Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. 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, Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.
Part I: Sailing the `3Cs´: Chromosome Conformation Capture and Its Variants
1. Quantitative Chromosome Conformation Capture (3C-qPCR)
Cosette Rebouissou, Séphora Sallis, and Thierry Forné
2. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-Seq
Mélanie Miranda, Daan Noordermeer, and Benoit Moindrot
3. Tough Tissue Hi-C
Stefan Grob
4. Mapping Mammalian 3D Genomes by Micro-C
Elena Slobodyanyuk, Claudia Cattoglio, and Tsung-Han S. Hsieh
Part II: Targeted Hi-C Approaches
5. Targeted Chromosome Conformation Capture (HiCap)
Artemy Zhigulev and Pelin Sahlén
6. Assessment of Higher-Order, Multi-Way Interactions with Tri-C
A. Marieke Oudelaar, Damien J. Downes, and Jim R. Hughes
7. Assessing Specific Networks of Chromatin Interactions with HiChIP
Dafne Campigli Di Giammartino, Alexander Polyzos, and Effie Apostolou
Part III: Sequencing-Based Approaches to Assess Nuclear Environment
8. Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-Seq
Liguo Zhang, Yu Chen, and Andrew S. Belmont
9. The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies
Cosette Rebouissou, Marie-Odile Baudement, and Thierry Forné
Part IV: Single-Cell Approaches
10. High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System
Wing Leung and Takashi Nagano
11. Simultaneous Quantification of Spatial Genome Positioning and Tranillegalscriptomics in Single Cells with scDam&T-Seq
Silke J.A. Lochs and Jop Kind
Part V: Visualizing Spatial Genome Organization
12. High-Throughput DNA FISH (hiFISH)
Elizabeth Finn, Tom Misteli, and Gianluca Pegoraro
13. Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells
Thomas Sabate, Christophe Zimmer, and Edouard Bertrand
Part VI: Functionally Dissecting Chromatin Architecture
14. CLOuD9: CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture
Wei Qiang Seow, Poonam Agarwal, and Kevin C. Wang
15. Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome
Michela Maresca, Ning Qing Liu, and Elzo de Wit
This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. 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,
Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.
Quantitative Chromosome Conformation Capture (3C-qPCR).- Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-Seq.- Tough Tissue Hi-C.- Mapping Mammalian 3D Genomes by Micro-C.- Targeted Chromosome Conformation Capture (HiCap).- Assessment of Higher-Order, Multi-Way Interactions with Tri-C.- Assessing Specific Networks of Chromatin Interactions with HiChIP.- Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-Seq.- The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies.- High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System.- Simultaneous Quantification of Spatial Genome Positioning and Tranillegalscriptomics in Single Cells with scDam&T-Seq.- High-Throughput DNA FISH (hiFISH).- Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells.- CLOuD9:CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture.- Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome.
Inhaltsverzeichnis
Part I: Sailing the '3Cs': Chromosome Conformation Capture and Its Variants
1. Quantitative Chromosome Conformation Capture (3C-qPCR)
Cosette Rebouissou, Séphora Sallis, and Thierry Forné
2. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-Seq
Mélanie Miranda, Daan Noordermeer, and Benoit Moindrot
3. Tough Tissue Hi-C
Stefan Grob
4. Mapping Mammalian 3D Genomes by Micro-C
Elena Slobodyanyuk, Claudia Cattoglio, and Tsung-Han S. Hsieh
Part II: Targeted Hi-C Approaches
5. Targeted Chromosome Conformation Capture (HiCap)
Artemy Zhigulev and Pelin Sahlén
6. Assessment of Higher-Order, Multi-Way Interactions with Tri-C
A. Marieke Oudelaar, Damien J. Downes, and Jim R. Hughes
7. Assessing Specific Networks of Chromatin Interactions with HiChIP
Dafne Campigli Di Giammartino, Alexander Polyzos, and Effie Apostolou
Part III: Sequencing-Based Approaches to Assess Nuclear Environment
8. Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-Seq
Liguo Zhang, Yu Chen, and Andrew S. Belmont
9. The High-Salt Recovered Sequence-Sequencing (HRS-seq) Method: Exploring Genome Association with Nuclear Bodies
Cosette Rebouissou, Marie-Odile Baudement, and Thierry Forné
Part IV: Single-Cell Approaches
10. High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System
Wing Leung and Takashi Nagano
11. Simultaneous Quantification of Spatial Genome Positioning and Tranillegalscriptomics in Single Cells with scDam&T-Seq
Silke J.A. Lochs and Jop Kind
Part V: Visualizing Spatial Genome Organization
12. High-Throughput DNA FISH (hiFISH)
Elizabeth Finn, Tom Misteli, and Gianluca Pegoraro
13. Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells
Thomas Sabate, Christophe Zimmer, and Edouard Bertrand
Part VI: Functionally Dissecting Chromatin Architecture
14. CLOuD9: CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture
Wei Qiang Seow, Poonam Agarwal, and Kevin C. Wang
15. Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome
Michela Maresca, Ning Qing Liu, and Elzo de Wit
Klappentext
This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. 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, Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.
Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
