The genome is organized in a hierarchical fashion within the nucleus in interphase. This nonrandom folding of the chromatin fiber is thought to play important roles in the processing of the genetic information. Therefore, a better knowledge of the mechanisms underlying the three-dimensional structure of the genome appears essential to fully understand the nuclear processes including transcription and replication. Fluorescent in situ hybridization (FISH) and molecular biology methods deriving from the Chromosome Conformation Capture technique are the methods of choice to study genome 3D organization at different levels. Although these single cell and population methods allowed to highlight similar chromatin structures, they also show frequent discrepancies which might be better understood by improving the capacity to generate actual 3D models of organization based on the different types of data available. This review aims at giving an overview of the principles, advantages, and limits of microscopy and molecular biology methods of analysis of genome structure and at discussing the different approaches of modeling of chromatin classically used and the improvements that are necessary to reach a better understanding on the links between chromatin structure and its spatial organization.

This review has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement 609989. We acknowledge funding from the Spanish Ministry of Economy and Competitiveness (BFU2013-47736-P) and the European Union's Horizon 2020 research and innovation programme under grant agreement No 676556 and support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and of the CERCA Programme/Generalitat de Catalunya to the CRG