Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

Microarray hybridizations are reproducible and paint a reliable picture of origin distributions in the genome. (A) Early S-phase HeLa microarray data at different stages of analysis. (A1) Zoomed-in view of normalized, smoothed, log₂ ratios of bubble fragments over genomic control from the Rp1 hybridization for a 78-kb region in Enr333 (33,698,3332–33,777,011), which illustrates details of the array signals and their strict tracking with individual EcoRI fragments (EcoRI sites shown in green at the top). (A2) Log₂ median signals (zero cut-off) within EcoRI fragments (medRI) from the Rp1 hybridization for the entire 500-kb Enr333 region (33,304,929–33,804,928), showing the EcoRI sites at the top; the location of the expanded region in A1 is indicated with the red bracket. (A3) MedRI data for the Tt1 hybridization. (A4) Averaged medRI values of Rp1 and Tt1 replicates; the green dots indicate calls that would not survive the 0.2 cut-off value. (B) The corresponding genomic fragments for selected positive and negative fragments from panel A4 were analyzed on 2D gels, with the Y and N below the images indicating whether the 2D gel result concords with the microarray call.