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Stevenson ZC, Moerdyk-Schauwecker MJ, Banse SA, Patel DS, Lu H, Phillips PC. High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS). eLife 2023; 12:RP84831. [PMID: 37401921 PMCID: PMC10328503 DOI: 10.7554/elife.84831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.
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Affiliation(s)
| | | | - Stephen A Banse
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
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2
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Bodofsky S, Liberatore K, Pioppo L, Lapadula D, Thompson L, Birnbaum S, McClung G, Kartik A, Clever S, Wightman B. A tissue-specific enhancer of the C. elegans nhr-67/tailless gene drives coordinated expression in uterine stem cells and the differentiated anchor cell. Gene Expr Patterns 2018; 30:71-81. [PMID: 30404043 PMCID: PMC6373727 DOI: 10.1016/j.gep.2018.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/27/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
Abstract
The nhr-67 nuclear receptor gene of Caenorhabditis elegans encodes the ortholog of the Drosophila tailless and vertebrate Tlx genes. In C. elegans, nhr-67 plays multiple roles in the development of the uterus during L2 and L3 larval stages. Four pre-VU cells are born in the L2 stage and form the precursor complement for the ventral surface of the mature uterus. One of the four pre-VU cells becomes the anchor cell (AC), which exits the cell cycle and differentiates, while the remaining three VU cells serve as stem cells that populate the ventral uterus. The nhr-67 gene functions in the development of both VU cell lineages and AC differentiation. Hypomorphic mutations in nhr-67 identify a 276bp region of the distal promoter that is sufficient to activate nhr-67 expression in pre-VU cells and the AC. The 276bp region includes 8 conserved potential cis-acting sites, including two E boxes and a nuclear receptor binding site. Mutational analysis demonstrates that the two E boxes are required for expression of nhr-67 in uterine precursor cells. The E/daughterless ortholog HLH-2 binds these sites as a homodimer, thus playing a central role in activating nhr-67 expression in the uterine precursors. At least two other binding activities, one of which may be the nhr-25/Ftz-F1 nuclear receptor transcription factor, also contribute to uterine precursor cell expression. The organization of the nhr-67 uterine precursor enhancer is compared to similar conserved enhancers in the egl-43, lag-2, and lin-3 genes, which contain the same HLH-2-binding E boxes and are similarly expressed in both pre-VU cells and the AC. This basic regulatory module allows the coordinated expression of at least four genes. Expression of genes in different cells that must coordinate to form a mature organ is driven by a shared set of promoter elements, which integrate multiple transcription factor inputs.
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Affiliation(s)
- Shari Bodofsky
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | | | - Lauren Pioppo
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - Dominic Lapadula
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - Lily Thompson
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - Susanna Birnbaum
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - George McClung
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - Akshara Kartik
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - Sheila Clever
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
| | - Bruce Wightman
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA.
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3
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Intron-specific patterns of divergence of lin-11 regulatory function in the C. elegans nervous system. Dev Biol 2017; 424:90-103. [DOI: 10.1016/j.ydbio.2017.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 12/19/2022]
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4
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Lussi YC, Mariani L, Friis C, Peltonen J, Myers TR, Krag C, Wong G, Salcini AE. Impaired removal of H3K4 methylation affects cell fate determination and gene transcription. Development 2016; 143:3751-3762. [PMID: 27578789 DOI: 10.1242/dev.139139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/20/2016] [Indexed: 01/30/2023]
Abstract
Methylation of histone 3 lysine 4 (H3K4) is largely associated with promoters and enhancers of actively transcribed genes and is finely regulated during development by the action of histone methyltransferases and demethylases. H3K4me3 demethylases of the KDM5 family have been previously implicated in development, but how the regulation of H3K4me3 level controls developmental processes is not fully established. Here, we show that the H3K4 demethylase RBR-2, the unique member of the KDM5 family in C. elegans, acts cell-autonomously and in a catalytic-dependent manner to control vulva precursor cells fate acquisition, by promoting the LIN-12/Notch pathway. Using genome-wide approaches, we show that RBR-2 reduces the H3K4me3 level at transcription start sites (TSSs) and in regions upstream of the TSSs, and acts both as a transcription repressor and activator. Analysis of the lin-11 genetic locus, a direct RBR-2 target gene required for vulva precursor cell fate acquisition, shows that RBR-2 controls the epigenetic signature of the lin-11 vulva-specific enhancer and lin-11 expression, providing in vivo evidence that RBR-2 can positively regulate transcription and cell fate acquisition by controlling enhancer activity.
