Chromosome conformation is thought to play an important role in gene expression regulation. Chromosome conformation capture (3C), circular chromosome conformation capture (4C), 3C-carbon copy (5C), ChIP-loop assay, ChIA-PET and Hi-C method were developed to study spatial organization of long genomic regions in living cells. All steps of 3C, those 3C-based methods and key procedures in experiment were also discussed. The aim of this paper is to introduce some new methods to study gene regulation in 3D.