Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis
Tài liệu tham khảo
Albert, 2000, Error and attack tolerance of complex networks, Nature, 406, 378, 10.1038/35019019
Aquino-Nunez, 2020, cnd-1/NeuroD1 functions with the homeobox gene ceh-5/Vax2 and hox gene ceh-13/labial to specify aspects of RME and DD neuron fate in Caenorhabditis elegans, G3 (Bethesda), 10, 3071, 10.1534/g3.120.401515
Bachir, 2017, Actin-based adhesion modules mediate cell interactions with the extracellular matrix and neighboring cells, Cold Spring Harb. Perspect. Biol., 9, 10.1101/cshperspect.a023234
Bao, 2011, Mounting Caenorhabditis elegans embryos for live imaging of embryogenesis, Cold Spring Harb. Protoc., 2011, 10.1101/pdb.prot065599
Bao, 2006, Automated cell lineage tracing in Caenorhabditis elegans, Proc. Natl. Acad. Sci. USA, 103, 2707, 10.1073/pnas.0511111103
Bao, 2008, Control of cell cycle timing during C. elegans embryogenesis, Dev. Biol., 318, 65, 10.1016/j.ydbio.2008.02.054
Barone, 2012, Cell adhesion in embryo morphogenesis, Curr. Opin. Cell Biol., 24, 148, 10.1016/j.ceb.2011.11.006
Barriga, 2018, Tissue stiffening coordinates morphogenesis by triggering collective cell migration in vivo, Nature, 554, 523, 10.1038/nature25742
Bei, 2002, SRC-1 and Wnt signaling act together to specify endoderm and to control cleavage orientation in early C. elegans embryos, Dev. Cell, 3, 113, 10.1016/S1534-5807(02)00185-5
Benkemoun, 2014, PAR-4/LKB1 regulates DNA replication during asynchronous division of the early C. elegans embryo, J. Cell Biol., 205, 447, 10.1083/jcb.201312029
Blanpain, 2014, Stem cell plasticity. Plasticity of epithelial stem cells in tissue regeneration, Science, 344, 1242281, 10.1126/science.1242281
Boeck, 2016, The time-resolved transcriptome of C. elegans, Genome Res., 26, 1441, 10.1101/gr.202663.115
Boyle, 2006, AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis, BMC Bioinformatics, 7, 275, 10.1186/1471-2105-7-275
Brauchle, 2003, Differential activation of the DNA replication checkpoint contributes to asynchrony of cell division in C. elegans embryos, Curr. Biol., 13, 819, 10.1016/S0960-9822(03)00295-1
Burga, 2011, Predicting mutation outcome from early stochastic variation in genetic interaction partners, Nature, 480, 250, 10.1038/nature10665
Chen, 2018, Establishment of signaling interactions with cellular resolution for every cell cycle of embryogenesis, Genetics, 209, 37, 10.1534/genetics.118.300820
Chera, 2014, Diabetes recovery by age-dependent conversion of pancreatic delta-cells into insulin producers, Nature, 514, 503, 10.1038/nature13633
Choi, 2015, A conserved phosphorylation switch controls the interaction between cadherin and beta-catenin in vitro and in vivo, Dev. Cell, 33, 82, 10.1016/j.devcel.2015.02.005
Davis, 2022, WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans, Genetics, 220, iyac003, 10.1093/genetics/iyac003
Dietzl, 2007, A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila, Nature, 448, 151, 10.1038/nature05954
Du, 2015, E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis, Dev. Biol., 398, 267, 10.1016/j.ydbio.2014.12.009
Du, 2015, The regulatory landscape of lineage differentiation in a metazoan embryo, Dev. Cell, 34, 592, 10.1016/j.devcel.2015.07.014
Du, 2014, De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis, Cell, 156, 359, 10.1016/j.cell.2013.11.046
Edgar, 1988, DNA synthesis and the control of embryonic gene expression in C. elegans, Cell, 53, 589, 10.1016/0092-8674(88)90575-2
El-Brolosy, 2019, Genetic compensation triggered by mutant mRNA degradation, Nature, 568, 193, 10.1038/s41586-019-1064-z
El-Brolosy, 2017, Genetic compensation: a phenomenon in search of mechanisms, PLoS Genet., 13, e1006780, 10.1371/journal.pgen.1006780
