1
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Stefanakis N, Jiang J, Liang Y, Shaham S. LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior. EMBO J 2024; 43:956-992. [PMID: 38360995 PMCID: PMC10943081 DOI: 10.1038/s44318-024-00049-w] [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: 09/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
While most glial cell types in the central nervous system (CNS) arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which envelop the brain neuropil and separate it from the circulatory system cavity. Transcriptome analysis shows that GLR glia combine astrocytic and endothelial characteristics, which are relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor also expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, the UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naive cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and promotes salt-induced paralysis, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neuronal differentiation, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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Affiliation(s)
- Nikolaos Stefanakis
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Jessica Jiang
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yupu Liang
- Research Bioinformatics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Alexion Pharmaceuticals, Boston, MA, 02135, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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2
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Cole AG, Hashimshony T, Du Z, Yanai I. Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo. eLife 2024; 12:RP87099. [PMID: 38284404 PMCID: PMC10945703 DOI: 10.7554/elife.87099] [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] [Indexed: 01/30/2024] Open
Abstract
Pattern formation originates during embryogenesis by a series of symmetry-breaking steps throughout an expanding cell lineage. In Drosophila, classic work has shown that segmentation in the embryo is established by morphogens within a syncytium, and the subsequent action of the gap, pair-rule, and segment polarity genes. This classic model however does not translate directly to species that lack a syncytium - such as Caenorhabditis elegans - where cell fate is specified by cell-autonomous cell lineage programs and their inter-signaling. Previous single-cell RNA-Seq studies in C. elegans have analyzed cells from a mixed suspension of cells from many embryos to study late differentiation stages, or individual early stage embryos to study early gene expression in the embryo. To study the intermediate stages of early and late gastrulation (28- to 102-cells stages) missed by these approaches, here we determine the transcriptomes of the 1- to 102-cell stage to identify 119 embryonic cell states during cell fate specification, including 'equivalence-group' cell identities. We find that gene expression programs are modular according to the sub-cell lineages, each establishing a set of stripes by combinations of transcription factor gene expression across the anterior-posterior axis. In particular, expression of the homeodomain genes establishes a comprehensive lineage-specific positioning system throughout the embryo beginning at the 28-cell stage. Moreover, we find that genes that segment the entire embryo in Drosophila have orthologs in C. elegans that exhibit sub-lineage-specific expression. These results suggest that the C. elegans embryo is patterned by a juxtaposition of distinct lineage-specific gene regulatory programs each with a unique encoding of cell location and fate. This use of homologous gene regulatory patterning codes suggests a deep homology of cell fate specification programs across diverse modes of development.
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Affiliation(s)
- Alison G Cole
- Department of Molecular Evolution and Development, University of ViennaViennaAustria
- University of ViennaViennaAustria
| | - Tamar Hashimshony
- Department of Biology, Technion – Israel Institute of TechnologyHaifaIsrael
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Itai Yanai
- Institute for Computational Medicine, NYU School of MedicineNew YorkUnited States
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3
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Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH. Binding profiles for 954 Drosophila and C. elegans transcription factors reveal tissue specific regulatory relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576242. [PMID: 38293065 PMCID: PMC10827215 DOI: 10.1101/2024.01.18.576242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the modERN (model organism Encyclopedia of Regulatory Networks) consortium that systematically assayed TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). We describe key features of these datasets, comprising 604 TFs identifying 3.6M sites in the fly and 350 TFs identifying 0.9 M sites in the worm. Applying a machine learning model to these data identifies sets of TFs with a prominent role in promoting target gene expression in specific cell types. TF binding data are available through the ENCODE Data Coordinating Center and at https://epic.gs.washington.edu/modERNresource, which provides access to processed and summary data, as well as widgets to probe cell type-specific TF-target relationships. These data are a rich resource that should fuel investigations into TF function during development.
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Affiliation(s)
- Michelle Kudron
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Louis Gevirtzman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Alec Victorsen
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN 55455
| | - Bridget C. Lear
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Jiahao Gao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Jinrui Xu
- Department of Biology, Howard University, Washington, District of Columbia 20059, USA
- Center for Applied Data Science and Analytics, Howard University, Washington, District of Columbia 20059, USA
| | - Swapna Samanta
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Emily Frink
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Adri Tran-Pearson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Chau Huynh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Dionne Vafeados
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Ann Hammonds
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - William Fisher
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Martha Wall
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Greg Wesseling
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Vanessa Hernandez
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Zhichun Lin
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Mary Kasparian
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Kevin White
- Department of Biochemistry and Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
- Department of Statistics and Data Science, Yale University, New Haven, Connecticut 06520, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Susan E. Celniker
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Valerie Reinke
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
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4
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Pons C, van Leeuwen J. Meta-analysis of dispensable essential genes and their interactions with bypass suppressors. Life Sci Alliance 2024; 7:e202302192. [PMID: 37918966 PMCID: PMC10622647 DOI: 10.26508/lsa.202302192] [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: 05/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
Genes have been historically classified as essential or non-essential based on their requirement for viability. However, genomic mutations can sometimes bypass the requirement for an essential gene, challenging the binary classification of gene essentiality. Such dispensable essential genes represent a valuable model for understanding the incomplete penetrance of loss-of-function mutations often observed in natural populations. Here, we compiled data from multiple studies on essential gene dispensability in Saccharomyces cerevisiae to comprehensively characterize these genes. In analyses spanning different evolutionary timescales, dispensable essential genes exhibited distinct phylogenetic properties compared with other essential and non-essential genes. Integration of interactions with suppressor genes that can bypass the gene essentiality revealed the high functional modularity of the bypass suppression network. Furthermore, dispensable essential and bypass suppressor gene pairs reflected simultaneous changes in the mutational landscape of S. cerevisiae strains. Importantly, species in which dispensable essential genes were non-essential tended to carry bypass suppressor mutations in their genomes. Overall, our study offers a comprehensive view of dispensable essential genes and illustrates how their interactions with bypass suppressors reflect evolutionary outcomes.
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Affiliation(s)
- Carles Pons
- https://ror.org/01z1gye03 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
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5
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Stefanakis N, Jiang J, Liang Y, Shaham S. LET-381/FoxF and UNC-30/Pitx2 control the development of C. elegans mesodermal glia that regulate motor behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563501. [PMID: 37961181 PMCID: PMC10634723 DOI: 10.1101/2023.10.23.563501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
While most CNS glia arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which ensheath the brain neuropil and separate it from the circulatory-system cavity. Transcriptome analysis suggests GLR glia merge astrocytic and endothelial characteristics relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naïve cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and induces salt hypersensitivity, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neurons, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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Soni P, Edwards H, Anupom T, Rahman M, Lesanpezeshki L, Blawzdziewicz J, Cope H, Gharahdaghi N, Scott D, Toh LS, Williams PM, Etheridge T, Szewczyk N, Willis CRG, Vanapalli SA. Spaceflight Induces Strength Decline in Caenorhabditis elegans. Cells 2023; 12:2470. [PMID: 37887314 PMCID: PMC10605753 DOI: 10.3390/cells12202470] [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: 09/15/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Background: Understanding and countering the well-established negative health consequences of spaceflight remains a primary challenge preventing safe deep space exploration. Targeted/personalized therapeutics are at the forefront of space medicine strategies, and cross-species molecular signatures now define the 'typical' spaceflight response. However, a lack of direct genotype-phenotype associations currently limits the robustness and, therefore, the therapeutic utility of putative mechanisms underpinning pathological changes in flight. Methods: We employed the worm Caenorhabditis elegans as a validated model of space biology, combined with 'NemaFlex-S' microfluidic devices for assessing animal strength production as one of the most reproducible physiological responses to spaceflight. Wild-type and dys-1 (BZ33) strains (a Duchenne muscular dystrophy (DMD) model for comparing predisposed muscle weak animals) were cultured on the International Space Station in chemically defined media before loading second-generation gravid adults into NemaFlex-S devices to assess individual animal strength. These same cultures were then frozen on orbit before returning to Earth for next-generation sequencing transcriptomic analysis. Results: Neuromuscular strength was lower in flight versus ground controls (16.6% decline, p < 0.05), with dys-1 significantly more (23% less strength, p < 0.01) affected than wild types. The transcriptional gene ontology signatures characterizing both strains of weaker animals in flight strongly corroborate previous results across species, enriched for upregulated stress response pathways and downregulated mitochondrial and cytoskeletal processes. Functional gene cluster analysis extended this to implicate decreased neuronal function, including abnormal calcium handling and acetylcholine signaling, in space-induced strength declines under the predicted control of UNC-89 and DAF-19 transcription factors. Finally, gene modules specifically altered in dys-1 animals in flight again cluster to neuronal/neuromuscular pathways, suggesting strength loss in DMD comprises a strong neuronal component that predisposes these animals to exacerbated strength loss in space. Conclusions: Highly reproducible gene signatures are strongly associated with space-induced neuromuscular strength loss across species and neuronal changes in calcium/acetylcholine signaling require further study. These results promote targeted medical efforts towards and provide an in vivo model for safely sending animals and people into deep space in the near future.