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Affiliation(s)
- Yvonne C Lussi
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Luca Mariani
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Carsten Friis
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Juhani Peltonen
- A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Kuopio 70211, Finland
| | - Toshia R Myers
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Claudia Krag
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Garry Wong
- A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Kuopio 70211, Finland
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark .,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
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5
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Thomas CG, Wang W, Jovelin R, Ghosh R, Lomasko T, Trinh Q, Kruglyak L, Stein LD, Cutter AD. Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis. Genome Res 2015; 25:667-78. [PMID: 25783854 PMCID: PMC4417115 DOI: 10.1101/gr.187237.114] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/12/2015] [Indexed: 12/19/2022]
Abstract
The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.
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Affiliation(s)
- Cristel G Thomas
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Rajarshi Ghosh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tatiana Lomasko
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
| | - Quang Trinh
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
| | - Leonid Kruglyak
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Departments of Human Genetics and Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095, USA
| | - Lincoln D Stein
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Bioinformatics and Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
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Barrière A, Ruvinsky I. Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes. PLoS Genet 2014; 10:e1004435. [PMID: 24968346 PMCID: PMC4072541 DOI: 10.1371/journal.pgen.1004435] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/28/2014] [Indexed: 12/18/2022] Open
Abstract
Because there is considerable variation in gene expression even between closely related species, it is clear that gene regulatory mechanisms evolve relatively rapidly. Because primary sequence conservation is an unreliable proxy for functional conservation of cis-regulatory elements, their assessment must be carried out in vivo. We conducted a survey of cis-regulatory conservation between C. elegans and closely related species C. briggsae, C. remanei, C. brenneri, and C. japonica. We tested enhancers of eight genes from these species by introducing them into C. elegans and analyzing the expression patterns they drove. Our results support several notable conclusions. Most exogenous cis elements direct expression in the same cells as their C. elegans orthologs, confirming gross conservation of regulatory mechanisms. However, the majority of exogenous elements, when placed in C. elegans, also directed expression in cells outside endogenous patterns, suggesting functional divergence. Recurrent ectopic expression of different promoters in the same C. elegans cells may reflect biases in the directions in which expression patterns can evolve due to shared regulatory logic of coexpressed genes. The fact that, despite differences between individual genes, several patterns repeatedly emerged from our survey, encourages us to think that general rules governing regulatory evolution may exist and be discoverable.
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Affiliation(s)
- Antoine Barrière
- Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (AB); (IR)
| | - Ilya Ruvinsky
- Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (AB); (IR)
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Ranawade AV, Cumbo P, Gupta BP. Caenorhabditis elegans histone deacetylase hda-1 is required for morphogenesis of the vulva and LIN-12/Notch-mediated specification of uterine cell fates. G3 (BETHESDA, MD.) 2013; 3:1363-74. [PMID: 23797102 PMCID: PMC3737176 DOI: 10.1534/g3.113.006999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 06/02/2013] [Indexed: 01/03/2023]
Abstract
Chromatin modification genes play crucial roles in development and disease. In Caenorhabditis elegans, the class I histone deacetylase family member hda-1, a component of the nucleosome remodeling and deacetylation complex, has been shown to control cell proliferation. We recovered hda-1 in an RNA interference screen for genes involved in the morphogenesis of the egg-laying system. We found that hda-1 mutants have abnormal vulva morphology and vulval-uterine connections (i.e., no uterine-seam cell). We characterized the vulval defects by using cell fate-specific markers and found that hda-1 is necessary for the specification of all seven vulval cell types. The analysis of the vulval-uterine connection defect revealed that hda-1 is required for the differentiation of the gonadal anchor cell (AC), which in turn induces ventral uterine granddaughters to adopt π fates, leading to the formation of the uterine-seam cell. Consistent with these results, hda-1 is expressed in the vulva and AC. A search for hda-1 target genes revealed that fos-1 (fos proto-oncogene family) acts downstream of hda-1 in vulval cells, whereas egl-43 (evi1 proto-oncogene family) and nhr-67 (tailless homolog, NHR family) mediate hda-1 function in the AC. Furthermore, we showed that AC expression of hda-1 plays a crucial role in the regulation of the lin-12/Notch ligand lag-2 to specify π cell fates. These results demonstrate the pivotal role of hda-1 in the formation of the vulva and the vulval-uterine connection. Given that hda-1 homologs are conserved across the phyla, our findings are likely to provide a better understanding of HDAC1 function in development and disease.
