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This detailed book presents an up-to-date view on methods and experimental approaches developed to identify and explore the chromothripsis phenomenon. Beginning with a section exploring the genesis and impact of chromothripsis, the collection continues by covering the identification of chromothripsis, the causal mechanisms of chromothripsis, the bioinformatics tools for chromothripsis analysis, and experimental systems recently developed for the in vitro investigation of chromothripsis. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Chromothripsis: Methods and Protocols serves as a vital resource for cell biologists, molecular biologists, cytogeneticists, and geneticists investigating chromothripsis, but also for students and researchers new to the field of chromothripsis and genomic instability.
List of contents
The Genomic Characteristics and Origin of Chromothripsis.- Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events.- Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo.- Chromothripsis and the Macroevolution Theory.- Analysis of Chromothripsis by Combined FISH and Microarray Analysis.- Chromothripsis Detectable in Small Supernumerary Marker Chromosomes (sSMC) Using Fluorescence In Situ Hybridization (FISH).- Identification of Chromothripsis in Biopsy Using SNP-Based Microarray.- Detection of Chromothripsis in Plants.- RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis.- Experimental Determination of Checkpoint Adaptation by Mitotic Shake-Off and Microscopy.- A Role for Retrotransposons in Chromothripsis.- Generation of Micronuclei and Detection of Chromosome Pulverization.- Detection of Impaired DNA Replication and Repair in Micronuclei as Indicators of Genomic Instability and Chromothripsis.- Study of Telomere Dysfunction in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability.- Genes, Proteins, and Biological Pathways Preventing Chromothripsis.- Expression of Genes Associated with Telomere Homeostasis in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability.- Chromothripsis Detection and Characterization Using the CTLPScanner Web Server.- ChromothripsisDB: A Curated Database for the Documentation, Visualization, and Mining of Chromothripsis Data.- Time-Lapse Imaging for the Detection of Chromosomal Abnormalities in Primate Pre-Implantation Embryos.- Correlative Live Imaging and Immunofluorescence for Analysis of Chromosome Segregation in Mouse Preimplantation Embryos.- Experimental Induction of Genome Chaos.- Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Changes Analysis in Complex Chromosomal Rearrangements and Chromothripsis.
Summary
This detailed book presents an up-to-date view on methods and experimental approaches developed to identify and explore the chromothripsis phenomenon. Beginning with a section exploring the genesis and impact of chromothripsis, the collection continues by covering the identification of chromothripsis, the causal mechanisms of chromothripsis, the bioinformatics tools for chromothripsis analysis, and experimental systems recently developed for the
in vitro
investigation of chromothripsis. Written for the highly successful
Methods in Molecular Biology
series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical,
Chromothripsis: Methods and Protocols
serves as a vital resource for cell biologists, molecular biologists, cytogeneticists, and geneticists investigating chromothripsis, but also for students and researchers new to the field of chromothripsis and genomic instability.