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Affiliation(s)
- Purushottam Soni
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA; (P.S.); (M.R.); (L.L.)
| | - Hunter Edwards
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA;
| | - Taslim Anupom
- Department of Electrical Engineering, Texas Tech University, Lubbock, TX 79409, USA;
| | - Mizanur Rahman
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA; (P.S.); (M.R.); (L.L.)
| | - Leila Lesanpezeshki
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA; (P.S.); (M.R.); (L.L.)
| | - Jerzy Blawzdziewicz
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, USA;
- Department of Physics and Astronomy, Texas Tech University, Lubbock, TX 79409, USA
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK; (H.C.); (N.G.)
| | - Nima Gharahdaghi
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK; (H.C.); (N.G.)
| | - Daniel Scott
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK;
| | - Li Shean Toh
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (L.S.T.); (P.M.W.)
| | - Philip M. Williams
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (L.S.T.); (P.M.W.)
| | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK;
| | - Nathaniel Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK; (H.C.); (N.G.)
- Ohio Musculoskeletal and Neurological Institute, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Craig R. G. Willis
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK;
| | - Siva A. Vanapalli
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA; (P.S.); (M.R.); (L.L.)
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7
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Perez MF, Sarkies P. Histone methyltransferase activity affects metabolism in human cells independently of transcriptional regulation. PLoS Biol 2023; 21:e3002354. [PMID: 37883365 PMCID: PMC10602318 DOI: 10.1371/journal.pbio.3002354] [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: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
The N-terminal tails of eukaryotic histones are frequently posttranslationally modified. The role of these modifications in transcriptional regulation is well-documented. However, the extent to which the enzymatic processes of histone posttranslational modification might affect metabolic regulation is less clear. Here, we investigated how histone methylation might affect metabolism using metabolomics, proteomics, and RNA-seq data from cancer cell lines, primary tumour samples and healthy tissue samples. In cancer, the expression of histone methyltransferases (HMTs) was inversely correlated to the activity of NNMT, an enzyme previously characterised as a methyl sink that disposes of excess methyl groups carried by the universal methyl donor S-adenosyl methionine (SAM or AdoMet). In healthy tissues, histone methylation was inversely correlated to the levels of an alternative methyl sink, PEMT. These associations affected the levels of multiple histone marks on chromatin genome-wide but had no detectable impact on transcriptional regulation. We show that HMTs with a variety of different associations to transcription are co-regulated by the Retinoblastoma (Rb) tumour suppressor in human cells. Rb-mutant cancers show increased total HMT activity and down-regulation of NNMT. Together, our results suggest that the total activity of HMTs affects SAM metabolism, independent of transcriptional regulation.
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Affiliation(s)
- Marcos Francisco Perez
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Department of Cells and Tissues, Instituto de Biologia Molecular de Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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8
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [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: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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9
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Athanasouli M, Akduman N, Röseler W, Theam P, Rödelsperger C. Thousands of Pristionchus pacificus orphan genes were integrated into developmental networks that respond to diverse environmental microbiota. PLoS Genet 2023; 19:e1010832. [PMID: 37399201 DOI: 10.1371/journal.pgen.1010832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023] Open
Abstract
Adaptation of organisms to environmental change may be facilitated by the creation of new genes. New genes without homologs in other lineages are known as taxonomically-restricted orphan genes and may result from divergence or de novo formation. Previously, we have extensively characterized the evolution and origin of such orphan genes in the nematode model organism Pristionchus pacificus. Here, we employ large-scale transcriptomics to establish potential functional associations and to measure the degree of transcriptional plasticity among orphan genes. Specifically, we analyzed 24 RNA-seq samples from adult P. pacificus worms raised on 24 different monoxenic bacterial cultures. Based on coexpression analysis, we identified 28 large modules that harbor 3,727 diplogastrid-specific orphan genes and that respond dynamically to different bacteria. These coexpression modules have distinct regulatory architecture and also exhibit differential expression patterns across development suggesting a link between bacterial response networks and development. Phylostratigraphy revealed a considerably high number of family- and even species-specific orphan genes in certain coexpression modules. This suggests that new genes are not attached randomly to existing cellular networks and that integration can happen very fast. Integrative analysis of protein domains, gene expression and ortholog data facilitated the assignments of biological labels for 22 coexpression modules with one of the largest, fast-evolving module being associated with spermatogenesis. In summary, this work presents the first functional annotation for thousands of P. pacificus orphan genes and reveals insights into their integration into environmentally responsive gene networks.
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Affiliation(s)
- Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Nermin Akduman
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Waltraud Röseler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Penghieng Theam
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
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10
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AlHarbi S, Frøkjær-Jensen C. Characterizing a standardized BioPart for PVQ-specific expression in C. elegans. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000870. [PMID: 37426742 PMCID: PMC10326622 DOI: 10.17912/micropub.biology.000870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023]
Abstract
Synthetic biology relies on standardized biological parts (BioParts), and we aim to identify cell-specific promoters for every class of neuron in C. elegans . Here, we characterize a short BioPart (P nlp-17 , 300 bp) for PVQ-specific expression. P nlp-17 ::mScarlet showed bright, persistent, and specific expression in hermaphrodite and male PVQ neurons from multicopy arrays and single-copy insertions starting from the comma stage. We generated standardized P nlp-17 cloning vectors with gfp and mScarlet compatible with single-copy or array expression for PVQ-specific transgene expression or identification. To facilitate gene synthesis, we have incorporated P nlp-17 as a standard BioPart in our online transgene design tool (www.wormbuilder.org/transgenebuilder).
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Affiliation(s)
- Sarah AlHarbi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal, 23955-6900, Saudi Arabia
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal, 23955-6900, Saudi Arabia
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11
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Miles J, Townend S, Milonaitytė D, Smith W, Hodge F, Westhead DR, van Oosten-Hawle P. Transcellular chaperone signaling is an intercellular stress-response distinct from the HSF-1-mediated heat shock response. PLoS Biol 2023; 21:e3001605. [PMID: 36780563 PMCID: PMC9956597 DOI: 10.1371/journal.pbio.3001605] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 02/24/2023] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
Organismal proteostasis is maintained by intercellular signaling processes including cell nonautonomous stress responses such as transcellular chaperone signaling (TCS). When TCS is activated upon tissue-specific knockdown of hsp-90 in the Caenorhabditis elegans intestine, heat-inducible hsp-70 is induced in muscle cells at the permissive temperature resulting in increased heat stress resistance and lifespan extension. However, our understanding of the molecular mechanism and signaling factors mediating transcellular activation of hsp-70 expression from one tissue to another is still in its infancy. Here, we conducted a combinatorial approach using transcriptome RNA-Seq profiling and a forward genetic mutagenesis screen to elucidate how stress signaling from the intestine to the muscle is regulated. We find that the TCS-mediated "gut-to-muscle" induction of hsp-70 expression is suppressed by HSF-1 and instead relies on transcellular-X-cross-tissue (txt) genes. We identify a key role for the PDZ-domain guanylate cyclase txt-1 and the homeobox transcription factor ceh-58 as signaling hubs in the stress receiving muscle cells to initiate hsp-70 expression and facilitate TCS-mediated heat stress resistance and lifespan extension. Our results provide a new view on cell-nonautonomous regulation of "inter-tissue" stress responses in an organism that highlight a key role for the gut. Our data suggest that the HSF-1-mediated heat shock response is switched off upon TCS activation, in favor of an intercellular stress-signaling route to safeguard survival.
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Affiliation(s)
- Jay Miles
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sarah Townend
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Dovilė Milonaitytė
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - William Smith
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Francesca Hodge
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David R. Westhead
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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12
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Wu T, Ge M, Wu M, Duan F, Liang J, Chen M, Gracida X, Liu H, Yang W, Dar AR, Li C, Butcher RA, Saltzman AL, Zhang Y. Pathogenic bacteria modulate pheromone response to promote mating. Nature 2023; 613:324-331. [PMID: 36599989 PMCID: PMC10732163 DOI: 10.1038/s41586-022-05561-9] [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: 12/26/2021] [Accepted: 11/11/2022] [Indexed: 01/05/2023]
Abstract
Pathogens generate ubiquitous selective pressures and host-pathogen interactions alter social behaviours in many animals1-4. However, very little is known about the neuronal mechanisms underlying pathogen-induced changes in social behaviour. Here we show that in adult Caenorhabditis elegans hermaphrodites, exposure to a bacterial pathogen (Pseudomonas aeruginosa) modulates sensory responses to pheromones by inducing the expression of the chemoreceptor STR-44 to promote mating. Under standard conditions, C. elegans hermaphrodites avoid a mixture of ascaroside pheromones to facilitate dispersal5-13. We find that exposure to the pathogenic Pseudomonas bacteria enables pheromone responses in AWA sensory neurons, which mediate attractive chemotaxis, to suppress the avoidance. Pathogen exposure induces str-44 expression in AWA neurons, a process regulated by a transcription factor zip-5 that also displays a pathogen-induced increase in expression in AWA. STR-44 acts as a pheromone receptor and its function in AWA neurons is required for pathogen-induced AWA pheromone response and suppression of pheromone avoidance. Furthermore, we show that C. elegans hermaphrodites, which reproduce mainly through self-fertilization, increase the rate of mating with males after pathogen exposure and that this increase requires str-44 in AWA neurons. Thus, our results uncover a causal mechanism for pathogen-induced social behaviour plasticity, which can promote genetic diversity and facilitate adaptation of the host animals.
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Affiliation(s)
- Taihong Wu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Minghai Ge
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Min Wu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Fengyun Duan
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jingting Liang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Maoting Chen
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Xicotencatl Gracida
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - He Liu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Wenxing Yang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Chengyin Li
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Arneet L Saltzman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Yun Zhang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Center for Brain Science, Harvard University, Cambridge, MA, USA.
