The structural insights gleaned from 3C methods naturally raise questions about the principles underlying establishment of chromosomal domains, the functions of such domains, and how they relate to other aspects of chromosomal processes such as chromatin state (see below) and replication timing. Much progress is being made toward understanding the molecular basis for chromosome folding, as Hi-C maps have been generated in a variety of cell types, at interesting cell stages such as mitosis, and in an ever-expanding range of mutants. In contrast, the functional consequences of chromosomal domains remain challenging to investigate, although deletion of well-defined boundary elements and artificial loop insertion provide some tools for addressing the regulatory implications of TADs and other chromosomal domains.
