1
|
Jackson EW, Romero E, Kling S, Lee Y, Tjeerdema E, Hamdoun A. Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin Lytechinus pictus. Development 2024; 151:dev202991. [PMID: 39023164 DOI: 10.1242/dev.202991] [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: 04/25/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Stable transgenesis is a transformative tool in model organism biology. Although the sea urchin is one of the oldest animal models in cell and developmental biology, studies in this animal have largely relied on transient manipulation of wild animals, without a strategy for stable transgenesis. Here, we build on recent progress to develop a more genetically tractable sea urchin species, Lytechinus pictus, and establish a robust transgene integration method. Three commonly used transposons (Minos, Tol2 and piggyBac) were tested for non-autonomous transposition, using plasmids containing a polyubiquitin promoter upstream of a H2B-mCerulean nuclear marker. Minos was the only transposable element that resulted in significant expression beyond metamorphosis. F0 animals were raised to sexual maturity, and spawned to determine germline integration and transgene inheritance frequency, and to characterize expression patterns of the transgene in F1 progeny. The results demonstrate transgene transmission through the germline, the first example of a germline transgenic sea urchin and, indeed, of any echinoderm. This milestone paves the way for the generation of diverse transgenic resources that will dramatically enhance the utility, reproducibility and efficiency of sea urchin research.
Collapse
Affiliation(s)
- Elliot W Jackson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Emilio Romero
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Svenja Kling
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Yoon Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Evan Tjeerdema
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| |
Collapse
|
2
|
Bernadskaya YY, Kuan A, Tjärnberg A, Brandenburg J, Zheng P, Wiechecki K, Kaplan N, Failla M, Bikou M, Madilian O, Wang W, Christiaen L. Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604718. [PMID: 39091743 PMCID: PMC11291048 DOI: 10.1101/2024.07.23.604718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10 (+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process "transcriptome maturation", and identified candidate "mature genes", including the Rho GAP-coding gene Depdc1 , which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. eLife 2024; 12:RP92093. [PMID: 38717010 PMCID: PMC11078544 DOI: 10.7554/elife.92093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here, I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors, and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode Caenorhabditis elegans. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
Collapse
|
5
|
Ohta N, Christiaen L. Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline. EMBO Rep 2024; 25:2188-2201. [PMID: 38649664 PMCID: PMC11094015 DOI: 10.1038/s44319-024-00139-0] [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: 01/30/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription control is a major determinant of cell fate decisions in somatic tissues. By contrast, early germline fate specification in numerous vertebrate and invertebrate species relies extensively on RNA-level regulation, exerted on asymmetrically inherited maternal supplies, with little-to-no zygotic transcription. However delayed, a maternal-to-zygotic transition is nevertheless poised to complete the deployment of pre-gametic programs in the germline. Here, we focus on early germline specification in the tunicate Ciona to study zygotic genome activation. We first demonstrate that a peculiar cellular remodeling event excludes localized postplasmic Pem-1 mRNA, which encodes the general inhibitor of transcription. Subsequently, zygotic transcription begins in Pem-1-negative primordial germ cells (PGCs), as revealed by histochemical detection of elongating RNA Polymerase II, and nascent Mef2 transcripts. In addition, we uncover a provisional antagonism between JAK and MEK/BMPRI/GSK3 signaling, which controls the onset of zygotic gene expression, following cellular remodeling of PGCs. We propose a 2-step model for the onset of zygotic transcription in the Ciona germline and discuss the significance of germ plasm dislocation and remodeling in the context of developmental fate specification.
Collapse
Affiliation(s)
- Naoyuki Ohta
- Michael Sars Centre, University of Bergen, Bergen, Norway.
| | - Lionel Christiaen
- Michael Sars Centre, University of Bergen, Bergen, Norway.
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA.
| |
Collapse
|
6
|
Hogan MP, Holding ML, Nystrom GS, Colston TJ, Bartlett DA, Mason AJ, Ellsworth SA, Rautsaw RM, Lawrence KC, Strickland JL, He B, Fraser P, Margres MJ, Gilbert DM, Gibbs HL, Parkinson CL, Rokyta DR. The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom. Proc Natl Acad Sci U S A 2024; 121:e2313440121. [PMID: 38578985 PMCID: PMC11032440 DOI: 10.1073/pnas.2313440121] [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: 08/08/2023] [Accepted: 03/13/2024] [Indexed: 04/07/2024] Open
Abstract
Developmental phenotypic changes can evolve under selection imposed by age- and size-related ecological differences. Many of these changes occur through programmed alterations to gene expression patterns, but the molecular mechanisms and gene-regulatory networks underlying these adaptive changes remain poorly understood. Many venomous snakes, including the eastern diamondback rattlesnake (Crotalus adamanteus), undergo correlated changes in diet and venom expression as snakes grow larger with age, providing models for identifying mechanisms of timed expression changes that underlie adaptive life history traits. By combining a highly contiguous, chromosome-level genome assembly with measures of expression, chromatin accessibility, and histone modifications, we identified cis-regulatory elements and trans-regulatory factors controlling venom ontogeny in the venom glands of C. adamanteus. Ontogenetic expression changes were significantly correlated with epigenomic changes within genes, immediately adjacent to genes (e.g., promoters), and more distant from genes (e.g., enhancers). We identified 37 candidate transcription factors (TFs), with the vast majority being up-regulated in adults. The ontogenetic change is largely driven by an increase in the expression of TFs associated with growth signaling, transcriptional activation, and circadian rhythm/biological timing systems in adults with corresponding epigenomic changes near the differentially expressed venom genes. However, both expression activation and repression contributed to the composition of both adult and juvenile venoms, demonstrating the complexity and potential evolvability of gene regulation for this trait. Overall, given that age-based trait variation is common across the tree of life, we provide a framework for understanding gene-regulatory-network-driven life-history evolution more broadly.
Collapse
Affiliation(s)
- Michael P. Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Matthew L. Holding
- Department of Biological Science, Florida State University, Tallahassee, FL32306
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Timothy J. Colston
- Department of Biological Science, Florida State University, Tallahassee, FL32306
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, PR00681
| | - Daniel A. Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH43210
| | - Schyler A. Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- School of Biological Sciences, Washington State University, Pullman, WA99164
| | - Kylie C. Lawrence
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Biology, University of South Alabama, Mobile, AL36688
| | - Bing He
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Mark J. Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
| | - David M. Gilbert
- Laboratory of Chromosome Replication and Epigenome Regulation, San Diego Biomedical Research Institute, San Diego, CA92121
| | - H. Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH43210
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC29634
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| |
Collapse
|
7
|
Ertl HA, Bayala EX, Siddiq MA, Wittkopp PJ. Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588430. [PMID: 38645200 PMCID: PMC11030446 DOI: 10.1101/2024.04.07.588430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly ( Drosophila melanogaster ) and worm ( Caenorhabditis elegans ) Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic D. melanogaster . We found that the Caenorhabditis elegans ortholog rescued cuticle development but not full embryonic viability in Drosophila melanogaster grh null mutants. At the molecular level, the C. elegans ortholog only partially rescued chromatin accessibility and gene expression. Divergence in the disordered N-terminus of the Grh protein contributes to these differences in embryonic viability and molecular phenotypes. These data show how pioneer factors can diverge in sequence and function at the molecular level while retaining conserved developmental functions at the organismal level. SUMMARY STATEMENT Despite divergence in a disordered region that affects function at both molecular and organismal levels, the Caenorhabditis elegans Grainy head (Grh) protein rescued cuticle morphology in D. melanogaster embryos.