Fan, 2019, A multicellular rosette-mediated collective dendrite extension, eLife, 8, e38065, 10.7554/eLife.38065
Félix, 2015, Pervasive robustness in biological systems, Nat. Rev. Genet., 16, 483, 10.1038/nrg3949
Félix, 2008, Robustness and evolution: concepts, insights and challenges from a developmental model system, Heredity (Edinb), 100, 132, 10.1038/sj.hdy.6800915
Fraser, 2000, Functional genomic analysis of C. elegans chromosome I by systematic RNA interference, Nature, 408, 325, 10.1038/35042517
Gerstein, 2010, Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project, Science, 330, 1775, 10.1126/science.1196914
Giaever, 2002, Functional profiling of the Saccharomyces cerevisiae genome, Nature, 418, 387, 10.1038/nature00935
Gibson, 2000, Canalization in evolutionary genetics: a stabilizing theory?, BioEssays, 22, 372, 10.1002/(SICI)1521-1878(200004)22:4<372::AID-BIES7>3.0.CO;2-J
Giurumescu, 2012, Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos, Development, 139, 4271, 10.1242/dev.086256
Goldstein, 1995, Cell contacts orient some cell division axes in the Caenorhabditis elegans embryo, J. Cell Biol., 129, 1071, 10.1083/jcb.129.4.1071
Gumbiner, 1996, Cell adhesion: the molecular basis of tissue architecture and morphogenesis, Cell, 84, 345, 10.1016/S0092-8674(00)81279-9
Hallam, 2000, The C. elegans NeuroD homolog cnd-1 functions in multiple aspects of motor neuron fate specification, Development, 127, 4239, 10.1242/dev.127.19.4239
Hashimshony, 2015, Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer, Nature, 519, 219, 10.1038/nature13996
Hebeisen, 2008, CDC-25.1 stability is regulated by distinct domains to restrict cell division during embryogenesis in C. elegans, Development, 135, 1259, 10.1242/dev.014969
Heisenberg, 2013, Forces in tissue morphogenesis and patterning, Cell, 153, 948, 10.1016/j.cell.2013.05.008
Hench, 2009, Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps, Dev. Biol., 333, 1, 10.1016/j.ydbio.2009.06.014
Hirsh, 2001, Protein dispensability and rate of evolution, Nature, 411, 1046, 10.1038/35082561
Ho, 2015, Systems-level quantification of division timing reveals a common genetic architecture controlling asynchrony and fate asymmetry, Mol. Syst. Biol., 11, 814, 10.15252/msb.20145857
Howe, 2011, RNA-Seq analysis in MeV, Bioinformatics, 27, 3209, 10.1093/bioinformatics/btr490
Hutter, 2016, GExplore 1.4: an expanded web interface for queries on Caenorhabditis elegans protein and gene function, Worm, 5, e1234659, 10.1080/21624054.2016.1234659
Ingolia, 2004, Topology and robustness in the Drosophila segment polarity network, PLoS Biol., 2, e123, 10.1371/journal.pbio.0020123
Jelier, 2016, Compensatory cell movements confer robustness to mechanical deformation during embryonic development, Cell Syst., 3, 160, 10.1016/j.cels.2016.07.005
Kamath, 2003, Systematic functional analysis of the Caenorhabditis elegans genome using RNAi, Nature, 421, 231, 10.1038/nature01278
Katzman, 2018, AceTree: a major update and case study in the long term maintenance of open-source scientific software, BMC Bioinformatics, 19, 121, 10.1186/s12859-018-2127-0
Kitano, 2004, Biological robustness, Nat. Rev. Genet., 5, 826, 10.1038/nrg1471
Knight, 1998, Gastrulation initiation in Caenorhabditis elegans requires the function of gad-1, which encodes a protein with WD repeats, Dev. Biol., 198, 253
Lee, 2006, Wnt/Frizzled signaling controls C. elegans gastrulation by activating actomyosin contractility, Curr. Biol., 16, 1986, 10.1016/j.cub.2006.08.090
Li, 2019, Systems properties and spatiotemporal regulation of cell position variability during embryogenesis, Cell Rep., 26, 313, 10.1016/j.celrep.2018.12.052
Lu, 2009, Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition, Development, 136, 2101, 10.1242/dev.034421
