The methodology study of three-dimensional (3D) genome research

Multiple dimensions of genome organization play critical roles in the regulation of non-coding regions in gene expression in cell/organ development and pathogenesis. Precise measurements of multi-dimensional genome structure ensure data quality and fully depend upon the study design. We here overview the number of methodologies used in the detection and analysis of genome structure and compare advantages and disadvantages of 3C-based, PCR amplification-based, and sequencing-based measurements. We discuss about the optimization of various techniques according to targeted genomic sites, the required resolution, and possible technique biases. Comparison of different analysis tools and computational system-based automatic analysis is evaluated to define more opportunities and challenges of data analysis in 3D genome research. The genome structure is visualized in levels of single genome organized by enhancer-promoter interactions, TAD, and intra-chromosomal and inter-chromosomal interactions between TADs. Thus, methodologies of genome organization multi-dimensions are not only critical in studies on 3D genome-regulated transcriptions, but also in the discovery of disease-specific biomarkers and targets for diagnosis and therapies.