematics and Statistics, University of Sheffield, Hicks Building, Sheffield S3 7RH, UK
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24
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Díaz-Valenzuela E, Sawers RH, Cibrián-Jaramillo A. Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit. Mol Biol Evol 2021; 37:1593-1603. [PMID: 32031611 PMCID: PMC7253206 DOI: 10.1093/molbev/msaa027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The process of domestication requires the rapid transformation of the wild morphology into the cultivated forms that humans select for. This process often takes place through changes in the regulation of genes, yet, there is no definite pattern on the role of cis- and trans-acting regulatory variations in the domestication of the fruit among crops. Using allele-specific expression and network analyses, we characterized the regulatory patterns and the inheritance of gene expression in wild and cultivated accessions of chili pepper, a crop with remarkable fruit morphological variation. We propose that gene expression differences associated to the cultivated form are best explained by cis-regulatory hubs acting through trans-regulatory cascades. We show that in cultivated chili, the expression of genes associated with fruit morphology is partially recessive with respect to those in the wild relative, consistent with the hybrid fruit phenotype. Decreased expression of fruit maturation and growth genes in cultivated chili suggest that selection for loss-of-function took place in its domestication. Trans-regulatory changes underlie the majority of the genes showing regulatory divergence and had larger effect sizes on gene expression than cis-regulatory variants. Network analysis of selected cis-regulated genes, including ARP9 and MED25, indicated their interaction with many transcription factors involved in organ growth and fruit ripening. Differentially expressed genes linked to cis-regulatory variants and their interactions with downstream trans-acting genes have the potential to drive the morphological differences observed between wild and cultivated fruits and provide an attractive mechanism of morphological transformation during the domestication of the chili pepper.
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Affiliation(s)
- Erik Díaz-Valenzuela
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Guanajuato, México
| | - Ruairidh H Sawers
- Department of Plant Science, The Pennsylvania State University, University Park State College, University Park, PA
| | - Angélica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Guanajuato, México
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25
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Reeves WM, Shimai K, Winkley KM, Veeman MT. Brachyury controls Ciona notochord fate as part of a feed-forward network. Development 2021; 148:dev195230. [PMID: 33419874 PMCID: PMC7875503 DOI: 10.1242/dev.195230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022]
Abstract
The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes is unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators, and find that combinatorial cocktails are more effective at reprogramming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a and other components of the notochord gene regulatory network, and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically defined master regulator.
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Affiliation(s)
- Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kotaro Shimai
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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26
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Masullo T, Biondo G, Natale MD, Tagliavia M, Bennici CD, Musco M, Ragusa MA, Costa S, Cuttitta A, Nicosia A. Gene Expression Changes after Parental Exposure to Metals in the Sea Urchin Affect Timing of Genetic Programme of Embryo Development. BIOLOGY 2021; 10:biology10020103. [PMID: 33535713 PMCID: PMC7912929 DOI: 10.3390/biology10020103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022]
Abstract
It is widely accepted that phenotypic traits can be modulated at the epigenetic level so that some conditions can affect the progeny of exposed individuals. To assess if the exposure of adult animals could result in effects on the offspring, the Mediterranean sea urchin and its well-characterized gene regulatory networks (GRNs) was chosen as a model. Adult animals were exposed to known concentrations of zinc and cadmium (both individually and in combination) for 10 days, and the resulting embryos were followed during the development. The oxidative stress occurring in parental gonads, embryo phenotypes and mortality, and the expression level of a set of selected genes, including members of the skeletogenic and endodermal GRNs, were evaluated. Increased oxidative stress at F0, high rates of developmental aberration with impaired gastrulation, in association to deregulation of genes involved in skeletogenesis (dri, hex, sm50, p16, p19, msp130), endodermal specification (foxa, hox11/13b, wnt8) and epigenetic regulation (kat2A, hdac1, ehmt2, phf8 and UBE2a) occurred either at 24 or 48 hpf. Results strongly indicate that exposure to environmental pollutants can affect not only directly challenged animals but also their progeny (at least F1), influencing optimal timing of genetic programme of embryo development, resulting in an overall impairment of developmental success.
