Figure 6
Figure 6. Erythroid enhancers are co-occupied by GATA-1, SCL, and Ldb1. Sixty-one DNA segments occupied in vivo by GATA-1, whose enhancer activities were determined by Cheng et al,63 were evaluated for co-occupancy by SCL and Ldb1, based on the ChIP-on-chip results. The distribution of results after transient transfection of K562 cells (range of 8 to 24 determinations for each GATA-1–occupied DNA segment) is shown as a box plot, with the internal line indicating the median, the box extending to the first and third quartiles, and the whiskers extending to the most extreme data point that is no more than 1.5 times the interquartile range. Black boxes represent DNA segments co-occupied by GATA-1, SCL, and Ldb1; white boxes represent sequences that are occupied only by GATA-1. The gray box represents a segment that was not called as an SCL peak in ChIP-on-chip but was shown by quantitative PCR (qPCR) to be occupied by SCL. The horizontal line demarcates the threshold for enhancer activity. The results were partitioned into DNA segments with no enhancer activity (class I), activity clustering around the threshold (class II), and more than 2-fold activity (class III; see bottom panel for a summary of the results). Class I and class III are statistically different, tested by both χ2 test and Fisher exact test (P < .001).

Erythroid enhancers are co-occupied by GATA-1, SCL, and Ldb1. Sixty-one DNA segments occupied in vivo by GATA-1, whose enhancer activities were determined by Cheng et al,63  were evaluated for co-occupancy by SCL and Ldb1, based on the ChIP-on-chip results. The distribution of results after transient transfection of K562 cells (range of 8 to 24 determinations for each GATA-1–occupied DNA segment) is shown as a box plot, with the internal line indicating the median, the box extending to the first and third quartiles, and the whiskers extending to the most extreme data point that is no more than 1.5 times the interquartile range. Black boxes represent DNA segments co-occupied by GATA-1, SCL, and Ldb1; white boxes represent sequences that are occupied only by GATA-1. The gray box represents a segment that was not called as an SCL peak in ChIP-on-chip but was shown by quantitative PCR (qPCR) to be occupied by SCL. The horizontal line demarcates the threshold for enhancer activity. The results were partitioned into DNA segments with no enhancer activity (class I), activity clustering around the threshold (class II), and more than 2-fold activity (class III; see bottom panel for a summary of the results). Class I and class III are statistically different, tested by both χ2 test and Fisher exact test (P < .001).

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