Figure 1. The Solexa Sequencing Tags Define Nucleosome Boundaries in the Human Genome.
(A) Nucleosome profile at the FZD2 promoter. The mononucleosome-sized DNA was isolated from MNase-digested chromatin of human T cells and sequenced to read 25 bp from the end using the Solexa sequencing technique. The sequence reads mapped to a given region were used to generate the nucleosome profiles using a scoring function (see Experimental Procedures) as shown by the black track. Blue ovals indicate inferred nucleosome positions in this study and red ovals indicate nucleosome positions identified previously (Ozsolak et al., 2007).
(B) Nucleosome profile at the BRCA1 and NBR2 promoters.
(C) Nucleosomes identified in the gene body of NBPF10 (region shown is chr1:16763501–16764673).
(D) Confirmation of nucleosome boundaries using LM-PCR. The mononucleosome DNA was ligated to a pair of Solexa adaptors, followed by amplification using one Solexa primer and one sequence-specific primer recognizing one of the nucleosomes indicated in Figure 1C. The product was labeled using a 32P-labeled nested primer, resolved by polyacrylamide gel electrophoresis, and visualized by exposing to X-ray films. An arrowhead indicates the major nucleosome boundaries.