Table 1.

Significant bins of the overlap test between H3K27me3 segments and SINE repeats under various null models

Tracks to randomize	Preserve total number of base pairs covered	Preserve segment lengths, but randomize position	Preserve segment and intersegment lengths, but randomize positions
H3K27me3	10/19	1/19	0/19
SINE	10/19	5/19	4/19
H3K27me3 and SINE	10/19	5/19	4/19

The number of significant bins of the overlap test between H3K27me3 segments and SINE repeats under different preservation and randomization rules for the null model. The test was performed in 19 bins on mouse chromosome 17, with the MEFB1 cell line. (Use of the MEFF cell line gave similar results; Table S2 in Additional file 1). In this case, less preservation of biological structure leads to smaller P-values. Also, randomizing the SINE track gave smaller P-values than randomizing the H3K27me3 track (or both).