Collapse
|
8
|
Solra M, Kapila R, Das S, Bhatt P, Rana S. Transient Metallo-Lipidoid Assemblies Amplify Covalent Catalysis of Aqueous and Non-Aqueous Reactions. Angew Chem Int Ed Engl 2024; 63:e202400348. [PMID: 38315883 DOI: 10.1002/anie.202400348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
Dissipative supramolecular assemblies are hallmarks of living systems, contributing to their complex, dynamic structures and emerging functions. Living cells can spatiotemporally control diverse biochemical reactions in membrane compartments and condensates, regulating metabolite levels, signal transduction or remodeling of the cytoskeleton. Herein, we constructed membranous compartments using self-assembly of lipid-like amphiphiles (lipidoid) in aqueous medium. The new double-tailed lipidoid features Cu(II) coordinated with a tetravalent chelator that dictates the binding of two amphiphilic ligands in cis-orientation. Hydrophobic interactions between the lipidoids coupled with intermolecular hydrogen bonding led to a well-defined bilayer vesicle structure. Oil-soluble SNAr reaction is efficiently upregulated in the hydrophobic cavity, acting as a catalytic crucible. The modular system allows easy incorporation of exposed primary amine groups, which augments the catalysis of retro aldol and C-N bond formation reactions. Moreover, a higher-affinity chelator enables consumption of the Cu(II) template leveraging the differential thermodynamic stability, which allows a controllable lifetime of the vesicular assemblies. Concomitant temporal upregulation of the catalytic reactions could be tuned by the metal ion concentration. This work offers new possibilities for metal ion-mediated dynamic supramolecular systems, opening up a massive repertoire of functionally active dynamic "life-like" materials.
Collapse
Affiliation(s)
- Manju Solra
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Rohit Kapila
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Sourav Das
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Preeti Bhatt
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Subinoy Rana
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| |
Collapse
|
9
|
Paczkó M, Vörös D, Szabó P, Jékely G, Szathmáry E, Szilágyi A. A neural network-based model framework for cell-fate decisions and development. Commun Biol 2024; 7:323. [PMID: 38486083 PMCID: PMC10940658 DOI: 10.1038/s42003-024-05985-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Gene regulatory networks (GRNs) fulfill the essential function of maintaining the stability of cellular differentiation states by sustaining lineage-specific gene expression, while driving the progression of development. However, accounting for the relative stability of intermediate differentiation stages and their divergent trajectories remains a major challenge for models of developmental biology. Here, we develop an empirical data-based associative GRN model (AGRN) in which regulatory networks store multilineage stage-specific gene expression profiles as associative memory patterns. These networks are capable of responding to multiple instructive signals and, depending on signal timing and identity, can dynamically drive the differentiation of multipotent cells toward different cell state attractors. The AGRN dynamics can thus generate diverse lineage-committed cell populations in a robust yet flexible manner, providing an attractor-based explanation for signal-driven cell fate decisions during differentiation and offering a readily generalizable modelling tool that can be applied to a wide variety of cell specification systems.
Collapse
Affiliation(s)
- Mátyás Paczkó
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Dániel Vörös
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Péter Szabó
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road 4QD, EX4, Exeter, UK
| | - Eörs Szathmáry
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary.
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Hindenburgstr. 15, 82343, Pöcking, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
| | - András Szilágyi
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
| |
Collapse
|
10
|
Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
Collapse
Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| |
Collapse
|
11
|
Gautam S, Fenner JL, Wang B, Range RC. Evolutionarily conserved Wnt/Sp5 signaling is critical for anterior-posterior axis patterning in sea urchin embryos. iScience 2024; 27:108616. [PMID: 38179064 PMCID: PMC10765061 DOI: 10.1016/j.isci.2023.108616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/30/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Studies across a diverse group of metazoan embryos indicate that Wnt signaling often activates the transcription factor Sp5, forming a signaling 'cassette' that plays critical roles in many developmental processes. This study explores the role of Wnt/Sp5 signaling during the specification and patterning of the primary germ layers during early anterior-posterior axis formation in the deuterostome sea urchin embryo. Our functional analyses show that Sp5 is critical for endomesoderm specification downstream of Wnt/β-catenin in posterior cells as well as anterior neuroectoderm patterning downstream of non-canonical Wnt/JNK signaling in anterior cells. Interestingly, expression and functional data comparisons show that Wnt/Sp5 signaling often plays similar roles in posterior endomesoderm as well as neuroectoderm patterning along the AP axis of several deuterostome embryos, including vertebrates. Thus, our findings provide strong support for the idea that Wnt-Sp5 signaling cassettes were critical for the establishment of early germ layers in the common deuterostome ancestor.
Collapse
Affiliation(s)
- Sujan Gautam
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer L. Fenner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Boyuan Wang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ryan C. Range
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Kim H, Choi H, Lee D, Kim J. A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing. Genes Genomics 2024; 46:1-11. [PMID: 38032470 DOI: 10.1007/s13258-023-01473-8] [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: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Understanding gene regulatory networks (GRNs) is essential for unraveling the molecular mechanisms governing cellular behavior. With the advent of high-throughput transcriptome measurement technology, researchers have aimed to reverse engineer the biological systems, extracting gene regulatory rules from their outputs, which represented by gene expression data. Bulk RNA sequencing, a widely used method for measuring gene expression, has been employed for GRN reconstruction. However, it falls short in capturing dynamic changes in gene expression at the level of individual cells since it averages gene expression across mixed cell populations. OBJECTIVE In this review, we provide an overview of 15 GRN reconstruction tools and discuss their respective strengths and limitations, particularly in the context of single cell RNA sequencing (scRNA-seq). METHODS Recent advancements in scRNA-seq break new ground of GRN reconstruction. They offer snapshots of the individual cell transcriptomes and capturing dynamic changes. We emphasize how these technological breakthroughs have enhanced GRN reconstruction. CONCLUSION GRN reconstructors can be classified based on their requirement for cellular trajectory, which represents a dynamical cellular process including differentiation, aging, or disease progression. Benchmarking studies support the superiority of GRN reconstructors that do not require trajectory analysis in identifying regulator-target relationships. However, methods equipped with trajectory analysis demonstrate better performance in identifying key regulatory factors. In conclusion, researchers should select a suitable GRN reconstructor based on their specific research objectives.
Collapse
Affiliation(s)
- Hyeonkyu Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Hwisoo Choi
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Daewon Lee
- School of Art and Technology, Chung-Ang University, 4726 Seodong-Daero, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea.
