ABSTRACT
Understanding the in vivo dynamics of protein localization and their physical interactions is important for many problems in biology. To enable systematic protein function interrogation in a multicellular context, we built a genome-scale transgenic platform for in vivo expression of fluorescent- and affinity-tagged proteins in Caenorhabditis elegans under endogenous cis regulatory control. The platform combines computer-assisted transgene design, massively parallel DNA engineering, and next-generation sequencing to generate a resource of 14,637 genomic DNA transgenes, which covers 73% of the proteome. The multipurpose tag used allows any protein of interest to be localized in vivo or affinity purified using standard tag-based assays. We illustrate the utility of the resource by systematic chromatin immunopurification and automated 4D imaging, which produced detailed DNA binding and cell/tissue distribution maps for key transcription factor proteins.
Subject(s)
Animals, Genetically Modified , Caenorhabditis elegans Proteins/analysis , Caenorhabditis elegans/genetics , Genetic Engineering/methods , Genome, Helminth , Transcription Factors/analysis , Animals , Caenorhabditis elegans/chemistry , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Transcription Factors/geneticsABSTRACT
A single mutagen can generate multiple different types of DNA lesions. How different repair pathways cooperate in complex DNA lesions, however, remains largely unclear. Here we measured, clustered, and modeled the kinetics of recruitment and dissociation of 70 DNA repair proteins to laser-induced DNA damage sites in HeLa cells. The precise timescale of protein recruitment reveals that error-prone translesion polymerases are considerably delayed compared to error-free polymerases. We show that this is ensured by the delayed recruitment of RAD18 to double-strand break sites. The time benefit of error-free polymerases disappears when PARP inhibition significantly delays PCNA recruitment. Moreover, removal of PCNA from complex DNA damage sites correlates with RPA loading during 5'-DNA end resection. Our systematic study of the dynamics of DNA repair proteins in complex DNA lesions reveals the multifaceted coordination between the repair pathways and provides a kinetics-based resource to study genomic instability and anticancer drug impact.
Subject(s)
DNA Breaks, Double-Stranded , DNA Repair , DNA-Binding Proteins/metabolism , Uterine Cervical Neoplasms/metabolism , DNA Breaks, Double-Stranded/drug effects , DNA Repair/drug effects , DNA-Binding Proteins/genetics , DNA-Directed DNA Polymerase/genetics , DNA-Directed DNA Polymerase/metabolism , Female , Genomic Instability , HeLa Cells , Humans , Kinetics , Models, Genetic , Phthalazines/pharmacology , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Proliferating Cell Nuclear Antigen/genetics , Proliferating Cell Nuclear Antigen/metabolism , Protein Binding , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Uterine Cervical Neoplasms/drug therapy , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/pathologyABSTRACT
The localization of a protein is intrinsically linked to its role in the structural and functional organization of the cell. Advances in transgenic technology have streamlined the use of protein localization as a function discovery tool. Here we review the use of large genomic DNA constructs such as bacterial artificial chromosomes as a transgenic platform for systematic tag-based protein function exploration.
Subject(s)
DNA, Complementary/genetics , Genetic Engineering/methods , Genomics/methods , Molecular Imaging/methods , Transgenes , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Chromosomes, Artificial, Bacterial/chemistry , Chromosomes, Artificial, Bacterial/metabolism , DNA, Complementary/metabolism , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Fluorescent Dyes/chemistry , Fluorescent Dyes/metabolism , Humans , Staining and Labeling/methodsABSTRACT
The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts.