Analysis of HMG-14/-17-Containing Chromatin

In chromatin, each nucleosome contains two specific binding sites for nonhistone chromosomal proteins HMG-14 or HMG-17; however, because the amount of these proteins in the nucleus is limited, only a small fraction of the nucleosomes contain these proteins. A central question on the role of HMG-14/-17 in chromatin structure and function is determination of the organization and distribution of nucleosomes containing these proteins along the chromatin fiber. Here we describe a method suitable to study these questions. It is important to note that the method described has general applicability and can be used to study the organization of any type of unusual nucleosomes in chromatin. For example, it is applicable to studies on the organization of nucleosomes containing minor species, acetylated, or otherwise modified histones, specific nonhistones, or even unusual or modified nucleotides.