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Affiliation(s)
| | - Philip Cumbo
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Bhagwati P. Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1 Canada
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8
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Cutter AD, Jovelin R, Dey A. Molecular hyperdiversity and evolution in very large populations. Mol Ecol 2013; 22:2074-95. [PMID: 23506466 PMCID: PMC4065115 DOI: 10.1111/mec.12281] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/24/2013] [Accepted: 01/29/2013] [Indexed: 02/06/2023]
Abstract
The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
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Sharanya D, Thillainathan B, Marri S, Bojanala N, Taylor J, Flibotte S, Moerman DG, Waterston RH, Gupta BP. Genetic control of vulval development in Caenorhabditis briggsae. G3 (BETHESDA, MD.) 2012; 2:1625-41. [PMID: 23275885 PMCID: PMC3516484 DOI: 10.1534/g3.112.004598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/19/2012] [Indexed: 01/23/2023]
Abstract
The nematode Caenorhabditis briggsae is an excellent model organism for the comparative analysis of gene function and developmental mechanisms. To study the evolutionary conservation and divergence of genetic pathways mediating vulva formation, we screened for mutations in C. briggsae that cause the egg-laying defective (Egl) phenotype. Here, we report the characterization of 13 genes, including three that are orthologs of Caenorhabditis elegans unc-84 (SUN domain), lin-39 (Dfd/Scr-related homeobox), and lin-11 (LIM homeobox). Based on the morphology and cell fate changes, the mutants were placed into four different categories. Class 1 animals have normal-looking vulva and vulva-uterine connections, indicating defects in other components of the egg-laying system. Class 2 animals frequently lack some or all of the vulval precursor cells (VPCs) due to defects in the migration of P-cell nuclei into the ventral hypodermal region. Class 3 animals show inappropriate fusion of VPCs to the hypodermal syncytium, leading to a reduced number of vulval progeny. Finally, class 4 animals exhibit abnormal vulval invagination and morphology. Interestingly, we did not find mutations that affect VPC induction and fates. Our work is the first study involving the characterization of genes in C. briggsae vulva formation, and it offers a basis for future investigations of these genes in C. elegans.
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Affiliation(s)
- Devika Sharanya
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Sujatha Marri
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Jon Taylor
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephane Flibotte
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Donald G. Moerman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065
| | - Bhagwati P. Gupta
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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Abstract
Perennial questions of evolutionary biology can be applied to gene regulatory systems using the abundance of experimental data addressing gene regulation in a comparative context. What is the tempo (frequency, rate) and mode (way, mechanism) of transcriptional regulatory evolution? Here we synthesize the results of 230 experiments performed on insects and nematodes in which regulatory DNA from one species was used to drive gene expression in another species. General principles of regulatory evolution emerge. Gene regulatory evolution is widespread and accumulates with genetic divergence in both insects and nematodes. Divergence in cis is more common than divergence in trans. Coevolution between cis and trans shows a particular increase over greater evolutionary timespans, especially in sex-specific gene regulation. Despite these generalities, the evolution of gene regulation is gene- and taxon-specific. The congruence of these conclusions with evidence from other types of experiments suggests that general principles are discoverable, and a unified view of the tempo and mode of regulatory evolution may be achievable.