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
| |
Collapse
|
14
|
Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544138. [PMID: 37333369 PMCID: PMC10274868 DOI: 10.1101/2023.06.07.544138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Such stable changes can (1) alter steady-state levels while preserving the architecture, (2) induce different architectures that persist for many generations, or (3) collapse the entire architecture. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that the evolution of mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of regulatory architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode C. elegans, which range from permanent silencing to recovery from silencing within a few generations and subsequent resistance to silencing. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
Collapse
|
15
|
Fitch WT. Cellular computation and cognition. Front Comput Neurosci 2023; 17:1107876. [PMID: 38077750 PMCID: PMC10702520 DOI: 10.3389/fncom.2023.1107876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 10/09/2023] [Indexed: 05/28/2024] Open
Abstract
Contemporary neural network models often overlook a central biological fact about neural processing: that single neurons are themselves complex, semi-autonomous computing systems. Both the information processing and information storage abilities of actual biological neurons vastly exceed the simple weighted sum of synaptic inputs computed by the "units" in standard neural network models. Neurons are eukaryotic cells that store information not only in synapses, but also in their dendritic structure and connectivity, as well as genetic "marking" in the epigenome of each individual cell. Each neuron computes a complex nonlinear function of its inputs, roughly equivalent in processing capacity to an entire 1990s-era neural network model. Furthermore, individual cells provide the biological interface between gene expression, ongoing neural processing, and stored long-term memory traces. Neurons in all organisms have these properties, which are thus relevant to all of neuroscience and cognitive biology. Single-cell computation may also play a particular role in explaining some unusual features of human cognition. The recognition of the centrality of cellular computation to "natural computation" in brains, and of the constraints it imposes upon brain evolution, thus has important implications for the evolution of cognition, and how we study it.
Collapse
Affiliation(s)
- W. Tecumseh Fitch
- Faculty of Life Sciences and Vienna Cognitive Science Hub, University of Vienna, Vienna, Austria
| |
Collapse
|
16
|
Wille CK, Zhang X, Haws SA, Denu JM, Sridharan R. DOT1L is a barrier to histone acetylation during reprogramming to pluripotency. SCIENCE ADVANCES 2023; 9:eadf3980. [PMID: 37976354 PMCID: PMC10656071 DOI: 10.1126/sciadv.adf3980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene activation-associated histone modifications. A striking exception is DOT1L-mediated H3K79 dimethylation (H3K79me2) that is considered a positive regulator of transcription. We find that ESCs are depleted for H3K79me2 at shared locations of enrichment with somatic cells, which are highly and ubiquitously expressed housekeeping genes, and have lower RNA polymerase II (RNAPII) at the transcription start site (TSS) despite greater nascent transcription. Inhibiting DOT1L increases the efficiency of reprogramming of somatic to induced pluripotent stem cells, enables an ESC-like RNAPII pattern at the TSS, and functionally compensates for enforced RNAPII pausing. DOT1L inhibition increases H3K27 methylation and RNAPII elongation-enhancing histone acetylation without changing the expression of the causal histone-modifying enzymes. Only the maintenance of elevated histone acetylation is essential for enhanced reprogramming and occurs at loci that are depleted for H3K79me2. Thus, DOT1L inhibition promotes the hyperacetylation and hypertranscription pluripotent properties.
Collapse
Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Xiaoya Zhang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Haws
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| |
Collapse
|
17
|
Kumar N, Mukhtar MS. Integrated Systems Biology Pipeline to Compare Co-Expression Networks in Plants and Elucidate Differential Regulators. PLANTS (BASEL, SWITZERLAND) 2023; 12:3618. [PMID: 37896081 PMCID: PMC10610404 DOI: 10.3390/plants12203618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
To identify sets of genes that exhibit similar expression characteristics, co-expression networks were constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse biotic, abiotic, and other environmental stresses. In addition, co-expression network analysis can provide deeper insights into gene regulation when combined with transcriptomics. The coordination and integration of all these complex networks to deduce gene regulation are major challenges for plant biologists. Python and R have emerged as major tools for managing complex scientific data over the past decade. In this study, we describe a reproducible protocol POTFUL (pant co-expression transcription factor regulators), implemented in Python 3, for integrating co-expression and transcription factor target protein networks to infer gene regulation.
Collapse
Affiliation(s)
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
18
|
Gorin G, Vastola JJ, Pachter L. Studying stochastic systems biology of the cell with single-cell genomics data. Cell Syst 2023; 14:822-843.e22. [PMID: 37751736 PMCID: PMC10725240 DOI: 10.1016/j.cels.2023.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.
Collapse
Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John J Vastola
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
19
|
Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
Collapse
Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
| |
Collapse
|
20
|
Zhao J, Wong CW, Ching WK, Cheng X. NG-SEM: an effective non-Gaussian structural equation modeling framework for gene regulatory network inference from single-cell RNA-seq data. Brief Bioinform 2023; 24:bbad369. [PMID: 37864293 DOI: 10.1093/bib/bbad369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
Inference of gene regulatory network (GRN) from gene expression profiles has been a central problem in systems biology and bioinformatics in the past decades. The tremendous emergency of single-cell RNA sequencing (scRNA-seq) data brings new opportunities and challenges for GRN inference: the extensive dropouts and complicated noise structure may also degrade the performance of contemporary gene regulatory models. Thus, there is an urgent need to develop more accurate methods for gene regulatory network inference in single-cell data while considering the noise structure at the same time. In this paper, we extend the traditional structural equation modeling (SEM) framework by considering a flexible noise modeling strategy, namely we use the Gaussian mixtures to approximate the complex stochastic nature of a biological system, since the Gaussian mixture framework can be arguably served as a universal approximation for any continuous distributions. The proposed non-Gaussian SEM framework is called NG-SEM, which can be optimized by iteratively performing Expectation-Maximization algorithm and weighted least-squares method. Moreover, the Akaike Information Criteria is adopted to select the number of components of the Gaussian mixture. To probe the accuracy and stability of our proposed method, we design a comprehensive variate of control experiments to systematically investigate the performance of NG-SEM under various conditions, including simulations and real biological data sets. Results on synthetic data demonstrate that this strategy can improve the performance of traditional Gaussian SEM model and results on real biological data sets verify that NG-SEM outperforms other five state-of-the-art methods.
Collapse
Affiliation(s)
- Jiaying Zhao
- Department of Mathematics, The University of Hongkong, Pokfulam road, Hong Kong
| | - Chi-Wing Wong
- Department of Mathematics, The University of Hongkong, Pokfulam road, Hong Kong
| | - Wai-Ki Ching
- Department of Mathematics, The University of Hongkong, Pokfulam road, Hong Kong
| | - Xiaoqing Cheng
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, ShaanXi, China
| |
Collapse
|
21
|
Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods 2023; 20:1368-1378. [PMID: 37537351 DOI: 10.1038/s41592-023-01971-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease. Despite decades of advancement, challenges remain in GRN inference, including dynamic rewiring, causal inference, feedback loop modeling and context specificity. To address these challenges, we develop Dictys, a dynamic GRN inference and analysis method that leverages multiomic single-cell assays of chromatin accessibility and gene expression, context-specific transcription factor footprinting, stochastic process network and efficient probabilistic modeling of single-cell RNA-sequencing read counts. Dictys improves GRN reconstruction accuracy and reproducibility and enables the inference and comparative analysis of context-specific and dynamic GRNs across developmental contexts. Dictys' network analyses recover unique insights in human blood and mouse skin development with cell-type-specific and dynamic GRNs. Its dynamic network visualizations enable time-resolved discovery and investigation of developmental driver transcription factors and their regulated targets. Dictys is available as a free, open-source and user-friendly Python package.