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13
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Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification. PLoS Genet 2022; 18:e1010372. [PMID: 36178933 PMCID: PMC9524666 DOI: 10.1371/journal.pgen.1010372] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans, each individual neuron class is defined by the expression of unique combinations of homeobox genes, prompting the question of whether each neuron class indeed requires a homeobox gene for its proper identity specification. We present here progress in addressing this question by extending previous mutant analysis of homeobox gene family members and describing multiple examples of homeobox gene function in different parts of the C. elegans nervous system. To probe homeobox function, we make use of a number of reporter gene tools, including a novel multicolor reporter transgene, NeuroPAL, which permits simultaneous monitoring of the execution of multiple differentiation programs throughout the entire nervous system. Using these tools, we add to the previous characterization of homeobox gene function by identifying neuronal differentiation defects for 14 homeobox genes in 24 distinct neuron classes that are mostly unrelated by location, function and lineage history. 12 of these 24 neuron classes had no homeobox gene function ascribed to them before, while in the other 12 neuron classes, we extend the combinatorial code of transcription factors required for specifying terminal differentiation programs. Furthermore, we demonstrate that in a particular lineage, homeotic identity transformations occur upon loss of a homeobox gene and we show that these transformations are the result of changes in homeobox codes. Combining the present with past analyses, 113 of the 118 neuron classes of C. elegans are now known to require a homeobox gene for proper execution of terminal differentiation programs. Such broad deployment indicates that homeobox function in neuronal identity specification may be an ancestral feature of animal nervous systems.
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14
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Riva C, Hajduskova M, Gally C, Suman SK, Ahier A, Jarriault S. A natural transdifferentiation event involving mitosis is empowered by integrating signaling inputs with conserved plasticity factors. Cell Rep 2022; 40:111365. [PMID: 36130499 PMCID: PMC9513805 DOI: 10.1016/j.celrep.2022.111365] [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: 08/16/2021] [Revised: 04/09/2022] [Accepted: 08/25/2022] [Indexed: 11/03/2022] Open
Abstract
Transdifferentiation, or direct cell reprogramming, is the conversion of one fully differentiated cell type into another. Whether core mechanisms are shared between natural transdifferentiation events when occurring with or without cell division is unclear. We have previously characterized the Y-to-PDA natural transdifferentiation in Caenorhabditis elegans, which occurs without cell division and requires orthologs of vertebrate reprogramming factors. Here, we identify a rectal-to-GABAergic transdifferentiation and show that cell division is required but not sufficient for conversion. We find shared mechanisms, including erasure of the initial identity, which requires the conserved reprogramming factors SEM-4/SALL, SOX-2, CEH-6/OCT, and EGL-5/HOX. We also find three additional and parallel roles of the Wnt signaling pathway: selection of a specific daughter, removal of the initial identity, and imposition of the precise final subtype identity. Our results support a model in which levels and antagonistic activities of SOX-2 and Wnt signaling provide a timer for the acquisition of final identity.
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Affiliation(s)
- Claudia Riva
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, Inserm U 1258, Université de Strasbourg, 67400 Illkirch, France
| | - Martina Hajduskova
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, Inserm U 1258, Université de Strasbourg, 67400 Illkirch, France
| | - Christelle Gally
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, Inserm U 1258, Université de Strasbourg, 67400 Illkirch, France.
| | - Shashi Kumar Suman
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, Inserm U 1258, Université de Strasbourg, 67400 Illkirch, France
| | - Arnaud Ahier
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, Inserm U 1258, Université de Strasbourg, 67400 Illkirch, France
| | - Sophie Jarriault
- Development and Stem Cells Department, IGBMC, CNRS UMR 7104, Inserm U 1258, Université de Strasbourg, 67400 Illkirch, France.
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15
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Rumley JD, Preston EA, Cook D, Peng FL, Zacharias AL, Wu L, Jileaeva I, Murray JI. pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo. Dev Biol 2022; 489:34-46. [PMID: 35660370 PMCID: PMC9378603 DOI: 10.1016/j.ydbio.2022.05.019] [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: 01/21/2022] [Revised: 04/21/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022]
Abstract
Patterning of the anterior-posterior axis is fundamental to animal development. The Wnt pathway plays a major role in this process by activating the expression of posterior genes in animals from worms to humans. This observation raises the question of whether the Wnt pathway or other regulators control the expression of the many anterior-expressed genes. We found that the expression of five anterior-specific genes in Caenorhabditis elegans embryos depends on the Wnt pathway effectors pop-1/TCF and sys-1/β-catenin. We focused further on one of these anterior genes, ref-2/ZIC, a conserved transcription factor expressed in multiple anterior lineages. Live imaging of ref-2 mutant embryos identified defects in cell division timing and position in anterior lineages. Cis-regulatory dissection identified three ref-2 transcriptional enhancers, one of which is necessary and sufficient for anterior-specific expression. This enhancer is activated by the T-box transcription factors TBX-37 and TBX-38, and surprisingly, concatemerized TBX-37/38 binding sites are sufficient to drive anterior-biased expression alone, despite the broad expression of TBX-37 and TBX-38. Taken together, our results highlight the diverse mechanisms used to regulate anterior expression patterns in the embryo.
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Affiliation(s)
- Jonathan D Rumley
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elicia A Preston
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dylan Cook
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Felicia L Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amanda L Zacharias
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Lucy Wu
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ilona Jileaeva
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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16
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Godini R, Fallahi H, Pocock R. The regulatory landscape of neurite development in Caenorhabditis elegans. Front Mol Neurosci 2022; 15:974208. [PMID: 36090252 PMCID: PMC9453034 DOI: 10.3389/fnmol.2022.974208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Neuronal communication requires precise connectivity of neurite projections (axons and dendrites). Developing neurites express cell-surface receptors that interpret extracellular cues to enable correct guidance toward, and connection with, target cells. Spatiotemporal regulation of neurite guidance molecule expression by transcription factors (TFs) is critical for nervous system development and function. Here, we review how neurite development is regulated by TFs in the Caenorhabditis elegans nervous system. By collecting publicly available transcriptome and ChIP-sequencing data, we reveal gene expression dynamics during neurite development, providing insight into transcriptional mechanisms governing construction of the nervous system architecture.
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Affiliation(s)
- Rasoul Godini
- Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- *Correspondence: Rasoul Godini,
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Roger Pocock
- Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Roger Pocock,
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17
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Rodriguez-Crespo D, Nanchen M, Rajopadhye S, Wicky C. The zinc-finger transcription factor LSL-1 is a major regulator of the germline transcriptional program in Caenorhabditis elegans. Genetics 2022; 221:iyac039. [PMID: 35262739 PMCID: PMC9071529 DOI: 10.1093/genetics/iyac039] [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: 01/10/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Specific gene transcriptional programs are required to ensure the proper proliferation and differentiation processes underlying the production of specialized cells during development. Gene activity is mainly regulated by the concerted action of transcription factors and chromatin proteins. In the nematode Caenorhabditis elegans, mechanisms that silence improper transcriptional programs in germline and somatic cells have been well studied, however, how are tissue-specific sets of genes turned on is less known. LSL-1 is herein defined as a novel crucial transcriptional regulator of germline genes in C. elegans. LSL-1 is first detected in the P4 blastomere and remains present at all stages of germline development, from primordial germ cell proliferation to the end of meiotic prophase. lsl-1 loss-of-function mutants exhibit many defects including meiotic prophase progression delay, a high level of germline apoptosis, and production of almost no functional gametes. Transcriptomic analysis and ChIP-seq data show that LSL-1 binds to promoters and acts as a transcriptional activator of germline genes involved in various processes, including homologous chromosome pairing, recombination, and genome stability. Furthermore, we show that LSL-1 functions by antagonizing the action of the heterochromatin proteins HPL-2/HP1 and LET-418/Mi2 known to be involved in the repression of germline genes in somatic cells. Based on our results, we propose LSL-1 to be a major regulator of the germline transcriptional program during development.
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Affiliation(s)
| | - Magali Nanchen
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| | - Shweta Rajopadhye
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| | - Chantal Wicky
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
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18
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Murray JI, Preston E, Crawford JP, Rumley JD, Amom P, Anderson BD, Sivaramakrishnan P, Patel SD, Bennett BA, Lavon TD, Hsiao E, Peng F, Zacharias AL. The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo. PLoS Genet 2022; 18:e1010187. [PMID: 35500030 PMCID: PMC9098060 DOI: 10.1371/journal.pgen.1010187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 05/12/2022] [Accepted: 04/04/2022] [Indexed: 12/18/2022] Open
Abstract
Hox transcription factors play a conserved role in specifying positional identity during animal development, with posterior Hox genes typically repressing the expression of more anterior Hox genes. Here, we dissect the regulation of the posterior Hox genes nob-1 and php-3 in the nematode C. elegans. We show that nob-1 and php-3 are co-expressed in gastrulation-stage embryos in cells that previously expressed the anterior Hox gene ceh-13. This expression is controlled by several partially redundant transcriptional enhancers. These enhancers act in a ceh-13-dependant manner, providing a striking example of an anterior Hox gene positively regulating a posterior Hox gene. Several other regulators also act positively through nob-1/php-3 enhancers, including elt-1/GATA, ceh-20/ceh-40/Pbx, unc-62/Meis, pop-1/TCF, ceh-36/Otx, and unc-30/Pitx. We identified defects in both cell position and cell division patterns in ceh-13 and nob-1;php-3 mutants, suggesting that these factors regulate lineage identity in addition to positional identity. Together, our results highlight the complexity and flexibility of Hox gene regulation and function and the ability of developmental transcription factors to regulate different targets in different stages of development.
