Chromatin: A Semi-Structured Polymer

DNA is the longest polymer present in a living cell. In humans, the 3 billion base pair double-stranded DNA (dsDNA) duplex would stretch out to 1 m for the haploid (gamete) and 2 m for a diploid (somatic cell), yet the dsDNA fits inside a nucleus with a diameter ranging from 6 to 8 µm for lymphocyte to HeLa cells. Here we review our current understanding on how chromatin structure is established. First we consider how the double stranded DNA (dsDNA) is wrapped up and packaged to form the nucleosome and how variations in the number of H1 histone proteins affects the spacing between nucleosomes. Next we describe how nucleosomes interact to form the local structure of chromatin, and finally how diverse parts of the chromatin fiber combine by mutual interaction via CTCF-cohesin binding. The crucial role of proteins in creating and maintaining this organization is highlighted and discussed in light of recent findings from Hi-C and ChIA-PET experiments. We also explain computational models for the genome wide study of chromatin and the formation of chromatin loops, which are consistent with the experimental data.

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