Collapse
Affiliation(s)
- Lingfei Wang
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Trasanidis
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Ting Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Guanlan Dong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA
| | - Michael Hu
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
22
|
Xue L, Wu Y, Lin Y. Dissecting and improving gene regulatory network inference using single-cell transcriptome data. Genome Res 2023; 33:1609-1621. [PMID: 37580132 PMCID: PMC10620053 DOI: 10.1101/gr.277488.122] [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: 11/09/2022] [Accepted: 08/07/2023] [Indexed: 08/16/2023]
Abstract
Single-cell transcriptome data has been widely used to reconstruct gene regulatory networks (GRNs) controlling critical biological processes such as development and differentiation. Although a growing list of algorithms has been developed to infer GRNs using such data, achieving an inference accuracy consistently higher than random guessing has remained challenging. To address this, it is essential to delineate how the accuracy of regulatory inference is limited. Here, we systematically characterized factors limiting the accuracy of inferred GRNs and demonstrated that using pre-mRNA information can help improve regulatory inference compared to the typically used information (i.e., mature mRNA). Using kinetic modeling and simulated single-cell data sets, we showed that target genes' mature mRNA levels often fail to accurately report upstream regulatory activities because of gene-level and network-level factors, which can be improved by using pre-mRNA levels. We tested this finding on public single-cell RNA-seq data sets using intronic reads as proxies of pre-mRNA levels and can indeed achieve a higher inference accuracy compared to using exonic reads (corresponding to mature mRNAs). Using experimental data sets, we further validated findings from the simulated data sets and identified factors such as transcription factor activity dynamics influencing the accuracy of pre-mRNA-based inference. This work delineates the fundamental limitations of gene regulatory inference and helps improve GRN inference using single-cell RNA-seq data.
Collapse
Affiliation(s)
- Lingfeng Xue
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871
| | - Yan Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China, 100871
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871;
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China, 100871
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871
| |
Collapse
|
23
|
Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 2023; 186:3810-3825.e18. [PMID: 37552983 PMCID: PMC10528910 DOI: 10.1016/j.cell.2023.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
Collapse
Affiliation(s)
- Meghan D J Bragdon
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Nikit Patel
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James Chuang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ethan Levien
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77030, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| |
Collapse
|
24
|
Williams RTP, King DC, Mastroianni IR, Hill JL, Apenes NW, Ramirez G, Miner EC, Moore A, Coleman K, Nishimura EO. Transcriptome profiling of the Caenorhabditis elegans intestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network. Genetics 2023; 224:iyad088. [PMID: 37183501 PMCID: PMC10411582 DOI: 10.1093/genetics/iyad088] [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: 03/06/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023] Open
Abstract
ELT-2 is the major transcription factor (TF) required for Caenorhabditis elegans intestinal development. ELT-2 expression initiates in embryos to promote development and then persists after hatching through the larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are known, an intestine-specific transcriptome profile spanning developmental time has been missing. We generated this dataset by performing Fluorescence Activated Cell Sorting on intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate the role of ELT-2 in directing the intestinal gene regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional TFs promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2's direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Additionally, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20-50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that the current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.
Collapse
Affiliation(s)
- Robert T P Williams
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - David C King
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Izabella R Mastroianni
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica L Hill
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Nicolai W Apenes
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriela Ramirez
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - E Catherine Miner
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Andrew Moore
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Karissa Coleman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
25
|
Kozol RA, Conith AJ, Yuiska A, Cree-Newman A, Tolentino B, Benesh K, Paz A, Lloyd E, Kowalko JE, Keene AC, Albertson C, Duboue ER. A brain-wide analysis maps structural evolution to distinct anatomical module. eLife 2023; 12:e80777. [PMID: 37498318 PMCID: PMC10435234 DOI: 10.7554/elife.80777] [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: 06/03/2022] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
The vertebrate brain is highly conserved topologically, but less is known about neuroanatomical variation between individual brain regions. Neuroanatomical variation at the regional level is hypothesized to provide functional expansion, building upon ancestral anatomy needed for basic functions. Classically, animal models used to study evolution have lacked tools for detailed anatomical analysis that are widely used in zebrafish and mice, presenting a barrier to studying brain evolution at fine scales. In this study, we sought to investigate the evolution of brain anatomy using a single species of fish consisting of divergent surface and cave morphs, that permits functional genetic testing of regional volume and shape across the entire brain. We generated a high-resolution brain atlas for the blind Mexican cavefish Astyanax mexicanus and coupled the atlas with automated computational tools to directly assess variability in brain region shape and volume across all populations. We measured the volume and shape of every grossly defined neuroanatomical region of the brain and assessed correlations between anatomical regions in surface fish, cavefish, and surface × cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted, while ventral regions have expanded, with F2 hybrid data providing support for developmental constraint along the dorsal-ventral axis. Furthermore, these dorsal-ventral relationships in anatomical variation show similar patterns for both volume and shape, suggesting that the anatomical evolution captured by these two parameters could be driven by similar developmental mechanisms. Together, these data demonstrate that A. mexicanus is a powerful system for functionally determining basic principles of brain evolution and will permit testing how genes influence early patterning events to drive brain-wide anatomical evolution.
Collapse
Affiliation(s)
- Robert A Kozol
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Andrew J Conith
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Anders Yuiska
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexia Cree-Newman
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Bernadeth Tolentino
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Kasey Benesh
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexandra Paz
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Evan Lloyd
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh UniversityBethlehemUnited States
| | - Alex C Keene
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Craig Albertson
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| |
Collapse
|
26
|
Bafna M, Li H, Zhang X. CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics. Bioinformatics 2023; 39:i484-i493. [PMID: 37387180 DOI: 10.1093/bioinformatics/btad269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Gene regulatory networks (GRNs) in a cell provide the tight feedback needed to synchronize cell actions. However, genes in a cell also take input from, and provide signals to other neighboring cells. These cell-cell interactions (CCIs) and the GRNs deeply influence each other. Many computational methods have been developed for GRN inference in cells. More recently, methods were proposed to infer CCIs using single cell gene expression data with or without cell spatial location information. However, in reality, the two processes do not exist in isolation and are subject to spatial constraints. Despite this rationale, no methods currently exist to infer GRNs and CCIs using the same model. RESULTS We propose CLARIFY, a tool that takes GRNs as input, uses them and spatially resolved gene expression data to infer CCIs, while simultaneously outputting refined cell-specific GRNs. CLARIFY uses a novel multi-level graph autoencoder, which mimics cellular networks at a higher level and cell-specific GRNs at a deeper level. We applied CLARIFY to two real spatial transcriptomic datasets, one using seqFISH and the other using MERFISH, and also tested on simulated datasets from scMultiSim. We compared the quality of predicted GRNs and CCIs with state-of-the-art baseline methods that inferred either only GRNs or only CCIs. The results show that CLARIFY consistently outperforms the baseline in terms of commonly used evaluation metrics. Our results point to the importance of co-inference of CCIs and GRNs and to the use of layered graph neural networks as an inference tool for biological networks. AVAILABILITY AND IMPLEMENTATION The source code and data is available at https://github.com/MihirBafna/CLARIFY.