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Affiliation(s)
- John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elicia Preston
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jeremy P. Crawford
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jonathan D. Rumley
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Prativa Amom
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Breana D. Anderson
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shaili D. Patel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barrington Alexander Bennett
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Teddy D. Lavon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erin Hsiao
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amanda L. Zacharias
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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19
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Ahn S, Yang H, Son S, Lee HS, Park D, Yim H, Choi HJ, Swoboda P, Lee J. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Rep 2022; 39:110661. [PMID: 35417689 DOI: 10.1016/j.celrep.2022.110661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Cilia are important for the interaction with environments and the proper function of tissues. While the basic structure of cilia is well conserved, ciliated cells have various functions. To understand the distinctive identities of ciliated cells, the identification of cell-specific proteins and its regulation is essential. Here, we report the mechanism that confers a specific identity on IL2 neurons in Caenorhabditis elegans, neurons important for the dauer larva-specific nictation behavior. We show that DAF-19M, an isoform of the sole C. elegans RFX transcription factor DAF-19, heads a regulatory subroutine, regulating target genes through an X-box motif variant under the control of terminal selector proteins UNC-86 and CFI-1 in IL2 neurons. Considering the conservation of DAF-19M module in IL2 neurons for nictation and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."
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Affiliation(s)
- Soungyub Ahn
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sangwon Son
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongjun Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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20
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Fischer F, Grigolon G, Benner C, Ristow M. Evolutionarily conserved transcription factors as regulators of longevity and targets for geroprotection. Physiol Rev 2022; 102:1449-1494. [PMID: 35343830 DOI: 10.1152/physrev.00017.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aging is the single largest risk factor for many debilitating conditions, including heart diseases, stroke, cancer, diabetes, and neurodegenerative disorders. While far from understood in its full complexity, it is scientifically well-established that aging is influenced by genetic and environmental factors, and can be modulated by various interventions. One of aging's early hallmarks are aberrations in transcriptional networks, controlling for example metabolic homeostasis or the response to stress. Evidence in different model organisms abounds that a number of evolutionarily conserved transcription factors, which control such networks, can affect lifespan and healthspan across species. These transcription factors thus potentially represent conserved regulators of longevity and are emerging as important targets in the challenging quest to develop treatments to mitigate age-related diseases, and possibly even to slow aging itself. This review provides an overview of evolutionarily conserved transcription factors that impact longevity or age-related diseases in at least one multicellular model organism (nematodes, flies, or mice), and/or are tentatively linked to human aging. Discussed is the general evidence for transcriptional regulation of aging and disease, followed by a more detailed look at selected transcription factor families, the common metabolic pathways involved, and the targeting of transcription factors as a strategy for geroprotective interventions.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Christoph Benner
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
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21
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Vidal B, Gulez B, Cao WX, Leyva-Diaz E, Reilly MB, Tekieli T, Hobert O. The enteric nervous system of the C. elegans pharynx is specified by the Sine oculis-like homeobox gene ceh-34. eLife 2022; 11:76003. [PMID: 35324425 PMCID: PMC8989417 DOI: 10.7554/elife.76003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/23/2022] [Indexed: 11/29/2022] Open
Abstract
Overarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode Caenorhabditis elegans that resides within the foregut (pharynx) of the worm. A C. elegans homolog of the Drosophila Sine oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine oculis homolog, our findings invite speculations about the early evolution of nervous systems.
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Affiliation(s)
- Berta Vidal
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Burcu Gulez
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Wen Xi Cao
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Eduardo Leyva-Diaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Tessa Tekieli
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
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22
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Wang X, Jiang Q, Song Y, He Z, Zhang H, Song M, Zhang X, Dai Y, Karalay O, Dieterich C, Antebi A, Wu L, Han JJ, Shen Y. Ageing induces tissue‐specific transcriptomic changes in
Caenorhabditis elegans. EMBO J 2022; 41:e109633. [PMID: 35253240 PMCID: PMC9016346 DOI: 10.15252/embj.2021109633] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/09/2022] Open
Abstract
Ageing is a complex process with common and distinct features across tissues. Unveiling the underlying processes driving ageing in individual tissues is indispensable to decipher the mechanisms of organismal longevity. Caenorhabditis elegans is a well‐established model organism that has spearheaded ageing research with the discovery of numerous genetic pathways controlling its lifespan. However, it remains challenging to dissect the ageing of worm tissues due to the limited description of tissue pathology and access to tissue‐specific molecular changes during ageing. In this study, we isolated cells from five major tissues in young and old worms and profiled the age‐induced transcriptomic changes within these tissues. We observed a striking diversity of ageing across tissues and identified different sets of longevity regulators therein. In addition, we found novel tissue‐specific factors, including irx‐1 and myrf‐2, which control the integrity of the intestinal barrier and sarcomere structure during ageing respectively. This study demonstrates the complexity of ageing across worm tissues and highlights the power of tissue‐specific transcriptomic profiling during ageing, which can serve as a resource to the field.
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Affiliation(s)
- Xueqing Wang
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
- Peking‐Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB) Peking University Beijing China
| | - Yuanyuan Song
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Zhidong He
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Hongdao Zhang
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Mengjiao Song
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Xiaona Zhang
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Yumin Dai
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Oezlem Karalay
- Max Planck Institute for Biology of Ageing Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III University Hospital Heidelberg Heidelberg Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Ligang Wu
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Jing‐Dong J Han
- CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
- Peking‐Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB) Peking University Beijing China
| | - Yidong Shen
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
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23
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Jimeno-Martín A, Sousa E, Brocal-Ruiz R, Daroqui N, Maicas M, Flames N. Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity. Genome Res 2022; 32:459-473. [PMID: 35074859 PMCID: PMC8896470 DOI: 10.1101/gr.275623.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022]
Abstract
To systematically investigate the complexity of neuron specification regulatory networks, we performed an RNA interference (RNAi) screen against all 875 transcription factors (TFs) encoded in Caenorhabditis elegans genome and searched for defects in nine different neuron types of the monoaminergic (MA) superclass and two cholinergic motoneurons. We identified 91 TF candidates to be required for correct generation of these neuron types, of which 28 were confirmed by mutant analysis. We found that correct reporter expression in each individual neuron type requires at least nine different TFs. Individual neuron types do not usually share TFs involved in their specification but share a common pattern of TFs belonging to the five most common TF families: homeodomain (HD), basic helix loop helix (bHLH), zinc finger (ZF), basic leucine zipper domain (bZIP), and nuclear hormone receptors (NHR). HD TF members are overrepresented, supporting a key role for this family in the establishment of neuronal identities. These five TF families are also prevalent when considering mutant alleles with previously reported neuronal phenotypes in C. elegans, Drosophila, and mouse. In addition, we studied terminal differentiation complexity focusing on the dopaminergic terminal regulatory program. We found two HD TFs (UNC-62 and VAB-3) that work together with known dopaminergic terminal selectors (AST-1, CEH-43, CEH-20). Combined TF binding sites for these five TFs constitute a cis-regulatory signature enriched in the regulatory regions of dopaminergic effector genes. Our results provide new insights on neuron-type regulatory programs in C. elegans that could help better understand neuron specification and evolution of neuron types.
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Affiliation(s)
- Angela Jimeno-Martín
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Noemi Daroqui
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
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24
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Zheng L, Liu J, Niu L, Kamran M, Yang AWH, Jolma A, Dai Q, Hughes TR, Patel DJ, Zhang L, Prasanth SG, Yu Y, Ren A, Lai EC. Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. Genes Dev 2022; 36:225-240. [PMID: 35144965 PMCID: PMC8887127 DOI: 10.1101/gad.348993.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/05/2022] [Indexed: 11/24/2022]
Abstract
The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. We conducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.
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Affiliation(s)
- Luqian Zheng
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jingjing Liu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Lijie Niu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Mohammad Kamran
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ally W H Yang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Arttu Jolma
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Qi Dai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Dinshaw J Patel
- Structural Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Long Zhang
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Yu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
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25
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Gal C, Carelli FN, Appert A, Cerrato C, Huang N, Dong Y, Murphy J, Frapporti A, Ahringer J. DREAM represses distinct targets by cooperating with different THAP domain proteins. Cell Rep 2021; 37:109835. [PMID: 34686342 PMCID: PMC8552245 DOI: 10.1016/j.celrep.2021.109835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/03/2021] [Accepted: 09/24/2021] [Indexed: 01/09/2023] Open
Abstract
The DREAM (dimerization partner [DP], retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell-cycle and other genes, but its mechanism of action is unclear. Here, we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell-cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline-specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell-cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.
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Affiliation(s)
- Csenge Gal
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesco Nicola Carelli
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alex Appert
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ni Huang
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jane Murphy
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Andrea Frapporti
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK.
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26
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Godini R, Handley A, Pocock R. Transcription Factors That Control Behavior-Lessons From C. elegans. Front Neurosci 2021; 15:745376. [PMID: 34646119 PMCID: PMC8503520 DOI: 10.3389/fnins.2021.745376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/02/2021] [Indexed: 11/15/2022] Open
Abstract
Behavior encompasses the physical and chemical response to external and internal stimuli. Neurons, each with their own specific molecular identities, act in concert to perceive and relay these stimuli to drive behavior. Generating behavioral responses requires neurons that have the correct morphological, synaptic, and molecular identities. Transcription factors drive the specific gene expression patterns that define these identities, controlling almost every phenomenon in a cell from development to homeostasis. Therefore, transcription factors play an important role in generating and regulating behavior. Here, we describe the transcription factors, the pathways they regulate, and the neurons that drive chemosensation, mechanosensation, thermosensation, osmolarity sensing, complex, and sex-specific behaviors in the animal model Caenorhabditis elegans. We also discuss the current limitations in our knowledge, particularly our minimal understanding of how transcription factors contribute to the adaptive behavioral responses that are necessary for organismal survival.
