Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development

[1]  H. Boda,et al.  Elimination of Mutant mtDNA by an Optimized mpTALEN Restores Differentiation Capacities of Heteroplasmic MELAS-iPSCs , 2020, Molecular therapy. Methods & clinical development.

[2]  J. Teodoro,et al.  Mitohormesis , 2021, Mitochondrial Physiology and Vegetal Molecules.

[3]  J. Lukeš,et al.  RNA Editing in Mitochondria and Plastids: Weird and Widespread. , 2020, Trends in genetics : TIG.

[4]  Iain G. Johnston,et al.  Regulation of Mother-to-Offspring Transmission of mtDNA Heteroplasmy , 2019, Cell metabolism.

[5]  M. Torres,et al.  Insights into the quantitative and dynamic aspects of Cell Competition. , 2019, Current opinion in cell biology.

[6]  T. Rodríguez,et al.  Cell competition: the winners and losers of fitness selection , 2019, Development.

[7]  L. Scorrano,et al.  DRP1-mediated mitochondrial shape controls calcium homeostasis and muscle mass , 2019, Nature Communications.

[8]  E. Fuchs,et al.  Distinct modes of cell competition shape mammalian tissue morphogenesis , 2019, Nature.

[9]  Fabian J Theis,et al.  PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells , 2019, Genome biology.

[10]  B. Reinius,et al.  Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. , 2019, Cell reports.

[11]  Martin J. Aryee,et al.  Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics , 2019, Cell.

[12]  R. Gogna,et al.  Cell competition in development: information from flies and vertebrates. , 2018, Current opinion in cell biology.

[13]  H. Sasaki,et al.  Epiblast formation by Tead-Yap-dependent expression of pluripotency factors and competitive elimination of unspecified cells , 2018, bioRxiv.

[14]  L. Scorrano,et al.  Neuronal Mitochondrial Dysfunction Activates the Integrated Stress Response to Induce Fibroblast Growth Factor 21 , 2018, Cell reports.

[15]  C. Münch.  The different axes of the mammalian mitochondrial unfolded protein response , 2018, BMC Biology.

[16]  Gordon K Smyth,et al.  The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads , 2018, bioRxiv.

[17]  Iain G. Johnston,et al.  Large-scale genetic analysis reveals mammalian mtDNA heteroplasmy dynamics and variance increase through lifetimes and generations , 2018, Nature Communications.

[18]  P. Chinnery,et al.  The mitochondrial DNA genetic bottleneck: inheritance and beyond. , 2018, Essays in biochemistry.

[19]  T. Rodríguez,et al.  P53 and mTOR signalling determine fitness selection through cell competition during early mouse embryonic development , 2018, Nature Communications.

[20]  Luke Zappia,et al.  Clustering trees: a visualization for evaluating clusterings at multiple resolutions , 2018, bioRxiv.

[21]  Cole M. Haynes,et al.  UPRmt regulation and output: a stress response mediated by mitochondrial-nuclear communication , 2018, Cell Research.

[22]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[23]  M. Surani,et al.  Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos , 2018, Nature Cell Biology.

[24]  P. Chinnery,et al.  Mitochondrial DNA Heteroplasmy and Purifying Selection in the Mammalian Female Germ Line , 2018, Development, growth & differentiation.

[25]  Fabian J. Theis,et al.  PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells , 2017, Genome Biology.

[26]  T. Rodríguez,et al.  The Mitochondria and the Regulation of Cell Fitness During Early Mammalian Development. , 2018, Current topics in developmental biology.

[27]  N. Galtier,et al.  Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker , 2017, Molecular biology and evolution.

[28]  M. Montoya,et al.  Pluripotency Surveillance by Myc-Driven Competitive Elimination of Differentiating Cells. , 2017, Developmental cell.

[29]  H. McBride,et al.  The mitochondria-endoplasmic reticulum contact sites: a signalling platform for cell death. , 2017, Current opinion in cell biology.

[30]  I. Kucinski,et al.  Chronic activation of JNK JAK/STAT and oxidative stress signalling causes the loser cell status , 2017, Nature Communications.

[31]  Robert W. Williams,et al.  Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals , 2017, The Journal of cell biology.

[32]  J. Miyazaki,et al.  Cell competition with normal epithelial cells promotes apical extrusion of transformed cells through metabolic changes , 2017, Nature Cell Biology.

[33]  M. Fischer,et al.  Census and evaluation of p53 target genes , 2017, Oncogene.

[34]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[35]  Rob Patro,et al.  Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.

[36]  J. C. Belmonte,et al.  Mitochondrial replacement in human oocytes carrying pathogenic mitochondrial DNA mutations , 2016, Nature.

[37]  Laura C. Greaves,et al.  A Phenotype-Driven Approach to Generate Mouse Models with Pathogenic mtDNA Mutations Causing Mitochondrial Disease , 2016, Cell reports.

[38]  Davis J. McCarthy,et al.  A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.

[39]  A. Chacińska,et al.  Chatty Mitochondria: Keeping Balance in Cellular Protein Homeostasis. , 2016, Trends in cell biology.

[40]  Nicola K. Wilson,et al.  Resolving Early Mesoderm Diversification through Single Cell Expression Profiling , 2016, Nature.