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Affiliation(s)
- Tiziana Masullo
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Girolama Biondo
- Institute for Anthropic Impacts and Sustainability in Marine Environment-National Research Council (IAS-CNR), Detached Unit of Capo Granitola, Via del mare 3, 91021 Campobello di Mazara, Italy;
| | - Marilena Di Natale
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
- Department of Earth and Marine Science (DiSTeM), University of Palermo, Via Archirafi 20, 90123 Palermo, Italy
| | - Marcello Tagliavia
- Institute for Biomedical Research and Innovation-National Research Council-(IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
| | - Carmelo Daniele Bennici
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Marianna Musco
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy; (M.A.R.); (S.C.)
| | - Salvatore Costa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy; (M.A.R.); (S.C.)
| | - Angela Cuttitta
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
- Correspondence: (A.C.); (A.N.)
| | - Aldo Nicosia
- Institute for Biomedical Research and Innovation-National Research Council-(IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
- Correspondence: (A.C.); (A.N.)
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27
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Adonin L, Drozdov A, Barlev NA. Sea Urchin as a Universal Model for Studies of Gene Networks. Front Genet 2021; 11:627259. [PMID: 33552139 PMCID: PMC7854572 DOI: 10.3389/fgene.2020.627259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.
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Affiliation(s)
- Leonid Adonin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nickolai A Barlev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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28
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Azambuja AP, Simoes-Costa M. A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation. PLoS Genet 2021; 17:e1009296. [PMID: 33465092 PMCID: PMC7846109 DOI: 10.1371/journal.pgen.1009296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/29/2021] [Accepted: 12/05/2020] [Indexed: 01/15/2023] Open
Abstract
The process of cell fate commitment involves sequential changes in the gene expression profiles of embryonic progenitors. This is exemplified in the development of the neural crest, a migratory stem cell population derived from the ectoderm of vertebrate embryos. During neural crest formation, cells transition through distinct transcriptional states in a stepwise manner. The mechanisms underpinning these shifts in cell identity are still poorly understood. Here we employ enhancer analysis to identify a genetic sub-circuit that controls developmental transitions in the nascent neural crest. This sub-circuit links Wnt target genes in an incoherent feedforward loop that controls the sequential activation of genes in the neural crest lineage. By examining the cis-regulatory apparatus of Wnt effector gene AXUD1, we found that multipotency factor SP5 directly promotes neural plate border identity, while inhibiting premature expression of specification genes. Our results highlight the importance of repressive interactions in the neural crest gene regulatory network and illustrate how genes activated by the same upstream signal become temporally segregated during progressive fate restriction.
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Affiliation(s)
- Ana Paula Azambuja
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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29
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Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell 2021; 28:20-32. [PMID: 33417869 PMCID: PMC7799393 DOI: 10.1016/j.stem.2020.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area.