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27
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Glenwinkel L, Taylor SR, Langebeck-Jensen K, Pereira L, Reilly MB, Basavaraju M, Rafi I, Yemini E, Pocock R, Sestan N, Hammarlund M, Miller DM, Hobert O. In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system. eLife 2021; 10:e64906. [PMID: 34165430 PMCID: PMC8225391 DOI: 10.7554/elife.64906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The generation of the enormous diversity of neuronal cell types in a differentiating nervous system entails the activation of neuron type-specific gene batteries. To examine the regulatory logic that controls the expression of neuron type-specific gene batteries, we interrogate single cell expression profiles of all 118 neuron classes of the Caenorhabditis elegans nervous system for the presence of DNA binding motifs of 136 neuronally expressed C. elegans transcription factors. Using a phylogenetic footprinting pipeline, we identify cis-regulatory motif enrichments among neuron class-specific gene batteries and we identify cognate transcription factors for 117 of the 118 neuron classes. In addition to predicting novel regulators of neuronal identities, our nervous system-wide analysis at single cell resolution supports the hypothesis that many transcription factors directly co-regulate the cohort of effector genes that define a neuron type, thereby corroborating the concept of so-called terminal selectors of neuronal identity. Our analysis provides a blueprint for how individual components of an entire nervous system are genetically specified.
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Affiliation(s)
- Lori Glenwinkel
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | | | - Laura Pereira
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Manasa Basavaraju
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Roger Pocock
- Biotech Research and Innovation Centre, University of CopenhagenCopenhagenDenmark
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash UniversityMelbourneAustralia
| | - Nenad Sestan
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Marc Hammarlund
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
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28
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H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity. Nat Cell Biol 2021; 23:1163-1175. [PMID: 34737442 PMCID: PMC8572725 DOI: 10.1038/s41556-021-00776-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/17/2021] [Indexed: 01/05/2023]
Abstract
The developmental role of histone H3K9 methylation (H3K9me), which typifies heterochromatin, remains unclear. In Caenorhabditis elegans, loss of H3K9me leads to a highly divergent upregulation of genes with tissue and developmental-stage specificity. During development H3K9me is lost from differentiated cell type-specific genes and gained at genes expressed in earlier developmental stages or other tissues. The continuous deposition of H3K9me2 by the SETDB1 homolog MET-2 after terminal differentiation is necessary to maintain repression. In differentiated tissues, H3K9me ensures silencing by restricting the activity of a defined set of transcription factors at promoters and enhancers. Increased chromatin accessibility following the loss of H3K9me is neither sufficient nor necessary to drive transcription. Increased ATAC-seq signal and gene expression correlate at a subset of loci positioned away from the nuclear envelope, while derepressed genes at the nuclear periphery remain poorly accessible despite being transcribed. In conclusion, H3K9me deposition can confer tissue-specific gene expression and maintain the integrity of terminally differentiated muscle by restricting transcription factor activity.
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29
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Eurmsirilerd E, Maduro MF. Evolution of Developmental GATA Factors in Nematodes. J Dev Biol 2020; 8:jdb8040027. [PMID: 33207804 PMCID: PMC7712238 DOI: 10.3390/jdb8040027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.
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Affiliation(s)
- Ethan Eurmsirilerd
- Undergraduate Program in Biology, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA;
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Morris F. Maduro
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Correspondence:
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30
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Elliott KH, Chen X, Salomone J, Chaturvedi P, Schultz PA, Balchand SK, Servetas JD, Zuniga A, Zeller R, Gebelein B, Weirauch MT, Peterson KA, Brugmann SA. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. eLife 2020; 9:e56450. [PMID: 33006313 PMCID: PMC7556880 DOI: 10.7554/elife.56450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.
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Affiliation(s)
- Kelsey H Elliott
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Joseph Salomone
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
- Medical-Scientist Training Program, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Preston A Schultz
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Sai K Balchand
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Matthew T Weirauch
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Shriners Children’s HospitalCincinnatiUnited States
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31
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A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae. Nat Commun 2020; 11:4947. [PMID: 33009392 PMCID: PMC7532196 DOI: 10.1038/s41467-020-18744-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/08/2020] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas syringae is a Gram-negative and model pathogenic bacterium that causes plant diseases worldwide. Here, we set out to identify binding motifs for all 301 annotated transcription factors (TFs) of P. syringae using HT-SELEX. We successfully identify binding motifs for 100 TFs. We map functional interactions between the TFs and their targets in virulence-associated pathways, and validate many of these interactions and functions using additional methods such as ChIP-seq, electrophoretic mobility shift assay (EMSA), RT-qPCR, and reporter assays. Our work identifies 25 virulence-associated master regulators, 14 of which had not been characterized as TFs before. The authors set out to identify binding motifs for all 301 transcription factors of a plant pathogenic bacterium, Pseudomonas syringae, using HT-SELEX. They successfully identify binding motifs for 100 transcription factors, infer their binding sites on the genome, and validate the predicted interactions and functions.
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32
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Charest J, Daniele T, Wang J, Bykov A, Mandlbauer A, Asparuhova M, Röhsner J, Gutiérrez-Pérez P, Cochella L. Combinatorial Action of Temporally Segregated Transcription Factors. Dev Cell 2020; 55:483-499.e7. [PMID: 33002421 PMCID: PMC7704111 DOI: 10.1016/j.devcel.2020.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 09/01/2020] [Indexed: 01/05/2023]
Abstract
Combinatorial action of transcription factors (TFs) with partially overlapping expression is a widespread strategy to generate novel gene-expression patterns and, thus, cellular diversity. Known mechanisms underlying combinatorial activity require co-expression of TFs within the same cell. Here, we describe the mechanism by which two TFs that are never co-expressed generate a new, intersectional expression pattern in C. elegans embryos: lineage-specific priming of a gene by a transiently expressed TF generates a unique intersection with a second TF acting on the same gene four cell divisions later; the second TF is expressed in multiple cells but only activates transcription in those where priming occurred. Early induction of active transcription is necessary and sufficient to establish a competent state, maintained by broadly expressed regulators in the absence of the initial trigger. We uncover additional cells diversified through this mechanism. Our findings define a mechanism for combinatorial TF activity with important implications for generation of cell-type diversity. Lineage-specific priming enables asymmetric gene expression in L/R neuron pairs Transient, lineage-specific TFs prime a locus for later activation by a bilateral TF An early active transcriptional state is necessary and sufficient for priming Maintenance of asymmetric primed state occurs in a symmetric regulatory environment
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Affiliation(s)
- Julien Charest
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Thomas Daniele
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Aleksandr Bykov
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Ariane Mandlbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Mila Asparuhova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Josef Röhsner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Paula Gutiérrez-Pérez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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33
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Lancaster BR, McGhee JD. How affinity of the ELT-2 GATA factor binding to cis-acting regulatory sites controls Caenorhabditis elegans intestinal gene transcription. Development 2020; 147:dev190330. [PMID: 32586978 PMCID: PMC7390640 DOI: 10.1242/dev.190330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022]
Abstract
We define a quantitative relationship between the affinity with which the intestine-specific GATA factor ELT-2 binds to cis-acting regulatory motifs and the resulting transcription of asp-1, a target gene representative of genes involved in Caenorhabditis elegans intestine differentiation. By establishing an experimental system that allows unknown parameters (e.g. the influence of chromatin) to effectively cancel out, we show that levels of asp-1 transcripts increase monotonically with increasing binding affinity of ELT-2 to variant promoter TGATAA sites. The shape of the response curve reveals that the product of the unbound ELT-2 concentration in vivo [i.e. (ELT-2free) or ELT-2 'activity'] and the largest ELT-XXTGATAAXX association constant (Kmax) lies between five and ten. We suggest that this (unitless) product [Kmax×(ELT-2free) or the equivalent product for any other transcription factor] provides an important quantitative descriptor of transcription-factor/regulatory-motif interaction in development, evolution and genetic disease. A more complicated model than simple binding affinity is necessary to explain the fact that ELT-2 appears to discriminate in vivo against equal-affinity binding sites that contain AGATAA instead of TGATAA.
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Affiliation(s)
- Brett R Lancaster
- Department of Biochemistry and Molecular Biology, University of Calgary, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Calgary, Alberta T2N 4N1, Canada
| | - James D McGhee
- Department of Biochemistry and Molecular Biology, University of Calgary, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Calgary, Alberta T2N 4N1, Canada
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34
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Mueller AL, Corbi-Verge C, Giganti DO, Ichikawa DM, Spencer JM, MacRae M, Garton M, Kim PM, Noyes MB. The geometric influence on the Cys2His2 zinc finger domain and functional plasticity. Nucleic Acids Res 2020; 48:6382-6402. [PMID: 32383734 PMCID: PMC7293014 DOI: 10.1093/nar/gkaa291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/07/2020] [Accepted: 04/20/2020] [Indexed: 11/25/2022] Open
Abstract
The Cys2His2 zinc finger is the most common DNA-binding domain expanding in metazoans since the fungi human split. A proposed catalyst for this expansion is an arms race to silence transposable elements yet it remains poorly understood how this domain is able to evolve the required specificities. Likewise, models of its DNA binding specificity remain error prone due to a lack of understanding of how adjacent fingers influence each other's binding specificity. Here, we use a synthetic approach to exhaustively investigate binding geometry, one of the dominant influences on adjacent finger function. By screening over 28 billion protein–DNA interactions in various geometric contexts we find the plasticity of the most common natural geometry enables more functional amino acid combinations across all targets. Further, residues that define this geometry are enriched in genomes where zinc fingers are prevalent and specificity transitions would be limited in alternative geometries. Finally, these results demonstrate an exhaustive synthetic screen can produce an accurate model of domain function while providing mechanistic insight that may have assisted in the domains expansion.
