title: Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis.
abstract: Chromatin regulators are widely expressed proteins with diverse roles in gene expression, nuclear organization, cell cycle regulation, pluripotency, physiology and development, and are frequently mutated in human diseases such as cancer. Their inhibition often results in pleiotropic effects that are difficult to study using conventional approaches. We have developed a semi-automated nuclear tracking algorithm to quantify the divisions, movements and positions of all nuclei during the early development of Caenorhabditis elegans and have used it to systematically study the effects of inhibiting chromatin regulators. The resulting high dimensional datasets revealed that inhibition of multiple regulators, including F55A3.3 (encoding FACT subunit SUPT16H), lin-53 (RBBP4/7), rba-1 (RBBP4/7), set-16 (MLL2/3), hda-1 (HDAC1/2), swsn-7 (ARID2), and let-526 (ARID1A/1B) affected cell cycle progression and caused chromosome segregation defects. In contrast, inhibition of cir-1 (CIR1) accelerated cell division timing in specific cells of the AB lineage. The inhibition of RNA polymerase II also accelerated these division timings, suggesting that normal gene expression is required to delay cell cycle progression in multiple lineages in the early embryo. Quantitative analyses of the dataset suggested the existence of at least two functionally distinct SWI/SNF chromatin remodeling complex activities in the early embryo, and identified a redundant requirement for the egl-27 and lin-40 MTA orthologs in the development of endoderm and mesoderm lineages. Moreover, our dataset also revealed a characteristic rearrangement of chromatin to the nuclear periphery upon the inhibition of multiple general regulators of gene expression. Our systematic, comprehensive and quantitative datasets illustrate the power of single cell-resolution quantitative tracking and high dimensional phenotyping to investigate gene function. Furthermore, the results provide an overview of the functions of essential chromatin regulators during the early development of an animal.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; University Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Angela V
authors.initials: AV
authors.lastname: Krüger
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; University Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Rob
authors.initials: R
authors.lastname: Jelier
authors.affiliation: Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, the Netherlands.
authors.forename: Oleh
authors.initials: O
authors.lastname: Dzyubachyk
authors.affiliation: Advanced Light Microscopy Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Timo
authors.initials: T
authors.lastname: Zimmerman
authors.affiliation: Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, the Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Meijering
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; University Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain. Electronic address: ben.lehner@crg.eu.
authors.forename: Ben
authors.initials: B
authors.lastname: Lehner
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000166:cytology* / Q000196:embryology* / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism*; D002453:Cell Cycle; D019070:Cell Lineage; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D020090:Chromosome Segregation; D004625:Embryo, Nonmammalian / Q000166:cytology / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics; D004707:Endoderm / Q000166:cytology / Q000196:embryology; D018507:Gene Expression Regulation, Developmental; D017238:Genes, Helminth; D006801:Humans; D008648:Mesoderm / Q000166:cytology / Q000196:embryology; D034622:RNA Interference; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D029742:Caenorhabditis elegans Proteins; D002843:Chromatin
keywords: C. elegans; Chromatin regulators; Embryogenesis; Epigenetics; Gene expression; High dimensional phenotyping; Image analysis; Single-cell analysis