In order to untangle the interconnection of gene transcription and gene movement, live cell systems, in which one can follow the activation or silencing of individual endogenous genes with respect to their chromosome

territory or a nuclear compartment, will be required. These types of experiments will be critical to extending our understanding of the role of nuclear organization in the regulation of gene expression. In recent years, light microscopy and electron microscopy approaches, as well as the emergence of genome-wide 3C-related studies have broadened our understanding of the three-dimensional organization of chromatin within the nuclear space, and how it relates to transcriptional regulation. Sotrastaurin However, many fundamental questions Selleck SP600125 remain unanswered. Although increasing evidence from experiments that are close to the native chromatin state do not support the 40 year old concept of higher order chromatin structure, there is still a lack of understanding with regard to the structure of chromatin in

the living cell, and whether or not a 30 nm fiber or even higher order chromatin organization exists in live interphase mammalian cells. Chromatin may have very different structures within a cell depending on multiple factors, such as the radial position within the nucleus, the cell cycle stage, the differentiation state of the cell, transcriptional activity, nucleosome Progesterone occupancy, DNA and histone modifications, histone variants, long-range chromatin interactions, or any combination of these factors. Although 3C-related techniques

have provided significant insight into genome-wide chromatin association frequencies within a population of cells, these techniques currently do not tell us how dynamic such interactions are in and among single cells. It remains to be determined what the frequency and duration of these interactions are, how they relate to the cell cycle and differentiation, and if they are the cause or consequence of transcriptional regulation. While recent advances in imaging and molecular approaches have provided significant insights into chromatin organization and gene interactions, ongoing studies examining individual living and fixed cells will provide the basis for further advances. Papers of particular interest, published within the period of review, have been highlighted as: • of special interest We thank the members of the Spector lab for helpful discussions, Megan Bodnar and Cinthya Zepeda-Mendoza for critically reading the manuscript and James Duffy for help with preparing the figures. Research in the Spector lab is supported by grants from NIGMS42694, NCI5P01CA013106-40, and NCI 2P30CA45508-24.