[41]  J. Auwerx,et al.  Mitonuclear communication in homeostasis and stress , 2016, Nature Reviews Molecular Cell Biology.

[42]  Fabian J Theis,et al.  Diffusion pseudotime robustly reconstructs lineage branching , 2016, Nature Methods.

[43]  Afshin Samali,et al.  Endoplasmic reticulum stress-mediated induction of SESTRIN 2 potentiates cell survival , 2016, Oncotarget.

[44]  S. Dimauro,et al.  Mitochondrial diseases , 2016, Nature Reviews Disease Primers.

[45]  Sarah A Teichmann,et al.  Computational assignment of cell-cycle stage from single-cell transcriptome data. , 2015, Methods.

[46]  F. Meirelles,et al.  Real-Time PCR Quantification of Heteroplasmy in a Mouse Model with Mitochondrial DNA of C57BL/6 and NZB/BINJ Strains , 2015, PloS one.

[47]  Fabian J. Theis,et al.  destiny: diffusion maps for large-scale single-cell data in R , 2015, Bioinform..

[48]  Iain G. Johnston,et al.  Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism , 2015, eLife.

[49]  Evan G. Williams,et al.  Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research. , 2015, Cell reports.

[50]  Iain G. Johnston,et al.  Mitochondrial DNA disease and developmental implications for reproductive strategies , 2014, Molecular human reproduction.

[51]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[52]  Iain G. Johnston,et al.  MtDNA segregation in heteroplasmic tissues is common in vivo and modulated by haplotype differences and developmental stage. , 2014, Cell reports.

[53]  A. Czechanski,et al.  Derivation and characterization of mouse embryonic stem cells from permissive and nonpermissive strains , 2014, Nature Protocols.

[54]  Andreas Krämer,et al.  Causal analysis approaches in Ingenuity Pathway Analysis , 2013, Bioinform..

[55]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[56]  David A. Scott,et al.  Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.

[57]  L. Guarente,et al.  The NAD+/Sirtuin Pathway Modulates Longevity through Activation of Mitochondrial UPR and FOXO Signaling , 2013, Cell.

[58]  Aida Di-Gregorio,et al.  Competitive Interactions Eliminate Unfit Embryonic Stem Cells at the Onset of Differentiation , 2013, Developmental cell.

[59]  G. Giovinazzo,et al.  Myc-driven endogenous cell competition in the early mammalian embryo , 2013, Nature.

[60]  P. Chinnery,et al.  Mitochondrial genetics , 2013, British medical bulletin.

[61]  D. Greco,et al.  A Mitochondrial Ribosomal and RNA Decay Pathway Blocks Cell Proliferation , 2013, Current Biology.

[62]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[63]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[64]  M. Sharpley,et al.  Heteroplasmy of Mouse mtDNA Is Genetically Unstable and Results in Altered Behavior and Cognition , 2012, Cell.

[65]  T. Wai,et al.  Variation in germ line mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission , 2012, Nature Genetics.

[66]  Cole M. Haynes,et al.  Mitochondrial Import Efficiency of ATFS-1 Regulates Mitochondrial UPR Activation , 2012, Science.

[67]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[68]  S. Mitalipov,et al.  Rapid mitochondrial DNA segregation in primate preimplantation embryos precedes somatic and germline bottleneck. , 2012, Cell reports.

[69]  C. Ware,et al.  HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC‐to‐EpiSC/hESC transition , 2012, The EMBO journal.

[70]  Marcella Attimonelli,et al.  Primates and mouse NumtS in the UCSC Genome Browser , 2012, BMC Bioinformatics.

[71]  V. Venegas,et al.  Quantification of mtDNA mutation heteroplasmy (ARMS qPCR). , 2012, Methods in molecular biology.

[72]  Jaak Vilo,et al.  g:Profiler—a web server for functional interpretation of gene lists (2011 update) , 2011, Nucleic Acids Res..

[73]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[74]  M. Vannan,et al.  A Mouse Model of Mitochondrial Disease Reveals Germline Selection Against Severe mtDNA Mutations , 2008, Science.

[75]  H. Rajasimha,et al.  Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. , 2008, American journal of human genetics.

[76]  J. Elson,et al.  Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA , 2008, PLoS biology.

[77]  A. Dinnyés,et al.  Mitochondrial DNA heteroplasmy in ovine fetuses and sheep cloned by somatic cell nuclear transfer , 2007, BMC Developmental Biology.

[78]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[79]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[80]  Erik E. Griffin,et al.  Mitofusins Mfn1 and Mfn2 coordinately regulate mitochondrial fusion and are essential for embryonic development , 2003, The Journal of cell biology.

[81]  M. Ryan,et al.  A mitochondrial specific stress response in mammalian cells , 2002, The EMBO journal.

[82]  A. M. van der Bliek,et al.  Dynamin-related protein Drp1 is required for mitochondrial division in mammalian cells. , 2001, Molecular biology of the cell.

[83]  H. Coller,et al.  Mitochondrial mutational spectra in human cells and tissues. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[84]  S. Dimauro,et al.  Mitochondrial diseases. , 1989, Neurologic clinics.

[85]  G. Morata,et al.  Minutes: mutants of drosophila autonomously affecting cell division rate. , 1975, Developmental biology.