Supplementary Figure 2: SuRE genome coverage, reproducibility and peaks.
From: Genome-wide mapping of autonomous promoter activity in human cells
a. Coverage of the human genome by unique elements in the SuRE library. b. Distribution (fold enrichment) of SuRE peaks among the 25 types of chromatin1. c. Correlation of SuRE enrichment between biological replicates at TSSs. d. Correlation between CAGE1 and SuRE at the TSSs. e. Same as Fig. 1e but with Histone genes indicated in red. Correlation between relative promoter autonomy (log10(SuRE/GRO-cap)) and tissue specificity (number of cell types and tissues in which each TSS is active, out of 889 tested2). Grey line shows linear fit. f. Correlation between relative promoter autonomy and the total number of promoters (ENCODE chromatin type ‘Tss’) that are found in a fixed window of 5-50 kb from the TSS. g. Size distribution of genomic fragments in the SuRE library. h. Number of reads (per individual replicate) of barcodes in cDNA. Only barcodes linked to a unique genomic fragment were counted. i. Venn diagram representing the overlap between the summits of SuRE peaks as called by the MACS algorithm3 and ENCODE-annotated promoters (‘Tss’) and enhancers (‘Enh’ and ‘EnhW’ combined)1. Because >1 peak summit can overlap a ENCODE annotation, overlaps are given for each direction of the comparison in the color of the annotation. j. Relative SuRE expression (SuRE/GRO-cap) of SuRE fragments for which the 3’ ends either in an intron (black) or an exon (red). Expression is normalized to GRO-cap to avoid systematic biases resulting from possible correlations between gene structure and expression level. A LOESS curve was separately fit to the logratios for all exon- and intron-terminal fragments using the distance each fragment ended downstream of the corresponding TSS, then predicted ratios were normalized to a maximum of 1.
1. Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
2. FANTOM Consortium. A promoter-level mammalian expression atlas. Nature 507, 462-470 (2014).
3. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137 (2008).