Collapse
Affiliation(s)
- Mihir Bafna
- School of Computational Science and Engineering, College of Computing, Georgia Institute of Technology, Atlanta, GA, 30332, United States
| | - Hechen Li
- School of Computational Science and Engineering, College of Computing, Georgia Institute of Technology, Atlanta, GA, 30332, United States
| | - Xiuwei Zhang
- School of Computational Science and Engineering, College of Computing, Georgia Institute of Technology, Atlanta, GA, 30332, United States
| |
Collapse
|
27
|
Steimle JD, Kim C, Rowton M, Nadadur RD, Wang Z, Stocker M, Hoffmann AD, Hanson E, Kweon J, Sinha T, Choi K, Black BL, Cunningham JM, Moskowitz IP, Ikegami K. ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment. Cell Rep 2023; 42:112665. [PMID: 37330911 PMCID: PMC10592526 DOI: 10.1016/j.celrep.2023.112665] [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: 06/07/2021] [Revised: 03/14/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023] Open
Abstract
Mechanisms underlying distinct specification, commitment, and differentiation phases of cell fate determination remain undefined due to difficulties capturing these processes. Here, we interrogate the activity of ETV2, a transcription factor necessary and sufficient for hematoendothelial differentiation, within isolated fate intermediates. We observe transcriptional upregulation of Etv2 and opening of ETV2-binding sites, indicating new ETV2 binding, in a common cardiac-hematoendothelial progenitor population. Accessible ETV2-binding sites are active at the Etv2 locus but not at other hematoendothelial regulator genes. Hematoendothelial commitment coincides with the activation of a small repertoire of previously accessible ETV2-binding sites at hematoendothelial regulators. Hematoendothelial differentiation accompanies activation of a large repertoire of new ETV2-binding sites and upregulation of hematopoietic and endothelial gene regulatory networks. This work distinguishes specification, commitment, and sublineage differentiation phases of ETV2-dependent transcription and suggests that the shift from ETV2 binding to ETV2-bound enhancer activation, not ETV2 binding to target enhancers, drives hematoendothelial fate commitment.
Collapse
Affiliation(s)
- Jeffrey D Steimle
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Chul Kim
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Megan Rowton
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rangarajan D Nadadur
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Zhezhen Wang
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Stocker
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Andrew D Hoffmann
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Erika Hanson
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Junghun Kweon
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tanvi Sinha
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John M Cunningham
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Kohta Ikegami
- Division of Molecular and Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.
| |
Collapse
|
28
|
Gorin G, Vastola JJ, Pachter L. Studying stochastic systems biology of the cell with single-cell genomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541250. [PMID: 37292934 PMCID: PMC10245677 DOI: 10.1101/2023.05.17.541250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.
Collapse
Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125
| | - John J. Vastola
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125
| |
Collapse
|
29
|
Cai L, Wang Z, Kulathinal R, Kumar S, Ji S. Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:2528-2538. [PMID: 34487501 DOI: 10.1109/tnnls.2021.3106831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Predictive modeling is useful but very challenging in biological image analysis due to the high cost of obtaining and labeling training data. For example, in the study of gene interaction and regulation in Drosophila embryogenesis, the analysis is most biologically meaningful when in situ hybridization (ISH) gene expression pattern images from the same developmental stage are compared. However, labeling training data with precise stages is very time-consuming even for developmental biologists. Thus, a critical challenge is how to build accurate computational models for precise developmental stage classification from limited training samples. In addition, identification and visualization of developmental landmarks are required to enable biologists to interpret prediction results and calibrate models. To address these challenges, we propose a deep two-step low-shot learning framework to accurately classify ISH images using limited training images. Specifically, to enable accurate model training on limited training samples, we formulate the task as a deep low-shot learning problem and develop a novel two-step learning approach, including data-level learning and feature-level learning. We use a deep residual network as our base model and achieve improved performance in the precise stage prediction task of ISH images. Furthermore, the deep model can be interpreted by computing saliency maps, which consists of pixel-wise contributions of an image to its prediction result. In our task, saliency maps are used to assist the identification and visualization of developmental landmarks. Our experimental results show that the proposed model can not only make accurate predictions but also yield biologically meaningful interpretations. We anticipate our methods to be easily generalizable to other biological image classification tasks with small training datasets. Our open-source code is available at https://github.com/divelab/lsl-fly.
Collapse
|
30
|
Pandey AK, Loscalzo J. Network medicine: an approach to complex kidney disease phenotypes. Nat Rev Nephrol 2023:10.1038/s41581-023-00705-0. [PMID: 37041415 DOI: 10.1038/s41581-023-00705-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
Scientific reductionism has been the basis of disease classification and understanding for more than a century. However, the reductionist approach of characterizing diseases from a limited set of clinical observations and laboratory evaluations has proven insufficient in the face of an exponential growth in data generated from transcriptomics, proteomics, metabolomics and deep phenotyping. A new systematic method is necessary to organize these datasets and build new definitions of what constitutes a disease that incorporates both biological and environmental factors to more precisely describe the ever-growing complexity of phenotypes and their underlying molecular determinants. Network medicine provides such a conceptual framework to bridge these vast quantities of data while providing an individualized understanding of disease. The modern application of network medicine principles is yielding new insights into the pathobiology of chronic kidney diseases and renovascular disorders by expanding the understanding of pathogenic mediators, novel biomarkers and new options for renal therapeutics. These efforts affirm network medicine as a robust paradigm for elucidating new advances in the diagnosis and treatment of kidney disorders.
Collapse
Affiliation(s)
- Arvind K Pandey
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
31
|
Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
Collapse
Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| |
Collapse
|
32
|
Teague S, Primavera G, Chen B, Freeburne E, Khan H, Jo K, Johnson C, Heemskerk I. The time integral of BMP signaling determines fate in a stem cell model for early human development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536068. [PMID: 37090515 PMCID: PMC10120633 DOI: 10.1101/2023.04.10.536068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discovered that measured BMP signaling history correlates strongly with fate in individual cells. We found that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, we discovered that both the level and duration of signaling activity control cell fate choices only by changing the time integral of signaling and that duration and level are therefore interchangeable in this context. In a stem cell model for patterning of the human embryo, we showed that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Using an RNA-seq screen we then found that mechanistically, BMP signaling is integrated by SOX2.
Collapse
Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Gillian Primavera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Bohan Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hina Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Physics, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
33
|
Nolan TM, Vukašinović N, Hsu CW, Zhang J, Vanhoutte I, Shahan R, Taylor IW, Greenstreet L, Heitz M, Afanassiev A, Wang P, Szekely P, Brosnan A, Yin Y, Schiebinger G, Ohler U, Russinova E, Benfey PN. Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. Science 2023; 379:eadf4721. [PMID: 36996230 PMCID: PMC10119888 DOI: 10.1126/science.adf4721] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 04/01/2023]
Abstract
Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and cell elongation, through gene regulatory networks that vary in space and time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive gene expression specific to different cell types and developmental stages of the Arabidopsis root, we identified the elongating cortex as a site where brassinosteroids trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed HOMEOBOX FROM ARABIDOPSIS THALIANA 7 (HAT7) and GT-2-LIKE 1 (GTL1) as brassinosteroid-responsive transcription factors that regulate cortex cell elongation. These results establish the cortex as a site of brassinosteroid-mediated growth and unveil a brassinosteroid signaling network regulating the transition from proliferation to elongation, which illuminates aspects of spatiotemporal hormone responses.