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Affiliation(s)
- Patrick Cahan
- Institute for Cell Engineering, Department of Biomedical Engineering, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy d Department of Translational Medicine, University of Naples "Federico II," Naples, Italy
| | - Sara-Jane Dunn
- DeepMind, 14-18 Handyside Street, London N1C 4DN, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Samantha A Morris
- Department of Developmental Biology, Department of Genetics, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Owen J L Rackham
- Centre for Computational Biology and The Program for Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Belvaux 4366, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Clairambault J. Stepping From Modeling Cancer Plasticity to the Philosophy of Cancer. Front Genet 2020; 11:579738. [PMID: 33329717 PMCID: PMC7710795 DOI: 10.3389/fgene.2020.579738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/03/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jean Clairambault
- Laboratoire Jacques-Louis Lions, BC 187, Sorbonne Université, Paris, France.,Inria, Paris, France
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31
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Lilienthal S, Luo GF, Wang S, Yue L, Fischer A, Ehrlich A, Nahmias Y, Willner I. Constitutional Dynamic Networks-Guided Synthesis of Programmed "Genes", Transcription of mRNAs, and Translation of Proteins. J Am Chem Soc 2020; 142:21460-21468. [PMID: 33290051 DOI: 10.1021/jacs.0c10565] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inspired by nature, where dynamic networks control the levels of gene expression and the activities of transcribed/translated proteins, we introduce nucleic acid-based constitutional dynamic networks (CDNs) as functional modules mimicking native circuits by demonstrating CDNs-guided programmed synthesis of genes, controlled transcription of RNAs, and dictated transcription/translation synthesis of proteins. An auxiliary CDN consisting of four dynamically equilibrated constituents AA', AB', BA', and BB' is orthogonally triggered by two different inputs yielding two different compositionally reconfigured CDNs. Subjecting the parent auxiliary CDN to two hairpins, HA and HB, and two templates TA and TB and a nicking/replication machinery leads to the cleavage of the hairpins and to the activation of the nicking/replication machineries that synthesize two "genes", e.g., the histidine-dependent DNAzyme g1 and the Zn2+-ion-dependent DNAzyme g2. The triggered orthogonal reconfiguration of the parent CDN to the respective CDNs leads to the programmed preferred CDN-guided synthesis of g1 or g2. Similarly, the triggered reconfigured CDNs are subjected to two hairpins HC and HD, the templates I'/I and J'/J, and the RNA polymerase (RNAp)/NTPs machinery. While the cleavage of the hairpins by the constituents associated with the parent CDN leads to the transcription of the broccoli aptamer recognizing the DFHBI ligand and of the aptamer recognizing the malachite green (MG) ligand, the orthogonally triggered CDNs lead to the CDNs-guided enhanced transcription of either the DFHBI aptamer or the MG aptamer. In addition, subjecting the triggered reconfigured CDNs to predesigned hairpins HE and HF, the templates M'/M and N'/N, the RNAp/NTPs machinery, and the cell-free ribosome t-RNA machinery leads to the CDNs-guided transcription/translation of the green fluorescence protein (GFP) or red fluorescence protein (RFP).
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Affiliation(s)
- Sivan Lilienthal
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Guo-Feng Luo
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liang Yue
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Amit Fischer
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Avner Ehrlich
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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33
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Zeitlinger J. Seven myths of how transcription factors read the cis-regulatory code. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 23:22-31. [PMID: 33134611 PMCID: PMC7592701 DOI: 10.1016/j.coisb.2020.08.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genomics data are now being generated at large quantities, of exquisite high resolution and from single cells. They offer a unique opportunity to develop powerful machine learning algorithms, including neural networks, to uncover the rules of the cis-regulatory code. However, current modeling assumptions are often not based on state-of-the-art knowledge of the cis-regulatory code from transcription, developmental genetics, imaging and structural studies. Here I aim to fill this gap by giving a brief historical overview of the field, describing common misconceptions and providing knowledge that might help to guide computational approaches. I will describe the principles and mechanisms involved in the combinatorial requirement of transcription factor binding motifs for enhancer activity, including the role of chromatin accessibility, repressors and low-affinity motifs in the cis-regulatory code. Deciphering the cis-regulatory code would unlock an enormous amount of regulatory information in the genome and would allow us to locate cis-regulatory genetic variants involved in development and disease.
