Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells
Figure 7
Prediction of novel TSS and association with embryonic transcription.
(A) Enrichment for H3K4me3 and H3K9,14ac modifications relative to total H3 detected by ChIP. Values for the regions flanking Mecp2 and Zad20d1 CpG island-ORIs (ORIs 67276 and 105455, respectively) were considered as baseline. Q-PCR reactions were carried out in duplicate in three independent preparations of immunoprecipitated material. Standard deviation bars are indicated. (B) Expression levels relative to empty vector in transient transfection reporter assays. Constructs carrying the Notch2 and Aprt promoters cloned in the sense orientation were used as positive controls and a region at the first intron of the Notch2 gene cloned in both orientations as the negative one. Histograms represent the averaged normalised values of two independent transfections carried out in duplicate. Standard deviation bars are indicated. Primer pair sequences used and the sizes of the cloned fragments are listed in Table S3. (C) Frequency of promoter-ORIs relative to the number of mapped CAGE tags at each TSS [37]. Grey bars represent ORIs identified by the strict algorithm (n = 40) and white bars ORIs identified when applying a less stringent algorithm (n = 75). (D) Frequency of total promoters or promoter-ORIs transcriptionally active in early development [37]. A chi-square test was used to compare the frequency of tagged promoters between promoter-ORIs identified by the algorithms and the rest of promoters.