UC San Diego

Chronic myelogenous leukemia, a cancer of white blood cells, is characterized by a chromosome translocation between ABL and BCR due to their close proximity during BCR replication. Twenty seven DNA breakpoints are within a major breakpoint cluster region (M-BCR), but why these breakpoints are clustered remains unclear. Initially, a Monte-Carlo algorithm calculating the sequence-dependent bending energy was used to position nucleosomes simultaneously in (M-BCR). MNase digestion followed by adapter-mediated PCR was then used to map experimentally the nucleosome boundaries. The discrepancy prompted the development of a replication-directed (RD) algorithm predicting nucleosome positions from the replication origin, one after another, each at the local minimum of bending energy. The better agreement confirms the spatial and temporal importance in nucleosome assembly in vivo. Therefore, a stepwise model for coupled nucleosome disassembly/reassembly across a replication fork was proposed: Unwinding of DNA by helicases may generate positive superhelical tension to facilitate the disassembly of downstream nucleosomes, which in turn may facilitate the reassembly of upstream nucleosomes. The latter may include a DNA loop formation followed by a sequential closing of two DNA arms around each histone core. Chromatin conformation capturing PCR, involving cross-linking, AluI digestion, re-ligation and PCR, preserved the core DNA conformation in 3-D and confirmed a 292-bp nucleosome-excluded region (A-rich region) containing a stretch of 17 consecutive A (17-A). Nineteen breakpoints are upstream from this region: 6 are clustered immediately upstream to the 17-A, and 10 out of 13 further upstream ones are spread in 4 nucleosome cores. It is likely that (1) the long A-rich region may extrude from the chromatin fiber or form an empty loop or other unusual secondary structures, which may experience greater mechanical stress locally without the "protection" of a histone core; (2) DNA in the newly reassembled nucleosome cores upstream to the A-rich region may lose histone cores under mechanical stress or in a stalled replication. These mechanisms may account for most of the M-BCR breakpoints and at least two other diseases caused by chromosome translocation, suggesting a functional role for the histone core as a "uniform curvature controller" to minimize the DNA breakage