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Affiliation(s)
- Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA
- The University of Kansas Medical Center, Kansas City, KS, USA
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34
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Erwin DH. A conceptual framework of evolutionary novelty and innovation. Biol Rev Camb Philos Soc 2020; 96:1-15. [PMID: 32869437 DOI: 10.1111/brv.12643] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022]
Abstract
Since 1990 the recognition of deep homologies among metazoan developmental processes and the spread of more mechanistic approaches to developmental biology have led to a resurgence of interest in evolutionary novelty and innovation. Other evolutionary biologists have proposed central roles for behaviour and phenotypic plasticity in generating the conditions for the construction of novel morphologies, or invoked the accessibility of new regions of vast sequence spaces. These approaches contrast with more traditional emphasis on the exploitation of ecological opportunities as the primary source of novelty. This definitional cornucopia reflects differing stress placed on three attributes of novelties: their radical nature, the generation of new taxa, and ecological and evolutionary impact. Such different emphasis has led to conflating four distinct issues: the origin of novel attributes (genes, developmental processes, phenotypic characters), new functions, higher clades and the ecological impact of new structures and functions. Here I distinguish novelty (the origin of new characters, deep character transformations, or new combinations) from innovation, the ecological and evolutionary success of clades. Evidence from the fossil record of macroevolutionary lags between the origin of a novelty and its ecological success demonstrates that novelty may be decoupled from innovation, and only definitions of novelty based on radicality (rather than generativity or consequentiality) can be assessed without reference to the subsequent history of the clade to which a novelty belongs. These considerations suggest a conceptual framework for novelty and innovation, involving: (i) generation of the potential for novelty; (ii) the formation of novel attributes; (iii) refinement of novelties through adaptation; (iv) exploitation of novelties by a clade, which may coincide with a new round of ecological or environmental potentiation; followed by (v) the establishment of innovations through ecological processes. This framework recognizes that there is little empirical support for either the dominance of ecological opportunity, nor abrupt discontinuities (often caricatured as 'hopeful monsters'). This general framework may be extended to aspects of cultural and social innovation.
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Affiliation(s)
- Douglas H Erwin
- Department of Paleobiology, MRC-121 National Museum of Natural History, PO Box 37012, Washington, DC, 20013-7012, U.S.A.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, U.S.A
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35
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Peter IS. The function of architecture and logic in developmental gene regulatory networks. Curr Top Dev Biol 2020; 139:267-295. [PMID: 32450963 DOI: 10.1016/bs.ctdb.2020.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An important contribution of systems biology is the insight that biological systems depend on the function of molecular interactions and not just on individual molecules. System level mechanisms are particularly important in the development of animals and plants which depends not just on transcription factors and signaling molecules, but also on regulatory circuits and gene regulatory networks (GRNs). However, since GRNs consist of transcription factors, it can be challenging to assess the function of regulatory circuits independently of the function of regulatory factors. The comparison of different GRNs offers a way to do so and leads to several observations. First, similar regulatory circuits operate in various developmental contexts and in different species, and frequently, these circuits are associated with similar developmental functions. Second, given regulatory circuits are often used at particular positions within the GRN hierarchy. Third, in some GRNs, regulatory circuits are organized in a particular order in respect to each other. And fourth, the evolution of GRNs occurs not just by co-option of regulatory genes but also by rewiring of regulatory linkages between conserved regulatory genes, indicating that the organization of interactions is important. Thus, even though in most instances the function of regulatory circuits remains to be discovered, it becomes evident that the architecture and logic of GRNs are functionally important for the control of genome activity and for the specification of the body plan.
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Affiliation(s)
- Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
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36
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Paraiso KD, Cho JS, Yong J, Cho KWY. Early Xenopus gene regulatory programs, chromatin states, and the role of maternal transcription factors. Curr Top Dev Biol 2020; 139:35-60. [PMID: 32450966 DOI: 10.1016/bs.ctdb.2020.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For decades, the early development of the Xenopus embryo has been an essential model system to study the gene regulatory mechanisms that govern cellular specification. At the top of the hierarchy of gene regulatory networks, maternally deposited transcription factors initiate this process and regulate the expression of zygotic genes that give rise to three distinctive germ layer cell types (ectoderm, mesoderm, and endoderm), and subsequent generation of organ precursors. The onset of germ layer specification is also closely coupled with changes associated with chromatin modifications. This review will examine the timing of maternal transcription factors initiating the zygotic genome activation, the epigenetic landscape of embryonic chromatin, and the network structure that governs the process.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States; Center for Complex Biological Systems, University of California, Irvine, CA, United States
| | - Jin S Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States
| | - Junseok Yong
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States; Center for Complex Biological Systems, University of California, Irvine, CA, United States.
