Expression-dependent perturbation of nucleosomal phases at HS2 of the human beta-LCR: Possible correlation with periodic bent DNA

DNA bend sites appear periodically at average intervals of 680 bp, correspo nding to a length of four nucleosomes, in the human epsilon-, beta- and (G) gamma-(A)gamma-psi beta-globin gene regions. We found that the HS2 region f lanked by two DNA bend sites accommodated five nucleosomes and they were re gularly phased throughout the region with the exception of that located in the middle, which corresponded to the precise location of HS2 and included the binding site for NF-E2. There appeared to be several phases in this reg ion in the reconstituted chromatin and in erythroid K562 cells where the gl obin genes are expressed, whereas only one phase was adopted in non-erythro id HeLa cells. Meanwhile, almost unique phases were adopted at the flanking bend sites in vitro as well as in vivo. Sequences of 30 bp containing the bend centers cloned into the vector alone showed identical nucleosomal phas es to those observed with the in vitro and in vivo experiments and removing the bend sites caused disruption of the phases at the bend sites as well a s those in their direct vicinity. Finally, the nucleosome in this HS2 regio n had an inhibitory effect on NF-E2 binding, although remodeling occurred w ith the nuclear extract from K562 cells in the presence of ATP. This sugges ts that HS2 is placed at a region of weak nucleosome phasing activity along with factor binding sites. (C) 1998 Academic Press.