Collapse
Affiliation(s)
| | - Nemanja Vukašinović
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Che-Wei Hsu
- Department of Biology, Duke University, Durham, NC, USA
- Department of Biology, Humboldt Universitat zu Berlin, Berlin, Germany
- The Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | | | - Isabelle Vanhoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | | | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Matthieu Heitz
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Ping Wang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Pablo Szekely
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Aiden Brosnan
- Department of Biology, Duke University, Durham, NC, USA
| | - Yanhai Yin
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Uwe Ohler
- Department of Biology, Humboldt Universitat zu Berlin, Berlin, Germany
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
- Department of Computer Science, Humboldt Universitat zu Berlin, Berlin, Germany
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| |
Collapse
|
34
|
Hughes JT, Williams ME, Rebeiz M, Williams TM. Widespread cis- and trans-regulatory evolution underlies the origin, diversification, and loss of a sexually dimorphic fruit fly pigmentation trait. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:143-161. [PMID: 34254440 DOI: 10.1002/jez.b.23068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/08/2022]
Abstract
Changes in gene expression are a prominent feature of morphological evolution. These changes occur to hierarchical gene regulatory networks (GRNs) of transcription factor genes that regulate the expression of trait-building differentiation genes. While changes in the expression of differentiation genes are essential to phenotypic evolution, they can be caused by mutations within cis-regulatory elements (CREs) that drive their expression (cis-evolution) or within genes for CRE-interacting transcription factors (trans-evolution). Locating these mutations remains a challenge, especially when experiments are limited to one species that possesses the ancestral or derived phenotype. We investigated CREs that control the expression of the differentiation genes tan and yellow, the expression of which evolved during the gain, modification, and loss of dimorphic pigmentation among Sophophora fruit flies. We show these CREs to be necessary components of a pigmentation GRN, as deletion from Drosophila melanogaster (derived dimorphic phenotype) resulted in lost expression and lost male-specific pigmentation. We evaluated the ability of orthologous CRE sequences to drive reporter gene expression in species with modified (Drosophila auraria), secondarily lost (Drosophila ananassae), and ancestrally absent (Drosophila willistoni) pigmentation. We show that the transgene host frequently determines CRE activity, implicating trans-evolution as a significant factor for this trait's diversity. We validated the gain of dimorphic Bab transcription factor expression as a trans-change contributing to the dimorphic trait. Our findings suggest an amenability to change for the landscape of trans-regulators and begs for an explanation as to why this is so common compared to the evolution of differentiation gene CREs.
Collapse
Affiliation(s)
- Jesse T Hughes
- Department of Biology, University of Dayton, Dayton, Ohio, USA
| | | | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Thomas M Williams
- Department of Biology, University of Dayton, Dayton, Ohio, USA.,The Integrative Science and Engineering Center, University of Dayton, Dayton, Ohio, USA
| |
Collapse
|
35
|
Feigin C, Li S, Moreno J, Mallarino R. The GRN concept as a guide for evolutionary developmental biology. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:92-104. [PMID: 35344632 PMCID: PMC9515236 DOI: 10.1002/jez.b.23132] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022]
Abstract
Organismal phenotypes result largely from inherited developmental programs, usually executed during embryonic and juvenile life stages. These programs are not blank slates onto which natural selection can draw arbitrary forms. Rather, the mechanisms of development play an integral role in shaping phenotypic diversity and help determine the evolutionary trajectories of species. Modern evolutionary biology must, therefore, account for these mechanisms in both theory and in practice. The gene regulatory network (GRN) concept represents a potent tool for achieving this goal whose utility has grown in tandem with advances in "omic" technologies and experimental techniques. However, while the GRN concept is widely utilized, it is often less clear what practical implications it has for conducting research in evolutionary developmental biology. In this Perspective, we attempt to provide clarity by discussing how experiments and projects can be designed in light of the GRN concept. We first map familiar biological notions onto the more abstract components of GRN models. We then review how diverse functional genomic approaches can be directed toward the goal of constructing such models and discuss current methods for functionally testing evolutionary hypotheses that arise from them. Finally, we show how the major steps of GRN model construction and experimental validation suggest generalizable workflows that can serve as a scaffold for project design. Taken together, the practical implications that we draw from the GRN concept provide a set of guideposts for studies aiming at unraveling the molecular basis of phenotypic diversity.
Collapse
Affiliation(s)
- Charles Feigin
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA,School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Jorge Moreno
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| |
Collapse
|
36
|
Computational approaches to understand transcription regulation in development. Biochem Soc Trans 2023; 51:1-12. [PMID: 36695505 PMCID: PMC9988001 DOI: 10.1042/bst20210145] [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: 10/28/2022] [Revised: 01/07/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Gene regulatory networks (GRNs) serve as useful abstractions to understand transcriptional dynamics in developmental systems. Computational prediction of GRNs has been successfully applied to genome-wide gene expression measurements with the advent of microarrays and RNA-sequencing. However, these inferred networks are inaccurate and mostly based on correlative rather than causative interactions. In this review, we highlight three approaches that significantly impact GRN inference: (1) moving from one genome-wide functional modality, gene expression, to multi-omics, (2) single cell sequencing, to measure cell type-specific signals and predict context-specific GRNs, and (3) neural networks as flexible models. Together, these experimental and computational developments have the potential to significantly impact the quality of inferred GRNs. Ultimately, accurately modeling the regulatory interactions between transcription factors and their target genes will be essential to understand the role of transcription factors in driving developmental gene expression programs and to derive testable hypotheses for validation.
Collapse
|
37
|
Weinstein ML, Jaenke CM, Asma H, Spangler M, Kohnen KA, Konys CC, Williams ME, Williams AV, Rebeiz M, Halfon MS, Williams TM. A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait. PLoS Genet 2023; 19:e1010653. [PMID: 36795790 PMCID: PMC9977049 DOI: 10.1371/journal.pgen.1010653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/01/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Animal traits develop through the expression and action of numerous regulatory and realizator genes that comprise a gene regulatory network (GRN). For each GRN, its underlying patterns of gene expression are controlled by cis-regulatory elements (CREs) that bind activating and repressing transcription factors. These interactions drive cell-type and developmental stage-specific transcriptional activation or repression. Most GRNs remain incompletely mapped, and a major barrier to this daunting task is CRE identification. Here, we used an in silico method to identify predicted CREs (pCREs) that comprise the GRN which governs sex-specific pigmentation of Drosophila melanogaster. Through in vivo assays, we demonstrate that many pCREs activate expression in the correct cell-type and developmental stage. We employed genome editing to demonstrate that two CREs control the pupal abdomen expression of trithorax, whose function is required for the dimorphic phenotype. Surprisingly, trithorax had no detectable effect on this GRN's key trans-regulators, but shapes the sex-specific expression of two realizator genes. Comparison of sequences orthologous to these CREs supports an evolutionary scenario where these trithorax CREs predated the origin of the dimorphic trait. Collectively, this study demonstrates how in silico approaches can shed novel insights on the GRN basis for a trait's development and evolution.