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37
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Garte S, Albert A. Genotype Components as Predictors of Phenotype in Model Gene Regulatory Networks. Acta Biotheor 2019; 67:299-320. [PMID: 31286303 DOI: 10.1007/s10441-019-09350-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/04/2019] [Indexed: 10/26/2022]
Abstract
Models of gene regulatory networks (GRN) have proven useful for understanding many aspects of the highly complex behavior of biological control networks. Randomly generated non-Boolean networks were used in experimental simulations to generate data on dynamic phenotypes as a function of several genotypic parameters. We found that predictive relationships between some phenotypes and quantitative genotypic parameters such as number of network genes, interaction density, and initial condition could be derived depending on the strength of the topological (positional) genotype on specific phenotypes. We quantitated the strength of the topological genotype effect (TGE) on a number of phenotypes in multi-gene networks. For phenotypes with a low influence of topological genotype, derived and empirical relationships using quantitative genotype parameters were accurate in phenotypic outcomes. We found a number of dynamic network properties, including oscillation behaviors, that were largely dependent on genotype topology, and for which no such general quantitative relationships were determinable. It remains to be determined if these results are applicable to biological gene regulatory networks.
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38
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Abstract
Early embryogenesis is characterized by the segregation of cell lineages that fulfill critical roles in the establishment of pregnancy and development of the fetus. The formation of the blastocyst marks the emergence of extraembryonic precursors, needed for implantation, and of pluripotent cells, which differentiate toward the major lineages of the adult organism. The coordinated emergence of these cell types shows that these processes are broadly conserved in mammals. However, developmental heterochrony and changes in gene regulatory networks highlight unique evolutionary adaptations that may explain the diversity in placentation and in the mechanisms controlling pluripotency in mammals. The incorporation of new technologies, including single-cell omics, imaging, and gene editing, is instrumental for comparative embryology. Broadening the knowledge of mammalian embryology will provide new insights into the mechanisms driving evolution and development. This knowledge can be readily translated into biomedical and biotechnological applications in humans and livestock, respectively.
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Affiliation(s)
- Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
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39
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Hovland AS, Rothstein M, Simoes-Costa M. Network architecture and regulatory logic in neural crest development. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1468. [PMID: 31702881 DOI: 10.1002/wsbm.1468] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/25/2019] [Accepted: 10/11/2019] [Indexed: 12/31/2022]
Abstract
The neural crest is an ectodermal cell population that gives rise to over 30 cell types during vertebrate embryogenesis. These stem cells are formed at the border of the developing central nervous system and undergo extensive migration before differentiating into components of multiple tissues and organs. Neural crest formation and differentiation is a multistep process, as these cells transition through sequential regulatory states before adopting their adult phenotype. Such changes are governed by a complex gene regulatory network (GRN) that integrates environmental and cell-intrinsic inputs to regulate cell identity. Studies of neural crest cells in a variety of vertebrate models have elucidated the function and regulation of dozens of the molecular players that are part of this network. The neural crest GRN has served as a platform to explore the molecular control of multipotency, cell differentiation, and the evolution of vertebrates. In this review, we employ this genetic program as a stepping-stone to explore the architecture and the regulatory principles of developmental GRNs. We also discuss how modern genomic approaches can further expand our understanding of genetic networks in this system and others. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Fates Developmental Biology > Lineages Models of Systems Properties and Processes > Cellular Models.
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Affiliation(s)
- Austin S Hovland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Megan Rothstein
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
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40
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Abstract
Gastrulation is arguably the most important evolutionary innovation in the animal kingdom. This process provides the basic embryonic architecture, an inner layer separated from an outer layer, from which all animal forms arise. An extraordinarily simple and elegant process of gastrulation is observed in the sea urchin embryo. The cells participating in sea urchin gastrulation are specified early during cleavage. One outcome of that specification is the expression of transcription factors that control each of the many subsequent morphogenetic changes. The first of these movements is an epithelial-mesenchymal transition (EMT) of skeletogenic mesenchyme cells, then EMT of pigment cell progenitors. Shortly thereafter, invagination of the archenteron occurs. At the end of archenteron extension, a second wave of EMT occurs to release immune cells into the blastocoel and primordial germ cells that will home to the coelomic pouches. The archenteron then remodels to establish the three parts of the gut, and at the anterior end, the gut fuses with the stomodaeum to form the through-gut. As part of the anterior remodeling, mesodermal coelomic pouches bud off the lateral sides of the archenteron tip. Multiple cell biological processes conduct each of these movements and in some cases the upstream transcription factors controlling this process have been identified. Remarkably, each event seamlessly occurs at the right time to orchestrate formation of the primitive body plan. This review covers progress toward understanding many of the molecular mechanisms underlying this sequence of morphogenetic events.