Ma, 2021, A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis, Nat. Methods, 18, 893, 10.1038/s41592-021-01216-1
Ma, 2019, PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components, Nature, 568, 259, 10.1038/s41586-019-1057-y
Macneil, 2011, Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression, Genome Res., 21, 645, 10.1101/gr.097378.109
Masoudi, 2021, Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans, Development, 148, dev199224, 10.1242/dev.199224
Memar, 2019, Twenty million years of evolution: the embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence, Dev. Biol., 447, 182, 10.1016/j.ydbio.2018.12.022
Merrell, 2016, Adult cell plasticity in vivo: de-differentiation and transdifferentiation are back in style, Nat. Rev. Mol. Cell Biol., 17, 413, 10.1038/nrm.2016.24
Mickey, 1996, An inductive interaction in 4-cell stage C. elegans embryos involves APX-1 expression in the signalling cell, Development, 122, 1791, 10.1242/dev.122.6.1791
Mills, 2019, Nomenclature for cellular plasticity: are the terms as plastic as the cells themselves?, EMBO J., 38, e103148, 10.15252/embj.2019103148
Miroshnikova, 2018, Adhesion forces and cortical tension couple cell proliferation and differentiation to drive epidermal stratification, Nat. Cell Biol., 20, 69, 10.1038/s41556-017-0005-z
Moore, 2013, Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis, Development, 140, 3266, 10.1242/dev.096040
Murray, 2008, Automated analysis of embryonic gene expression with cellular resolution in C. elegans, Nat. Methods, 5, 703, 10.1038/nmeth.1228
Nair, 2013, Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification, Development, 140, 3385, 10.1242/dev.098012
Nijhout, 2002, The nature of robustness in development, BioEssays, 24, 553, 10.1002/bies.10093
Noatynska, 2013, Coordinating cell polarity and cell cycle progression: what can we learn from flies and worms?, Open Biol., 3, 130083, 10.1098/rsob.130083
Ohno, 2022, Small RNAs couple embryonic developmental programs to gut microbes, Sci. Adv., 8, eabl7663, 10.1126/sciadv.abl7663
Packer, 2019, A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution, Science, 365, eaax1971, 10.1126/science.aax1971
Papatheodorou, 2018, Expression Atlas: gene and protein expression across multiple studies and organisms, Nucleic Acids Res., 46, D246, 10.1093/nar/gkx1158
Pohl, 2012, Actomyosin-based self-organization of cell internalization during C. elegans gastrulation, BMC Biol., 10, 94, 10.1186/1741-7007-10-94
Poss, 2002, Heart regeneration in zebrafish, Science, 298, 2188, 10.1126/science.1077857
Priess, 2005, Notch signaling in the C. elegans embryo, WormBook, 2005, 1
Pryszcz, 2011, MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score, Nucleic Acids Res., 39, e32, 10.1093/nar/gkq953
Raj, 2010, Variability in gene expression underlies incomplete penetrance, Nature, 463, 913, 10.1038/nature08781
Ramani, 2012, The majority of animal genes are required for wild-type fitness, Cell, 148, 792, 10.1016/j.cell.2012.01.019
Richards, 2013, A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress, Dev. Biol., 374, 12, 10.1016/j.ydbio.2012.11.034
Rocheleau, 1997, Wnt signaling and an APC-related gene specify endoderm in early C. elegans embryos, Cell, 90, 707, 10.1016/S0092-8674(00)80531-0
Rossi, 2015, Genetic compensation induced by deleterious mutations but not gene knockdowns, Nature, 524, 230, 10.1038/nature14580
Rual, 2004, Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library, Genome Res., 14, 2162, 10.1101/gr.2505604
Santella, 2014, A semi-local neighborhood-based framework for probabilistic cell lineage tracing, BMC Bioinformatics, 15, 217, 10.1186/1471-2105-15-217
Santella, 2010, A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D, BMC Bioinformatics, 11, 580, 10.1186/1471-2105-11-580