Collapse
Affiliation(s)
- Michael L. Weinstein
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
| | - Chad M. Jaenke
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
| | - Hasiba Asma
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, New York, United States of America
| | - Matthew Spangler
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
| | - Katherine A. Kohnen
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
| | - Claire C. Konys
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
| | - Melissa E. Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
| | - Ashley V. Williams
- West Carrollton High School, 5833 Student St., Dayton, Ohio, United States of America
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marc S. Halfon
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, New York, United States of America
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, New York, United States of America
| | - Thomas M. Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
- The Integrative Science and Engineering Center, University of Dayton, 300 College Park, Dayton, Ohio, United States of America
- * E-mail:
| |
Collapse
|
38
|
Hellekes V, Claus D, Seiler J, Illner F, Schiffer PH, Kroiher M. CRISPR/Cas9 mediated gene editing in non-model nematode Panagrolaimus sp. PS1159. Front Genome Ed 2023; 5:1078359. [PMID: 36818277 PMCID: PMC9935820 DOI: 10.3389/fgeed.2023.1078359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The phylum Nematoda harbors a huge diversity of species in a broad range of ecosystems and habitats. Nematodes share a largely conserved Bauplan but major differences have been found in early developmental processes. The development of the nematode model organism Caenorhabditis elegans has been studied in great detail for decades. These efforts have provided the community with a large number of protocols and methods. Unfortunately, many of these tools are not easily applicable in non-Caenorhabditis nematodes. In recent years it has become clear that many crucial genes in the C. elegans developmental toolkit are absent in other nematode species. It is thus necessary to study the developmental program of other nematode species in detail to understand evolutionary conservation and novelty in the phylum. Panagrolaimus sp. PS1159 is a non-parasitic nematode exhibiting parthenogenetic reproduction and we are establishing the species to comparatively study evolution, biodiversity, and alternative reproduction and survival strategies. Here, we demonstrate the first successful application of the CRISPR/Cas9 system for genome editing in Panagrolaimus sp. PS1159 and the closely related hermaphroditic species Propanagrolaimus sp. JU765 applying the non-homologous end joining and the homology-directed repair (HDR) mechanisms. Using microinjections and modifying published protocols from C. elegans and P. pacificus we induced mutations in the orthologue of unc-22. This resulted in a visible uncoordinated twitching phenotype. We also compared the HDR efficiency following the delivery of different single-stranded oligodeoxynucleotides (ssODNs). Our work will expand the applicability for a wide range of non-model nematodes from across the tree and facilitate functional analysis into the evolution of parthenogenesis, changes in the developmental program of Nematoda, and cryptobiosis.
Collapse
Affiliation(s)
- Viktoria Hellekes
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany,Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany,*Correspondence: Viktoria Hellekes,
| | - Denise Claus
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Johanna Seiler
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Felix Illner
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Philipp H. Schiffer
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Michael Kroiher
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| |
Collapse
|
39
|
Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
Collapse
Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
40
|
GReNaDIne: A Data-Driven Python Library to Infer Gene Regulatory Networks from Gene Expression Data. Genes (Basel) 2023; 14:genes14020269. [PMID: 36833196 PMCID: PMC9957546 DOI: 10.3390/genes14020269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Context: Inferring gene regulatory networks (GRN) from high-throughput gene expression data is a challenging task for which different strategies have been developed. Nevertheless, no ever-winning method exists, and each method has its advantages, intrinsic biases, and application domains. Thus, in order to analyze a dataset, users should be able to test different techniques and choose the most appropriate one. This step can be particularly difficult and time consuming, since most methods' implementations are made available independently, possibly in different programming languages. The implementation of an open-source library containing different inference methods within a common framework is expected to be a valuable toolkit for the systems biology community. Results: In this work, we introduce GReNaDIne (Gene Regulatory Network Data-driven Inference), a Python package that implements 18 machine learning data-driven gene regulatory network inference methods. It also includes eight generalist preprocessing techniques, suitable for both RNA-seq and microarray dataset analysis, as well as four normalization techniques dedicated to RNA-seq. In addition, this package implements the possibility to combine the results of different inference tools to form robust and efficient ensembles. This package has been successfully assessed under the DREAM5 challenge benchmark dataset. The open-source GReNaDIne Python package is made freely available in a dedicated GitLab repository, as well as in the official third-party software repository PyPI Python Package Index. The latest documentation on the GReNaDIne library is also available at Read the Docs, an open-source software documentation hosting platform. Contribution: The GReNaDIne tool represents a technological contribution to the field of systems biology. This package can be used to infer gene regulatory networks from high-throughput gene expression data using different algorithms within the same framework. In order to analyze their datasets, users can apply a battery of preprocessing and postprocessing tools and choose the most adapted inference method from the GReNaDIne library and even combine the output of different methods to obtain more robust results. The results format provided by GReNaDIne is compatible with well-known complementary refinement tools such as PYSCENIC.
Collapse
|
41
|
Forbes Beadle L, Love JC, Shapovalova Y, Artemev A, Rattray M, Ashe HL. Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation. PLoS Biol 2023; 21:e3001956. [PMID: 36649329 PMCID: PMC9882958 DOI: 10.1371/journal.pbio.3001956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/27/2023] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling. Here, we use a non-invasive method for estimating half-lives for hundreds of mRNAs in the early Drosophila embryo. This approach uses the intronic and exonic reads from a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Using single-molecule imaging, we provide evidence that, for the mRNAs tested, there is a correlation between short half-life and mRNA association with P-bodies. Moreover, we detect an enrichment of mRNA 3' ends in P-bodies in the early embryo, consistent with 5' to 3' degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.
Collapse
Affiliation(s)
- Lauren Forbes Beadle
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jennifer C. Love
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Yuliya Shapovalova
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Artem Artemev
- Department of Computing, Imperial College London, London, United Kingdom
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (MR); (HLA)
| | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (MR); (HLA)
| |
Collapse
|
42
|
Amy Lyu MJ, Tang Q, Wang Y, Essemine J, Chen F, Ni X, Chen G, Zhu XG. Evolution of gene regulatory network of C 4 photosynthesis in the genus Flaveria reveals the evolutionary status of C 3-C 4 intermediate species. PLANT COMMUNICATIONS 2023; 4:100426. [PMID: 35986514 PMCID: PMC9860191 DOI: 10.1016/j.xplc.2022.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
C4 photosynthesis evolved from ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 metabolic pathway have been intensively studied and well documented; however, the transcription factors (TFs) that regulate these C4 metabolic genes are not yet well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolutionary process is unclear. Here, we constructed gene regulatory networks (GRNs) for four closely evolutionarily related species from the genus Flaveria, which represent four different evolutionary stages of C4 photosynthesis: C3 (F. robusta), type I C3-C4 (F. sonorensis), type II C3-C4 (F. ramosissima), and C4 (F. trinervia). Our results show that more than half of the co-regulatory relationships between TFs and core C4 metabolic genes are species specific. The counterparts of the C4 genes in C3 species were already co-regulated with photosynthesis-related genes, whereas the required TFs for C4 photosynthesis were recruited later. The TFs involved in C4 photosynthesis were widely recruited in the type I C3-C4 species; nevertheless, type II C3-C4 species showed a divergent GRN from C4 species. In line with these findings, a 13CO2 pulse-labeling experiment showed that the CO2 initially fixed into C4 acid was not directly released to the Calvin-Benson-Bassham cycle in the type II C3-C4 species. Therefore, our study uncovered dynamic changes in C4 genes and TF co-regulation during the evolutionary process; furthermore, we showed that the metabolic pathway of the type II C3-C4 species F. ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C3-C4 intermediate species.
Collapse
Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiming Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Yanjie Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Faming Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiang Ni
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
43
|
Copeland J, Merkuri F, Simoes-Costa M. ChIP-Seq Protocol for In Vitro Cell Differentiation Systems. Methods Mol Biol 2023; 2599:49-58. [PMID: 36427142 DOI: 10.1007/978-1-0716-2847-8_5] [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] [Indexed: 06/16/2023]
Abstract
In vitro differentiation systems provide a flexible platform for understanding complex developmental processes. Here, we provide a comprehensive protocol for the preparation and analysis of ChIP-seq libraries for human-induced neural crest cells (hiNCCs) from human embryonic stem cells (hESCs). This workflow is aimed at identifying interactions between transcription factors and cis regulatory elements, which serve as useful assays in uncovering gene regulatory principles during development.