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41
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Tempos and modes of collectivity in the history of life. Theory Biosci 2019; 140:343-351. [PMID: 31529373 DOI: 10.1007/s12064-019-00303-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
Collective integration and processing of information have increased through the history of life, through both the formation of aggregates in which the entities may have very different properties and which jointly coarse-grained environmental variables (ranging from widely varying metabolism in microbial consortia to the ecological diversity of species on reefs) and through collectives of similar entities (such as cells within an organism or social groups). Such increases have been implicated in significant transitions in the history of life, including aspects of the origin of life, the generation of pangenomes among microbes and microbial communities such as stromatolites, multicellularity and social insects. This contribution provides a preliminary overview of the dominant modes of collective information processing in the history of life, their phylogenetic distribution and extent of convergence, and the effects of new modes for integrating and acting upon information on the tempo of evolutionary change.
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42
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Schaffter SW, Schulman R. Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules. Nat Chem 2019; 11:829-838. [PMID: 31427767 DOI: 10.1038/s41557-019-0292-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/13/2019] [Indexed: 02/04/2023]
Abstract
The regulation of cellular dynamics and responses to stimuli by genetic regulatory networks suggests how in vitro chemical reaction networks might analogously direct the dynamics of synthetic materials or chemistries. A key step in developing genetic regulatory network analogues capable of this type of sophisticated regulation is the integration of multiple coordinated functions within a single network. Here, we demonstrate how such functional integration can be achieved using in vitro transcriptional genelet circuits that emulate essential features of cellular genetic regulatory networks. By successively incorporating functional genelet modules into a bistable circuit, we construct an integrated regulatory network that dynamically changes its state in response to upstream stimuli and coordinates the timing of downstream signal expression. We use quantitative models to guide module integration and develop strategies to mitigate undesired interactions between network components that arise as the size of the network increases. This approach could enable the construction of in vitro networks capable of multifaceted chemical and material regulation.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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43
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Torres Cleuren YN, Ewe CK, Chipman KC, Mears ER, Wood CG, Al-Alami CEA, Alcorn MR, Turner TL, Joshi PM, Snell RG, Rothman JH. Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network. eLife 2019; 8:48220. [PMID: 31414984 PMCID: PMC6754231 DOI: 10.7554/elife.48220] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm GRN. While some natural isolates show a nearly absolute requirement for these two regulators, in others, most embryos differentiate endoderm in their absence. GWAS and analysis of recombinant inbred lines reveal multiple genetic regions underlying this broad phenotypic variation. We observe a reciprocal trend, in which genomic variants, or knockdown of endoderm regulatory genes, that result in a high SKN-1 requirement often show low MOM-2/Wnt requirement and vice-versa, suggesting that cryptic variation in the endoderm GRN may be tuned by opposing requirements for these two key regulatory inputs. These findings reveal that while the downstream components in the endoderm GRN are common across metazoan phylogeny, initiating regulatory inputs are remarkably plastic even within a single species.
