Chromothripsis: Methods and Protocols

ISBN-13: 9781493977796 / Angielski / Twarda / 2018 / 367 str.

Franck Pellestor

Opis

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.

Spis treści

Part I: Genesis and Impact of Chromothripsis

 

1. The Genomic Characteristics and Origin of Chromothripsis

            Alessio Marcozzi, Franck Pellestor, and Wigard P. Kloosterman

 

2. Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events

            Maki Fukami and Hiroki Kurahashi

 

3. Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo

            Franck Pellestor and Vincent Gatinois

 

4. Chromothripsis and the Macroevolution Theory

            Franck Pellestor

 

Part II: The Identification of Chromothripsis

 

5. Analysis of Chromothripsis by Combined FISH and Microarray Analysis

            Ruth N. MacKinnon

 

6. Chromothripsis Detectable in Small Supernumerary Marker Chromosomes (sSMC) Using Fluorescence In Situ Hybridization (FISH)

            Thomas Liehr

 

7. Identification of Chromothripsis in Biopsy Using SNP-Based Microarray

            Veronica Ortega, Christina Mendiola, and Gopalrao Velagaleti

 

8. Detection of Chromothripsis in Plants

            Isabelle M. Henry, Luca Comai, and Ek Han Tan

 

9. RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis

            Anne-Laure Bougé, Florence Rufflé, Sébastien Riquier, Benoit Guibert, Jérôme Audoux, and Thérèse Commes

 

Part III: The Causal Mechanisms of Chromothripsis

 

10. Experimental Determination of Checkpoint Adaptation by Mitotic Shake-Off and Microscopy

            Lucy H. Swift and Roy M. Golsteyn

 

11. A Role for Retrotransposons in Chromothripsis

            Dustin C. Hancks

 

12. Generation of Micronuclei and Detection of Chromosome Pulverization

            Monique N.H. Luijten, Jeannie X.T. Lee, Sixun Chen, and Karen C. Crasta

 

13. Detection of Impaired DNA Replication and Repair in Micronuclei as Indicators of Genomic Instability and Chromothripsis

            Mariona Terradas, Marta Martín, and Anna Genescà

 

14. Study of Telomere Dysfunction in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability

            Oumar Samassekou, Nathalie Bastien, Ju Yan, Sabine Mai, and Régen Drouin

 

15. Genes, Proteins, and Biological Pathways Preventing Chromothripsis

            Martin Poot

 

16. Expression of Genes Associated with Telomere Homeostasis in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability

            Oumar Samassekou, Nathalie Bastien, Ju Yan, Sabine Mai, and Régen Drouin

 

Part IV: The Bioinformatic Tools for Chromothripsis Analysis

 

17. Chromothripsis Detection and Characterization Using the CTLPScanner Web Server

            Jian Yang, Bo Liu, and Haoyang Cai

 

18. ChromothripsisDB: A Curated Database for the Documentation, Visualization, and Mining of Chromothripsis Data

            Haoyang Cai

 

Part V: The Experimental Models

 

19. Time-Lapse Imaging for the Detection of Chromosomal Abnormalities in Primate Pre-Implantation Embryos

            Brittany L. Daughtry and Shawn L. Chavez

 

20. Correlative Live Imaging and Immunofluorescence for Analysis of Chromosome Segregation in Mouse Preimplantation Embryos

            Cayetana Vázquez-Diez and Greg FitzHarris

 

21. Experimental Induction of Genome Chaos

            Christine J. Ye, Guo Liu, and Henry H. Heng

 

22. Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Changes Analysis in Complex Chromosomal Rearrangements and Chromothripsis

            Kevin Yauy, Vincent Gatinois, Thomas Guignard, Satish Sati, Jacques Puechberty, Jean Baptiste Gaillard, Anouck Schneider, and Franck Pellestor

Blurb

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.