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Affiliation(s)
- April L Mueller
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - David O Giganti
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David M Ichikawa
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jeffrey M Spencer
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mark MacRae
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Michael Garton
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Marcus B Noyes
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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35
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Loss of an H3K9me anchor rescues laminopathy-linked changes in nuclear organization and muscle function in an Emery-Dreifuss muscular dystrophy model. Genes Dev 2020; 34:560-579. [PMID: 32139421 PMCID: PMC7111258 DOI: 10.1101/gad.332213.119] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/14/2020] [Indexed: 12/30/2022]
Abstract
In this study, Harr et al. use C. elegans to investigate the consequences of a missense mutation (Y45C) in lamin A (encoded by LMNA) found in the human Emery-Dreifuss muscular dystrophy (EDMD) syndrome. Using muscle-specific emerin Dam-ID and other in vivo approaches, the authors report that they were able to counteract the dominant muscle-specific defects provoked by LMNA mutation by the ablation of a lamin-associated H3K9me anchor, suggesting a novel therapeutic pathway for treating EDMD. Mutations in the nuclear structural protein lamin A produce rare, tissue-specific diseases called laminopathies. The introduction of a human Emery-Dreifuss muscular dystrophy (EDMD)-inducing mutation into the C. elegans lamin (LMN-Y59C), recapitulates many muscular dystrophy phenotypes, and correlates with hyper-sequestration of a heterochromatic array at the nuclear periphery in muscle cells. Using muscle-specific emerin Dam-ID in worms, we monitored the effects of the mutation on endogenous chromatin. An increased contact with the nuclear periphery along chromosome arms, and an enhanced release of chromosomal centers, coincided with the disease phenotypes of reduced locomotion and compromised sarcomere integrity. The coupling of the LMN-Y59C mutation with the ablation of CEC-4, a chromodomain protein that anchors H3K9-methylated chromatin at the nuclear envelope (NE), suppressed the muscle-associated disease phenotypes. Deletion of cec-4 also rescued LMN-Y59C-linked alterations in chromatin organization and some changes in transcription. Sequences that changed position in the LMN-Y59C mutant, are enriched for E2F (EFL-2)-binding sites, consistent with previous studies suggesting that altered Rb-E2F interaction with lamin A may contribute to muscle dysfunction. In summary, we were able to counteract the dominant muscle-specific defects provoked by LMNA mutation by the ablation of a lamin-associated H3K9me anchor, suggesting a novel therapeutic pathway for EDMD.
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36
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Rozanov L, Ravichandran M, Grigolon G, Zanellati MC, Mansfeld J, Zarse K, Barzilai N, Atzmon G, Fischer F, Ristow M. Redox-mediated regulation of aging and healthspan by an evolutionarily conserved transcription factor HLH-2/Tcf3/E2A. Redox Biol 2020; 32:101448. [PMID: 32203922 PMCID: PMC7096751 DOI: 10.1016/j.redox.2020.101448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/02/2020] [Indexed: 02/08/2023] Open
Abstract
Physiological aging is a complex process, influenced by a plethora of genetic and environmental factors. While being far from fully understood, a number of common aging hallmarks have been elucidated in recent years. Among these, transcriptomic alterations are hypothesized to represent a crucial early manifestation of aging. Accordingly, several transcription factors (TFs) have previously been identified as important modulators of lifespan in evolutionarily distant model organisms. Based on a set of TFs conserved between nematodes, zebrafish, mice, and humans, we here perform a RNA interference (RNAi) screen in C. elegans to discover evolutionarily conserved TFs impacting aging. We identify a basic helix-loop-helix TF, named HLH-2 in nematodes (Tcf3/E2A in mammals), to exert a pronounced lifespan-extending effect in C. elegans upon impairment. We further show that its impairment impacts cellular energy metabolism, increases parameters of healthy aging, and extends nematodal lifespan in a ROS-dependent manner. We then identify arginine kinases, orthologues of mammalian creatine kinases, as a target of HLH-2 transcriptional regulation, serving to mediate the healthspan-promoting effects observed upon impairment of hlh-2 expression. Consistently, HLH-2 is shown to epistatically interact with core components of known lifespan-regulating pathways, i.e. AAK-2/AMPK and LET-363/mTOR, as well as the aging-related TFs SKN-1/Nrf2 and HSF-1. Lastly, single-nucelotide polymorphisms (SNPs) in Tcf3/E2A are associated with exceptional longevity in humans. Together, these findings demonstrate that HLH-2 regulates energy metabolism via arginine kinases and thereby affects the aging phenotype dependent on ROS-signaling and established canonical effectors. A C. elegans RNAi screen identifies conserved aging-related transcription factors. Impairment of transcription factor hlh-2 has the most pronounced effect on lifespan. C. elegans HLH-2 affects cellular energy homeostasis and redox signaling. HLH-2 modulates arginine kinase to interact with downstream longevity pathways. Polymorphisms (SNPs) in the hlh-2 orthologue Tcf3/E2A are linked to human longevity.
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Affiliation(s)
- Leonid Rozanov
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Meenakshi Ravichandran
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Maria Clara Zanellati
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Johannes Mansfeld
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Nir Barzilai
- Albert Einstein College of Medicine, Departments of Genetics and of Medicine, Bronx, NY, 10461, USA
| | - Gil Atzmon
- Albert Einstein College of Medicine, Departments of Genetics and of Medicine, Bronx, NY, 10461, USA; University of Haifa, Faculty of Natural Sciences, Haifa, 3498838, Israel
| | - Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.
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37
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Leyva-Díaz E, Masoudi N, Serrano-Saiz E, Glenwinkel L, Hobert O. Brn3/POU-IV-type POU homeobox genes-Paradigmatic regulators of neuronal identity across phylogeny. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e374. [PMID: 32012462 DOI: 10.1002/wdev.374] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/18/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
One approach to understand the construction of complex systems is to investigate whether there are simple design principles that are commonly used in building such a system. In the context of nervous system development, one may ask whether the generation of its highly diverse sets of constituents, that is, distinct neuronal cell types, relies on genetic mechanisms that share specific common features. Specifically, are there common patterns in the function of regulatory genes across different neuron types and are those regulatory mechanisms not only used in different parts of one nervous system, but are they conserved across animal phylogeny? We address these questions here by focusing on one specific, highly conserved and well-studied regulatory factor, the POU homeodomain transcription factor UNC-86. Work over the last 30 years has revealed a common and paradigmatic theme of unc-86 function throughout most of the neuron types in which Caenorhabditis elegans unc-86 is expressed. Apart from its role in preventing lineage reiterations during development, UNC-86 operates in combination with distinct partner proteins to initiate and maintain terminal differentiation programs, by coregulating a vast array of functionally distinct identity determinants of specific neuron types. Mouse orthologs of unc-86, the Brn3 genes, have been shown to fulfill a similar function in initiating and maintaining neuronal identity in specific parts of the mouse brain and similar functions appear to be carried out by the sole Drosophila ortholog, Acj6. The terminal selector function of UNC-86 in many different neuron types provides a paradigm for neuronal identity regulation across phylogeny. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Invertebrate Organogenesis > Worms Nervous System Development > Vertebrates: Regional Development.
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Affiliation(s)
- Eduardo Leyva-Díaz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
| | - Neda Masoudi
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
| | | | - Lori Glenwinkel
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
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38
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Garrigues JM, Tsu BV, Daugherty MD, Pasquinelli AE. Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. eLife 2019; 8:51139. [PMID: 31825311 PMCID: PMC6927752 DOI: 10.7554/elife.51139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Heat Shock Factor 1 (HSF-1) is a key regulator of the heat shock response (HSR). Upon heat shock, HSF-1 binds well-conserved motifs, called Heat Shock Elements (HSEs), and drives expression of genes important for cellular protection during this stress. Remarkably, we found that substantial numbers of HSEs in multiple Caenorhabditis species reside within Helitrons, a type of DNA transposon. Consistent with Helitron-embedded HSEs being functional, upon heat shock they display increased HSF-1 and RNA polymerase II occupancy and up-regulation of nearby genes in C. elegans. Interestingly, we found that different genes appear to be incorporated into the HSR by species-specific Helitron insertions in C. elegans and C. briggsae and by strain-specific insertions among different wild isolates of C. elegans. Our studies uncover previously unidentified targets of HSF-1 and show that Helitron insertions are responsible for rewiring and diversifying the Caenorhabditis HSR.
