Capturing Chromosome Conformation : Methods and Protocols

1. Capturing Chromosome Conformation

Michel Puc?at



2. The Chromosome Conformation Capture (3C) in Drosophila melanogaster

Federica Lo Sardo



3. 4C-Seq: Interrogating Chromatin Looping with Circular Chromosome Conformation Capture

Nezih Karasu and Tom Sexton



4. Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments

Marco Di Stefano, David Castillo, Fran?ois Serra, Irene Farabella, Mike N. Goodstadt, and Marc A. Marti-Renom



5. Targeted DNase Hi-C

Zhijun Duan



6. C-HiC: A High Resolution Method for Unbiased Chromatin Conformation Capture Targeting Small Locus

J?r?me D. Robin



7. Computational Analysis of Hi-C Data

Mattia Forcato and Silvio Bicciato



8. Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP

Xue Qing David Wang, Christopher J.F. Cameron, Dana Segal, Denis Paquette, Mathieu Blanchette, and Jos?e Dostie



9. Single-Cell DamID to Capture Contacts between DNA and the Nuclear Lamina in Individual Mammalian Cells

Kim L. de Luca and Jop Kind



10. Formaldehyde-Mediated Snapshot of Nuclear Architecture

Federica Lucini, Andrea Bianchi, and Chiara Lanzuolo



11. Visualization of Chromatin Dynamics by Live Cell Microscopy Using CRISPR/Cas9 Gene Editing and ANCHOR Labeling

Ezio T. Fok, Stephanie Fanucchi, Kerstin Bystricky, and Musa M. Mhlanga



12. Preparing Map of Chromosome Territories Distribution Frequency

Paulina Nastaly and Paolo Maiuri



13. Higher-Order Chromatin Organization Using 3D DNA Fluorescent In Situ Hybridization

Quentin Szabo, Giacomo Cavalli, and Fr?d?ric Bantignies



14. 3D Immuno-DNA Fluorescence In Situ Hybridization (FISH) for Detection of HIV-1 and Cellular Genes in Primary CD4+ T Cells

Bojana Lucic, Julia Wegner, Mia Stanic, Katharina Laurence Jost, and Marina Lusic



15. Visualization of Nuclear and Cytoplasmic Long Noncoding RNAs at Single-Cell Level by RNA-FISH

Tiziana Santini, Julie Martone, and Monica Ballarino



16. 3D COMBO chrRNA-DNA-Immuno FISH

Federica Marasca, Alice Cortesi, and Beatrice Bodega



17. An Algorithm for the Analysis of the 3D Spatial Organization of the Genome

Francesco Gregoretti, Alice Cortesi, Gennaro Oliva, Beatrice Bodega, and Laura Antonelli