Collapse
Affiliation(s)
- Jacqueline Copeland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Fjodor Merkuri
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
44
|
Liao L, Yao Z, Kong J, Zhang X, Li H, Chen W, Xie Q. Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo. BMC Genomics 2022; 23:825. [PMID: 36513979 PMCID: PMC9746114 DOI: 10.1186/s12864-022-09054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo. RESULTS In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified. CONCLUSION Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
Collapse
Affiliation(s)
- Liqin Liao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Ziqi Yao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China
| | - Jie Kong
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Xinheng Zhang
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Hongxin Li
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Weiguo Chen
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Qingmei Xie
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022; 138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [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: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is an emblematic population of embryonic stem-like cells with remarkable migratory ability. These distinctive attributes have inspired the curiosity of developmental biologists for over 150 years, however only recently the regulatory mechanisms controlling the complex features of the NC have started to become elucidated at genomic scales. Regulatory control of NC development is achieved through combinatorial transcription factor binding and recruitment of associated transcriptional complexes to distal cis-regulatory elements. Together, they regulate when, where and to what extent transcriptional programmes are actively deployed, ultimately shaping ontogenetic processes. Here, we discuss how transcriptional networks control NC ontogeny, with a special emphasis on the molecular mechanisms underlying specification of the cephalic NC. We also cover emerging properties of transcriptional regulation revealed in diverse developmental systems, such as the role of three-dimensional conformation of chromatin, and how they are involved in the regulation of NC ontogeny. Finally, we highlight how advances in deciphering the NC transcriptional network have afforded new insights into the molecular basis of human diseases.
Collapse
Affiliation(s)
- Ivan L Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
| |
Collapse
|
47
|
Okubo K, Kaneko K. Heterosis of fitness and phenotypic variance in the evolution of a diploid gene regulatory network. PNAS NEXUS 2022; 1:pgac097. [PMID: 36741431 PMCID: PMC9896930 DOI: 10.1093/pnasnexus/pgac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/24/2022] [Indexed: 02/07/2023]
Abstract
Heterosis describes the phenomenon, whereby a hybrid population has higher fitness than an inbred population, which has previously been explained by either Mendelian dominance or overdominance under the general assumption of a simple genotype-phenotype relationship. However, recent studies have demonstrated that genes interact through a complex gene regulatory network (GRN). Furthermore, phenotypic variance is reportedly lower for heterozygotes, and the origin of such variance-related heterosis remains elusive. Therefore, a theoretical analysis linking heterosis to GRN evolution and stochastic gene expression dynamics is required. Here, we investigated heterosis related to fitness and phenotypic variance in a system with interacting genes by numerically evolving diploid GRNs. According to the results, the heterozygote population exhibited higher fitness than the homozygote population, indicating fitness-related heterosis resulting from evolution. In addition, the heterozygote population exhibited lower noise-related phenotypic variance in expression levels than the homozygous population, implying that the heterozygote population is more robust to noise. Furthermore, the distribution of the ratio of heterozygote phenotypic variance to homozygote phenotypic variance exhibited quantitative similarity with previous experimental results. By applying dominance and differential gene expression rather than only a single gene expression model, we confirmed the correlation between heterosis and differential gene expression. We explain our results by proposing that the convex high-fitness region is evolutionarily shaped in the genetic space to gain noise robustness under genetic mixing through sexual reproduction. These results provide new insights into the effects of GRNs on variance-related heterosis and differential gene expression.
Collapse
Affiliation(s)
- Kenji Okubo
- Research Center for Integrative Evolutionary Science, the Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa, 240-0193, Japan
| | | |
Collapse
|
48
|
Minelli A, Valero-Gracia A. Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution. Cells 2022; 11:cells11111790. [PMID: 35681485 PMCID: PMC9179533 DOI: 10.3390/cells11111790] [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] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022] Open
Abstract
Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.
Collapse
Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via U. Bassi 58B, 35132 Padova, Italy
- Correspondence:
| | - Alberto Valero-Gracia
- Natural History Museum, University of Oslo, Blindern, P.O. Box 1172, 0318 Oslo, Norway;
| |
Collapse
|
49
|
Amit G, Vaknin Ben Porath D, Levy O, Hamdi O, Bashan A. Global coordination level in single-cell transcriptomic data. Sci Rep 2022; 12:7547. [PMID: 35534606 PMCID: PMC9085802 DOI: 10.1038/s41598-022-11507-y] [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: 01/05/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022] Open
Abstract
Genes are linked by underlying regulatory mechanisms and by jointly implementing biological functions, working in coordination to apply different tasks in the cells. Assessing the coordination level between genes from single-cell transcriptomic data, without a priori knowledge of the map of gene regulatory interactions, is a challenge. A ‘top-down’ approach has recently been developed to analyze single-cell transcriptomic data by evaluating the global coordination level between genes (called GCL). Here, we systematically analyze the performance of the GCL in typical scenarios of single-cell RNA sequencing (scRNA-seq) data. We show that an individual anomalous cell can have a disproportionate effect on the GCL calculated over a cohort of cells. In addition, we demonstrate how the GCL is affected by the presence of clusters, which are very common in scRNA-seq data. Finally, we analyze the effect of the sampling size of the Jackknife procedure on the GCL statistics. The manuscript is accompanied by a description of a custom-built Python package for calculating the GCL. These results provide practical guidelines for properly pre-processing and applying the GCL measure in transcriptional data.
Collapse
|
50
|
Kinjo S, Kiyomoto M, Suzuki H, Yamamoto T, Ikeo K, Yaguchi S. TrBase: A genome and transcriptome database of Temnopleurus reevesii. Dev Growth Differ 2022; 64:210-218. [PMID: 35451498 DOI: 10.1111/dgd.12780] [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: 01/31/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/28/2022]
Abstract
Sea urchins have a long history as model organisms in biology, but their use in genetics is limited because of their long breeding cycle. In sea urchin genetics, genome editing technology was first established in Hemicentrotus pulcherrimus, whose genome has already been published. However, because this species also has a long breeding cycle, new model sea urchins that are more suitable for genetics have been sought. Here, we report a draft genome of another Western Pacific species, Temnopleurus reevesii, which we established as a new model sea urchin recently since this species has a comparable developmental process to other model sea urchins but a short breeding cycle of approximately half a year. The genome of T. reevesii was assembled into 28,742 scaffold sequences with an N50 length of 67.6 kb and an estimated genome size of 905.9 Mb. In the assembled genome, 27,064 genes were identified, 23,624 of which were expressed in at least one of the seven developmental stages. To provide genetic information, we constructed the genome database TrBase (https://cell-innovation.nig.ac.jp/Tree/). We also constructed the Western Pacific Sea Urchin Genome Database (WestPac-SUGDB) (https://cell-innovation.nig.ac.jp/WPAC/) with the aim of establishing a portal site for genetic information on sea urchins in the West Pacific. This site contains genomic information on two species, T. reevesii and H. pulcherrimus, and is equipped with homology search programs for comparing the two datasets. Therefore, TrBase and WestPac-SUGDB are expected to contribute not only to genetic research using sea urchins but also to comparative genomics and evolutionary research.
Collapse
Affiliation(s)
- Sonoko Kinjo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Masato Kiyomoto
- Institute for Marine and Coastal Research, Ochanomizu University, Tateyama, Japan
| | - Haruka Suzuki
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan.,PRESTO, JST, Kawaguchi, Japan
| |
Collapse
|