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Affiliation(s)
- Jacob M Garrigues
- Division of Biology, University of California, San Diego, San Diego, United States
| | - Brian V Tsu
- Division of Biology, University of California, San Diego, San Diego, United States
| | - Matthew D Daugherty
- Division of Biology, University of California, San Diego, San Diego, United States
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, San Diego, United States
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39
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Levine A, Grushko D, Cohen E. Gene expression modulation by the linker of nucleoskeleton and cytoskeleton complex contributes to proteostasis. Aging Cell 2019; 18:e13047. [PMID: 31576648 PMCID: PMC6826161 DOI: 10.1111/acel.13047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/19/2019] [Accepted: 09/08/2019] [Indexed: 01/08/2023] Open
Abstract
Cellular mechanisms that act in concert to maintain protein homeostasis (proteostasis) are vital for organismal functionality and survival. Nevertheless, subsets of aggregation-prone proteins form toxic aggregates (proteotoxicity) that in some cases, underlie the development of neurodegenerative diseases. Proteotoxic aggregates are often deposited in the vicinity of the nucleus, a process that is cytoskeleton-dependent. Accordingly, cytoskeletal dysfunction contributes to pathological hallmarks of various neurodegenerative diseases. Here, we asked whether the linker of nucleoskeleton and cytoskeleton (LINC) complex, which bridges these filaments across the nuclear envelope, is needed for the maintenance of proteostasis. Employing model nematodes, we discovered that knocking down LINC components impairs the ability of the worm to cope with proteotoxicity. Knocking down anc-1, which encodes a key component of the LINC complex, modulates the expression of transcription factors and E3 ubiquitin ligases, thereby affecting the rates of protein ubiquitination and impairing proteasome-mediated protein degradation. Our results establish a link between the LINC complex, protein degradation, and neurodegeneration-associated proteotoxicity.
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Affiliation(s)
- Amir Levine
- Department of Biochemistry and Molecular Biology The Institute for Medical Research Israel‐Canada The Hebrew University of Jerusalem Jerusalem Israel
| | - Danielle Grushko
- Department of Biochemistry and Molecular Biology The Institute for Medical Research Israel‐Canada The Hebrew University of Jerusalem Jerusalem Israel
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology The Institute for Medical Research Israel‐Canada The Hebrew University of Jerusalem Jerusalem Israel
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40
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Lee J, Taylor CA, Barnes KM, Shen A, Stewart EV, Chen A, Xiang YK, Bao Z, Shen K. A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes. eLife 2019; 8:e46703. [PMID: 31386623 PMCID: PMC6684318 DOI: 10.7554/elife.46703] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular differentiation requires both activation of target cell transcriptional programs and repression of non-target cell programs. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages from previously differentiated epithelial cells, including a neuron generated by a developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single-cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. ZTF-11 functions together with the MuvB corepressor complex to suppress the activation of non-neuronal genes in neurons. These results dovetail with the ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes.
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Affiliation(s)
- Joo Lee
- Department of BiochemistryStanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Caitlin A Taylor
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
| | | | - Ao Shen
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | | | - Allison Chen
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Yang K Xiang
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | - Zhirong Bao
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
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41
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Booth LN, Maures TJ, Yeo RW, Tantilert C, Brunet A. Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes. eLife 2019; 8:46418. [PMID: 31282863 PMCID: PMC6697445 DOI: 10.7554/elife.46418] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/02/2019] [Indexed: 12/19/2022] Open
Abstract
Sexual interactions have a potent influence on health in several species, including mammals. Previous work in C. elegans identified strategies used by males to accelerate the demise of the opposite sex (hermaphrodites). But whether hermaphrodites evolved counter-strategies against males remains unknown. Here we discover that young C. elegans hermaphrodites are remarkably resistant to brief sexual encounters with males, whereas older hermaphrodites succumb prematurely. Surprisingly, it is not their youthfulness that protects young hermaphrodites, but the fact that they have self-sperm. The beneficial effect of self-sperm is mediated by a sperm-sensing pathway acting on the soma rather than by fertilization. Activation of this pathway in females triggers protection from the negative impact of males. Interestingly, the role of self-sperm in protecting against the detrimental effects of males evolved independently in hermaphroditic nematodes. Endogenous strategies to delay the negative effect of mating may represent a key evolutionary innovation to maximize reproductive success. A nematode worm known as Caenorhabditis elegans is often used in the laboratory to study how animals grow and develop. There are two types of C. elegans worm: hermaphrodite individuals produce both female sex cells (eggs) and male sex cells (sperm), while male individuals only produce sperm. The hermaphrodite worms are able to reproduce without mating with another worm, allowing populations of C. elegans to grow rapidly when they are living in favorable conditions. However, when the hermaphrodites do mate with males they tend to produce more offspring. These offspring are also usually healthier because they receive a mixture of genetic material from two different parents. Although mating is beneficial for the survival of a species it can also harm an individual animal. Previous studies have shown that mating with male worms can accelerate aging of hermaphrodite worms and cause premature death. However, it remained unclear whether hermaphrodite worms have evolved any mechanisms to protect themselves after mating with a male. To address this question, Booth et al. used genetic techniques to study the lifespans of hermaphrodite worms. The experiments found that the hermaphrodites’ own sperm (known as self-sperm) regulated a sperm-sensing signaling pathway that protected them from the negative impact of mating with males. Hermaphrodites with self-sperm that mated with males lived for a similar length of time as hermaphrodites that did not mate. On the other hand, hermaphrodites that did not have self-sperm (because they were older or had a genetic mutation) had shorter lifespans after mating than worms that did not mate. Modulating the sperm-sensing signaling pathway in worms that lacked self-sperm was sufficient to protect them from the negative effects of mating with males. Further experiments found that the hermaphrodites of another nematode worm called C. briggsae – which evolved self-sperm independently of C. elegans – also protected themselves from the negative effects of mating with males in a similar way. This suggests that other animals may also have evolved similar mechanisms to protect themselves from harm when mating. A separate study by Shi et al. has found that the beneficial effects of self-sperm are mediated by a pathway linked to longevity that also exists in mammals. The results of both investigations combined suggest possible avenues for future research into the complex relationship between health, longevity, and reproduction.
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Affiliation(s)
- Lauren N Booth
- Department of Genetics, Stanford University, Stanford, United States
| | - Travis J Maures
- Department of Genetics, Stanford University, Stanford, United States
| | - Robin W Yeo
- Department of Genetics, Stanford University, Stanford, United States
| | - Cindy Tantilert
- Department of Genetics, Stanford University, Stanford, United States
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, United States.,Glenn Laboratories for the Biology of Aging at Stanford University, Stanford, United States
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42
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Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR. Similarity regression predicts evolution of transcription factor sequence specificity. Nat Genet 2019; 51:981-989. [PMID: 31133749 DOI: 10.1038/s41588-019-0411-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/04/2019] [Indexed: 11/09/2022]
Abstract
Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs in all sequenced eukaryotic genomes. There is ongoing controversy regarding the degree of motif diversification among related species that is, in part, because of uncertainty in motif prediction methods. Here we describe similarity regression, a significantly improved method for predicting motifs, which we use to update and expand the Cis-BP database. Similarity regression inherently quantifies TF motif evolution, and shows that previous claims of near-complete conservation of motifs between human and Drosophila are inflated, with nearly half of the motifs in each species absent from the other, largely due to extensive divergence in C2H2 zinc finger proteins. We conclude that diversification in DNA-binding motifs is pervasive, and present a new tool and updated resource to study TF diversity and gene regulation across eukaryotes.
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Affiliation(s)
- Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ally W H Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Sasse
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gwendolyn Cowley
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mihai Albu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Mark X Caddick
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Canadian Institutes For Advanced Research (CIFAR) Artificial Intelligence Chair, Vector Institute, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Matthew T Weirauch
- Divisions of Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. .,CIFAR, Toronto, Ontario, Canada.
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43
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Cabianca DS, Muñoz-Jiménez C, Kalck V, Gaidatzis D, Padeken J, Seeber A, Askjaer P, Gasser SM. Active chromatin marks drive spatial sequestration of heterochromatin in C. elegans nuclei. Nature 2019; 569:734-739. [PMID: 31118512 DOI: 10.1038/s41586-019-1243-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
The execution of developmental programs of gene expression requires an accurate partitioning of the genome into subnuclear compartments, with active euchromatin enriched centrally and silent heterochromatin at the nuclear periphery1. The existence of degenerative diseases linked to lamin A mutations suggests that perinuclear binding of chromatin contributes to cell-type integrity2,3. The methylation of lysine 9 of histone H3 (H3K9me) characterizes heterochromatin and mediates both transcriptional repression and chromatin anchoring at the inner nuclear membrane4. In Caenorhabditis elegans embryos, chromodomain protein CEC-4 bound to the inner nuclear membrane tethers heterochromatin through H3K9me3,5, whereas in differentiated tissues, a second heterochromatin-sequestering pathway is induced. Here we use an RNA interference screen in the cec-4 background and identify MRG-1 as a broadly expressed factor that is necessary for this second chromatin anchor in intestinal cells. However, MRG-1 is exclusively bound to euchromatin, suggesting that it acts indirectly. Heterochromatin detachment in double mrg-1; cec-4 mutants is rescued by depleting the histone acetyltransferase CBP-1/p300 or the transcription factor ATF-8, a member of the bZIP family (which is known to recruit CBP/p300). Overexpression of CBP-1 in cec-4 mutants is sufficient to delocalize heterochromatin in an ATF-8-dependent manner. CBP-1 and H3K27ac levels increase in heterochromatin upon mrg-1 knockdown, coincident with delocalization. This suggests that the spatial organization of chromatin in C. elegans is regulated both by the direct perinuclear attachment of silent chromatin, and by an active retention of CBP-1/p300 in euchromatin. The two pathways contribute differentially in embryos and larval tissues, with CBP-1 sequestration by MRG-1 having a major role in differentiated cells.