Santella, 2016, Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model, Nucleic Acids Res., 44, D781, 10.1093/nar/gkv1119
Sawa, 2012, Control of cell polarity and asymmetric division in C. elegans, Curr. Top. Dev. Biol., 101, 55, 10.1016/B978-0-12-394592-1.00003-X
Schlesinger, 1999, Wnt pathway components orient a mitotic spindle in the early Caenorhabditis elegans embryo without requiring gene transcription in the responding cell, Genes Dev., 13, 2028, 10.1101/gad.13.15.2028
Schnabel, 2006, Global cell sorting in the C. elegans embryo defines a new mechanism for pattern formation, Dev. Biol., 294, 418, 10.1016/j.ydbio.2006.03.004
Schnabel, 1997, Assessing normal embryogenesis in Caenorhabditis elegans using a 4D microscope: variability of development and regional specification, Dev. Biol., 184, 234, 10.1006/dbio.1997.8509
Segref, 2010, Fate specification and tissue-specific cell cycle control of the Caenorhabditis elegans intestine, Mol. Biol. Cell, 21, 725, 10.1091/mbc.e09-04-0268
Shah, 2017, PCP and SAX-3/Robo pathways cooperate to regulate convergent extension-based nerve cord assembly in C. elegans, Dev. Cell, 41, 195, 10.1016/j.devcel.2017.03.024
Sherman, 2022, DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update), Nucleic Acids Res., 10.1093/nar/gkac194
Smedley, 2015, The BioMart community portal: an innovative alternative to large, centralized data repositories, Nucleic Acids Res., 43, W589, 10.1093/nar/gkv350
Sönnichsen, 2005, Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans, Nature, 434, 462, 10.1038/nature03353
Spatz, 2021, Cellular plasticity at the nexus of development and disease, Development, 148, dev197392, 10.1242/dev.197392
Stelling, 2004, Robustness of cellular functions, Cell, 118, 675, 10.1016/j.cell.2004.09.008
Sulston, 1983, The embryonic cell lineage of the nematode Caenorhabditis elegans, Dev. Biol., 100, 64, 10.1016/0012-1606(83)90201-4
Tanaka, 2011, The cellular basis for animal regeneration, Dev. Cell, 21, 172, 10.1016/j.devcel.2011.06.016
Terry, 2020, Early C. elegans embryos modulate cell division timing to compensate for, and survive, the discordant conditions of a severe temperature gradient, bioRxiv
Tintori, 2016, A transcriptional lineage of the early C. elegans embryo, Dev. Cell, 38, 430, 10.1016/j.devcel.2016.07.025
Towbin, 2012, Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery, Cell, 150, 934, 10.1016/j.cell.2012.06.051
Waddington, 1942, Canalization of development and the inheritance of acquired characters, Nature, 150, 563, 10.1038/150563a0
Walston, 2004, Multiple Wnt signaling pathways converge to orient the mitotic spindle in early C. elegans embryos, Dev. Cell, 7, 831, 10.1016/j.devcel.2004.10.008
Wang, 2010, KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies, Genomics Proteomics Bioinformatics, 8, 77, 10.1016/S1672-0229(10)60008-3
Wang, 2019, A high-content imaging approach to profile C. elegans embryonic development, Development, 146, dev174029, 10.1242/dev.174029
Wang, 2009, Why is the correlation between gene importance and gene evolutionary rate so weak?, PLoS Genet., 5, e1000329, 10.1371/journal.pgen.1000329
Winzeler, 1999, Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis, Science, 285, 901, 10.1126/science.285.5429.901
Yuan, 2019, Cellular plasticity in cancer, Cancer Discov., 9, 837, 10.1158/2159-8290.CD-19-0015
Zhang, 2020, Regulation of gliogenesis by lin-32/Atoh1 in Caenorhabditis elegans, G3 (Bethesda), 10, 3271, 10.1534/g3.120.401547
Zhang, 2005, Significant impact of protein dispensability on the instantaneous rate of protein evolution, Mol. Biol. Evol., 22, 1147, 10.1093/molbev/msi101
Zhao, 2021, Single-cell dynamics of chromatin activity during cell lineage differentiation in Caenorhabditis elegans embryos, Mol. Syst. Biol., 17, e10075, 10.15252/msb.202010075