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Affiliation(s)
- Yamila N Torres Cleuren
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chee Kiang Ewe
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Kyle C Chipman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Emily R Mears
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cricket G Wood
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | | | - Melissa R Alcorn
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Thomas L Turner
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Pradeep M Joshi
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joel H Rothman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
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44
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Abstract
The regulatory genome controls genome activity throughout the life of an organism. This requires that complex information processing functions are encoded in, and operated by, the regulatory genome. Although much remains to be learned about how the regulatory genome works, we here discuss two cases where regulatory functions have been experimentally dissected in great detail and at the systems level, and formalized by computational logic models. Both examples derive from the sea urchin embryo, but assess two distinct organizational levels of genomic information processing. The first example shows how the regulatory system of a single gene, endo16, executes logic operations through individual transcription factor binding sites and cis-regulatory modules that control the expression of this gene. The second example shows information processing at the gene regulatory network (GRN) level. The GRN controlling development of the sea urchin endomesoderm has been experimentally explored at an almost complete level. A Boolean logic model of this GRN suggests that the modular logic functions encoded at the single-gene level show compositionality and suffice to account for integrated function at the network level. We discuss these examples both from a biological-experimental point of view and from a computer science-informational point of view, as both illuminate principles of how the regulatory genome works.
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Affiliation(s)
- Sorin Istrail
- Department of Computer Science, Brown University, Providence, Rhode Island
| | - Isabelle S Peter
- Division of Biology and Biological Engineering, MC156-29, California Institute of Technology, Pasadena, California
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45
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Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise. Nat Commun 2019; 10:2418. [PMID: 31160574 PMCID: PMC6546794 DOI: 10.1038/s41467-019-10388-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
In transcriptional regulatory networks (TRNs), a canonical 3-node feed-forward loop (FFL) is hypothesized to evolve to filter out short spurious signals. We test this adaptive hypothesis against a novel null evolutionary model. Our mutational model captures the intrinsically high prevalence of weak affinity transcription factor binding sites. We also capture stochasticity and delays in gene expression that distort external signals and intrinsically generate noise. Functional FFLs evolve readily under selection for the hypothesized function but not in negative controls. Interestingly, a 4-node “diamond” motif also emerges as a short spurious signal filter. The diamond uses expression dynamics rather than path length to provide fast and slow pathways. When there is no idealized external spurious signal to filter out, but only internally generated noise, only the diamond and not the FFL evolves. While our results support the adaptive hypothesis, we also show that non-adaptive factors, including the intrinsic expression dynamics, matter. Feed‐forward loops (FFLs) can filter out noise, but whether their overrepresentation in GRNs reflects adaptive evolution for this function is debated. Here, the authors develop a null model of regulatory evolution and find that FFLs evolve readily under selection for the noise filtering function.
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46
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Fernandez-Valverde SL, Aguilera F, Ramos-Díaz RA. Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era. Integr Comp Biol 2019; 58:640-653. [PMID: 29917089 DOI: 10.1093/icb/icy061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) technologies has revolutionized the way we understand the transformation of genetic information into morphological traits. Elucidating the network of interactions between genes that govern cell differentiation through development is one of the core challenges in genome research. These networks are known as developmental gene regulatory networks (dGRNs) and consist largely of the functional linkage between developmental control genes, cis-regulatory modules, and differentiation genes, which generate spatially and temporally refined patterns of gene expression. Over the last 20 years, great advances have been made in determining these gene interactions mainly in classical model systems, including human, mouse, sea urchin, fruit fly, and worm. This has brought about a radical transformation in the fields of developmental biology and evolutionary biology, allowing the generation of high-resolution gene regulatory maps to analyze cell differentiation during animal development. Such maps have enabled the identification of gene regulatory circuits and have led to the development of network inference methods that can recapitulate the differentiation of specific cell-types or developmental stages. In contrast, dGRN research in non-classical model systems has been limited to the identification of developmental control genes via the candidate gene approach and the characterization of their spatiotemporal expression patterns, as well as to the discovery of cis-regulatory modules via patterns of sequence conservation and/or predicted transcription-factor binding sites. However, thanks to the continuous advances in HTS technologies, this scenario is rapidly changing. Here, we give a historical overview on the architecture and elucidation of the dGRNs. Subsequently, we summarize the approaches available to unravel these regulatory networks, highlighting the vast range of possibilities of integrating multiple technical advances and theoretical approaches to expand our understanding on the global gene regulation during animal development in non-classical model systems. Such new knowledge will not only lead to greater insights into the evolution of molecular mechanisms underlying cell identity and animal body plans, but also into the evolution of morphological key innovations in animals.