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Affiliation(s)
- Daphne S Cabianca
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Celia Muñoz-Jiménez
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Véronique Kalck
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland.,Center for Advanced Imaging, Harvard University, Cambridge, MA, USA
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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Tzur YB, Winter E, Gao J, Hashimshony T, Yanai I, Colaiácovo MP. Spatiotemporal Gene Expression Analysis of the Caenorhabditis elegans Germline Uncovers a Syncytial Expression Switch. Genetics 2018; 210:587-605. [PMID: 30093412 PMCID: PMC6216576 DOI: 10.1534/genetics.118.301315] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/03/2018] [Indexed: 11/18/2022] Open
Abstract
Developmental programs are executed by tightly controlled gene regulatory pathways. Here, we combined the unique sample retrieval capacity afforded by laser capture microscopy with analysis of mRNA abundance by CEL-Seq (cell expression by linear amplification and sequencing) to generate a spatiotemporal gene expression map of the Caenorhabditis elegans syncytial germline from adult hermaphrodites and males. We found that over 6000 genes exhibit spatiotemporally dynamic expression patterns throughout the hermaphrodite germline, with two dominant groups of genes exhibiting reciprocal shifts in expression at late pachytene during meiotic prophase I. We found a strong correlation between restricted spatiotemporal expression and known developmental and cellular processes, indicating that these gene expression changes may be an important driver of germ cell progression. Analysis of the male gonad revealed a shift in gene expression at early pachytene and upregulation of subsets of genes following the meiotic divisions, specifically in early and late spermatids, mostly transcribed from the X chromosome. We observed that while the X chromosome is silenced throughout the first half of the gonad, some genes escape this control and are highly expressed throughout the germline. Although we found a strong correlation between the expression of genes corresponding to CSR-1-interacting 22G-RNAs during germ cell progression, we also found that a large fraction of genes may bypass the need for CSR-1-mediated germline licensing. Taken together, these findings suggest the existence of mechanisms that enable a shift in gene expression during prophase I to promote germ cell progression.
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Affiliation(s)
- Yonatan B Tzur
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem 91904, Israel
| | - Eitan Winter
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Jinmin Gao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Tamar Hashimshony
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Itai Yanai
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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Non-proteolytic activity of 19S proteasome subunit RPT-6 regulates GATA transcription during response to infection. PLoS Genet 2018; 14:e1007693. [PMID: 30265660 PMCID: PMC6179307 DOI: 10.1371/journal.pgen.1007693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/10/2018] [Accepted: 09/13/2018] [Indexed: 11/19/2022] Open
Abstract
GATA transcription factors play a crucial role in the regulation of immune functions across metazoans. In Caenorhabditis elegans, the GATA transcription factor ELT-2 is involved in the control of not only infections but also recovery after an infection. We identified RPT-6, part of the 19S proteasome subunit, as an ELT-2 binding partner that is required for the proper expression of genes required for both immunity against bacterial infections and recovery after infection. We found that the intact ATPase domain of RPT-6 is required for the interaction and that inhibition of rpt-6 affected the expression of ELT-2-controlled genes, preventing the appropriate immune response against Pseudomonas aeruginosa and recovery from infection by the pathogen. Further studies indicated that SKN-1, which is an Nrf transcription factor involved in the response to oxidative stress and infection, is activated by inhibition of rpt-6. Our results indicate that RPT-6 interacts with ELT-2 in vivo to control the expression of immune genes in a manner that is likely independent of the proteolytic activity of the proteasome. The conserved GATA transcription factor ELT-2 plays an important role in the control of genes required for both defense and recovery from infection. We show that RPT-6, a component of the 19S subunit, physically interacts with ELT-2 in vivo, controlling the expression of ELT-2-dependent genes and the response of the nematode Caenorhabditis elegans to bacterial infection. The proteolytic activity of the proteasome has surfaced as a key regulator of gene expression, but our results provide evidence indicating that a non-canonical activity of the 26S proteasome subunit plays an important role in the control of gene expression during the response to bacterial infection.
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FACT Sets a Barrier for Cell Fate Reprogramming in Caenorhabditis elegans and Human Cells. Dev Cell 2018; 46:611-626.e12. [PMID: 30078731 PMCID: PMC6137076 DOI: 10.1016/j.devcel.2018.07.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 05/08/2018] [Accepted: 07/03/2018] [Indexed: 01/04/2023]
Abstract
The chromatin regulator FACT (facilitates chromatin transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using Caenorhabditis elegans, we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACT's role as a barrier to cell fate conversion is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts. Such activity is unexpected because FACT is known as a positive regulator of gene expression, and previously described reprogramming barriers typically repress gene expression. While FACT depletion in human fibroblasts results in decreased expression of many genes, a number of FACT-occupied genes, including reprogramming-promoting factors, show increased expression upon FACT depletion, suggesting a repressive function of FACT. Our findings identify FACT as a cellular reprogramming barrier in C. elegans and humans, revealing an evolutionarily conserved mechanism for cell fate protection.
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47
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Abete-Luzi P, Eisenmann DM. Regulation ofC. elegansL4 cuticle collagen genes by the heterochronic protein LIN-29. Genesis 2018; 56. [DOI: 10.1002/dvg.23106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/12/2018] [Accepted: 03/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Patricia Abete-Luzi
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland 21250
| | - David M. Eisenmann
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland 21250
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48
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Ruan S, Swamidass SJ, Stormo GD. BEESEM: estimation of binding energy models using HT-SELEX data. Bioinformatics 2018; 33:2288-2295. [PMID: 28379348 DOI: 10.1093/bioinformatics/btx191] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/30/2017] [Indexed: 12/24/2022] Open
Abstract
Motivation Characterizing the binding specificities of transcription factors (TFs) is crucial to the study of gene expression regulation. Recently developed high-throughput experimental methods, including protein binding microarrays (PBM) and high-throughput SELEX (HT-SELEX), have enabled rapid measurements of the specificities for hundreds of TFs. However, few studies have developed efficient algorithms for estimating binding motifs based on HT-SELEX data. Also the simple method of constructing a position weight matrix (PWM) by comparing the frequency of the preferred sequence with single-nucleotide variants has the risk of generating motifs with higher information content than the true binding specificity. Results We developed an algorithm called BEESEM that builds on a comprehensive biophysical model of protein-DNA interactions, which is trained using the expectation maximization method. BEESEM is capable of selecting the optimal motif length and calculating the confidence intervals of estimated parameters. By comparing BEESEM with the published motifs estimated using the same HT-SELEX data, we demonstrate that BEESEM provides significant improvements. We also evaluate several motif discovery algorithms on independent PBM and ChIP-seq data. BEESEM provides significantly better fits to in vitro data, but its performance is similar to some other methods on in vivo data under the criterion of the area under the receiver operating characteristic curve (AUROC). This highlights the limitations of the purely rank-based AUROC criterion. Using quantitative binding data to assess models, however, demonstrates that BEESEM improves on prior models. Availability and Implementation Freely available on the web at http://stormo.wustl.edu/resources.html . Contact stormo@wustl.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis 63110, USA
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49
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Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston RH. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics 2018; 208:937-949. [PMID: 29284660 PMCID: PMC5844342 DOI: 10.1534/genetics.117.300657] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022] Open
Abstract
To develop a catalog of regulatory sites in two major model organisms, Drosophila melanogaster and Caenorhabditis elegans, the modERN (model organism Encyclopedia of Regulatory Networks) consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecessor, modENCODE (Model Organism ENCyclopedia Of DNA Elements), we now have data for 262 TFs identifying 1.23 M sites in the fly genome and 217 TFs identifying 0.67 M sites in the worm genome. Because sites from different TFs are often overlapping and tightly clustered, they fall into 91,011 and 59,150 regions in the fly and worm, respectively, and these binding sites span as little as 8.7 and 5.8 Mb in the two organisms. Clusters with large numbers of sites (so-called high occupancy target, or HOT regions) predominantly associate with broadly expressed genes, whereas clusters containing sites from just a few factors are associated with genes expressed in tissue-specific patterns. All of the strains expressing GFP-tagged TFs are available at the stock centers, and the chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center and also through a simple interface (http://epic.gs.washington.edu/modERN/) that facilitates rapid accessibility of processed data sets. These data will facilitate a vast number of scientific inquiries into the function of individual TFs in key developmental, metabolic, and defense and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks and globally across the life spans of these two key model organisms.
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Affiliation(s)
- Michelle M Kudron
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Alec Victorsen
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Louis Gevirtzman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - William W Fisher
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Dionne Vafeados
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Matt Kirkey
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Ann S Hammonds
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jeffery Gersch
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Haneen Ammouri
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Martha L Wall
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Jennifer Moran
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - David Steffen
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Matt Szynkarek
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Samantha Seabrook-Sturgis
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Nader Jameel
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Madhura Kadaba
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Jaeda Patton
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Robert Terrell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Mitch Corson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Timothy J Durham
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Soo Park
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Swapna Samanta
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Mei Han
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Koon-Kiu Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Susan E Celniker
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kevin P White
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Lijia Ma
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
- Department of Computer Science, Yale University, New Haven, Connecticut 06520
| | - Valerie Reinke
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Robert H Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
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50
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Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 2018; 32:202-223. [PMID: 29491135 PMCID: PMC5859963 DOI: 10.1101/gad.310367.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.
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Affiliation(s)
- Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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