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Brabin C, Appleford PJ, Woollard A. The Caenorhabditis elegans GATA factor ELT-1 works through the cell proliferation regulator BRO-1 and the Fusogen EFF-1 to maintain the seam stem-like fate. PLoS Genet 2011; 7:e1002200. [PMID: 21829390 PMCID: PMC3150447 DOI: 10.1371/journal.pgen.1002200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/08/2011] [Indexed: 11/18/2022] Open
Abstract
Seam cells in Caenorhabditis elegans provide a paradigm for the stem cell mode of division, with the ability to both self-renew and produce daughters that differentiate. The transcription factor RNT-1 and its DNA binding partner BRO-1 (homologues of the mammalian cancer-associated stem cell regulators RUNX and CBFβ, respectively) are known rate-limiting regulators of seam cell proliferation. Here, we show, using a combination of comparative genomics and DNA binding assays, that bro-1 expression is directly regulated by the GATA factor ELT-1. elt-1(RNAi) animals display similar seam cell lineage defects to bro-1 mutants, but have an additional phenotype in which seam cells lose their stem cell-like properties and differentiate inappropriately by fusing with the hyp7 epidermal syncytium. This phenotype is dependent on the fusogen EFF-1, which we show is repressed by ELT-1 in seam cells. Overall, our data suggest that ELT-1 has dual roles in the stem-like seam cells, acting both to promote proliferation and prevent differentiation. Stem cells can both produce differentiated cells and self-renew, producing more stem cells. Choosing between these opposing options is critical for development. Here, we have investigated the molecular genetics underlying this choice in the nematode worm, C. elegans, using the seam cells as a model of stem cell divisions. The transcription factor RNT-1 works together with BRO-1 (homologues of mammalian RUNX and CBFβ genes, respectively) to regulate proliferation of the seam cells, reflecting the roles of RUNX/CBFβ in mammalian stem cells. To better understand how bro-1 is regulated, we looked for conserved regions of non-coding DNA, likely to be of functional importance. We identified a 122 bp conserved non-coding element that is necessary and sufficient for bro-1 expression. Subsequent analysis suggested that the GATA transcription factor ELT-1 directly regulates bro-1. We have found that ELT-1 actually performs two distinct roles, promoting proliferation of seam cells while also preventing them from inappropriately fusing with surrounding tissue and losing their stem-like properties. Furthermore, we propose a link between the retention of stem cell properties and the maintenance of seam cells in a distinct compartment, in which they are protected from differentiation.
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Affiliation(s)
- Charles Brabin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Peter J. Appleford
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alison Woollard
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
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12
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Nokes EB, Van Der Linden AM, Winslow C, Mukhopadhyay S, Ma K, Sengupta P. Cis-regulatory mechanisms of gene expression in an olfactory neuron type in Caenorhabditis elegans. Dev Dyn 2010; 238:3080-92. [PMID: 19924784 DOI: 10.1002/dvdy.22147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The generation of cellular diversity is dependent on the precise spatiotemporal regulation of gene expression by both cis- and trans-acting mechanisms. The developmental principles regulating expression of specific gene subsets in individual cell types are not fully understood. Here we define the cis-regulatory mechanisms driving expression of cell-selective and broadly expressed genes in vivo in the AWB olfactory neuron subtype in C. elegans. We identify an element that is necessary to drive expression of neuron-selective chemoreceptor genes in the AWB neurons, and show that this element functions in a context-dependent manner. We find that the expression of broadly expressed sensory neuronal genes in the AWB neurons is regulated by diverse cis- and trans-regulatory mechanisms that act partly in parallel to the pathways governing expression of AWB-selective genes. We further demonstrate that cis-acting mechanisms driving gene expression in the AWB neurons appear to have diverged in related nematode species. Our results provide insights into the cis-regulatory logic driving cell-specific gene expression, and suggest that variations in this logic contribute to the generation of functional diversity.
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Affiliation(s)
- Eva B Nokes
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
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