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Affiliation(s)
- Selene L Fernandez-Valverde
- CONACYT, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - René Alexander Ramos-Díaz
- CONACYT, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
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Li L, Rispoli R, Patient R, Ciau-Uitz A, Porcher C. Etv6 activates vegfa expression through positive and negative transcriptional regulatory networks in Xenopus embryos. Nat Commun 2019; 10:1083. [PMID: 30842454 PMCID: PMC6403364 DOI: 10.1038/s41467-019-09050-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/15/2019] [Indexed: 01/09/2023] Open
Abstract
VEGFA signaling controls physiological and pathological angiogenesis and hematopoiesis. Although many context-dependent signaling pathways downstream of VEGFA have been uncovered, vegfa transcriptional regulation in vivo remains unclear. Here, we show that the ETS transcription factor, Etv6, positively regulates vegfa expression during Xenopus blood stem cell development through multiple transcriptional inputs. In agreement with its established repressive functions, Etv6 directly inhibits expression of the repressor foxo3, to prevent Foxo3 from binding to and repressing the vegfa promoter. Etv6 also directly activates expression of the activator klf4; reflecting a genome-wide paucity in ETS-binding motifs in Etv6 genomic targets, Klf4 then recruits Etv6 to the vegfa promoter to activate its expression. These two mechanisms (double negative gate and feed-forward loop) are classic features of gene regulatory networks specifying cell fates. Thus, Etv6's dual function, as a transcriptional repressor and activator, controls a major signaling pathway involved in endothelial and blood development in vivo.
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Affiliation(s)
- Lei Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Rossella Rispoli
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Division of Genetics and Molecular Medicine, NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, SE1 9RT, UK
| | - Roger Patient
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Aldo Ciau-Uitz
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Catherine Porcher
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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Abstract
Echinoderms are important research models for a wide range of biological questions. In particular, echinoderm embryos are exemplary models for dissecting the molecular and cellular processes that drive development and testing how these processes can be modified through evolution to produce the extensive morphological diversity observed in the phylum. Modern attempts to characterize these processes depend on some level of genomic analysis; from querying annotated gene sets to functional genomics experiments to identify candidate cis-regulatory sequences. Given how essential these data have become, it is important that researchers using available datasets or performing their own genome-scale experiments understand the nature and limitations of echinoderm genomic analyses. In this chapter we highlight the current state of echinoderm genomic data and provide methodological considerations for common approaches, including analysis of transcriptome and functional genomics datasets.
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Erkenbrack EM, Davidson EH, Peter IS. Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids. Development 2018; 145:dev.167288. [PMID: 30470703 DOI: 10.1242/dev.167288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
Abstract
Evolution of the animal body plan is driven by changes in developmental gene regulatory networks (GRNs), but how networks change to control novel developmental phenotypes remains, in most cases, unresolved. Here, we address GRN evolution by comparing the endomesoderm GRN in two echinoid sea urchins, Strongylocentrotus purpuratus and Eucidaris tribuloides, with at least 268 million years of independent evolution. We first analyzed the expression of twelve transcription factors and signaling molecules of the S. purpuratus GRN in E. tribuloides embryos, showing that orthologous regulatory genes are expressed in corresponding endomesodermal cell fates in the two species. However, perturbation of regulatory genes revealed that important regulatory circuits of the S. purpuratus GRN are significantly different in E. tribuloides For example, mesodermal Delta/Notch signaling controls exclusion of alternative cell fates in E. tribuloides but controls mesoderm induction and activation of a positive feedback circuit in S. purpuratus These results indicate that the architecture of the sea urchin endomesoderm GRN evolved by extensive gain and loss of regulatory interactions between a conserved set of regulatory factors that control endomesodermal cell fate specification.
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Affiliation(s)
- Eric M Erkenbrack
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Eric H Davidson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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