A matter of scale: how emerging technologies are redefining our view of chromosome architecture

•Genomewide technologies reveal the 3D folding of chromosomes at kbp resolution.•Recent use of single molecule and super-resolution microscopies has begun to uncover principles of chromatin organization with unprecedented spatial and temporal resolution.•DNA is packaged into discrete, physically isolated chromosomal modules often associated with specific epigenetic markers.

The 3D folding of the genome and its relation to fundamental processes such as gene regulation, replication, and segregation remains one of the most puzzling and exciting questions in genetics. In this review, we describe how the use of new technologies is starting to revolutionize the field of chromosome organization, and to shed light on the mechanisms of transcription, replication, and repair. In particular, we concentrate on recent studies using genome-wide methods, single-molecule technologies, and super-resolution microscopy (SRM). We summarize some of the main concerns when employing these techniques, and discuss potential new and exciting perspectives that illuminate the connection between 3D genomic organization and gene regulation.