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Figure S7. Three Classes of Genes in Human ES cells.
Our results suggest that most protein coding genes in human cells, including most genes thought to be transcriptionally inactive, experience the hallmarks of transcription initiation. To estimate the fraction of genes in each class, we used a simple voting mechanism to assign every gene as either active or inactive by calling a gene active if one Affymetrix probe for a given gene was detected in at least half of the experiments we analyzed (left, Supplemental text). Using this algorithm, ~50% of genes were considered active, over 90% of which had H3K4me3-modified nucleosomes at one of their promoters in ES cells. Among the remaining half of the genes, 60% had H3K4me3-modified nucleosomes at the transcription start site where regulation of events subsequent to transcription initiation must play important roles in preventing production or accumulation of transcripts. The final 20% of the total population where the promoters did not contain H3K4me3-modified nucleosomes consists of genes that are excluded from experiencing transcriptional initiation, where mechanisms that prevent transcription initiation must predominate. Schematics of the expected binding for several complexes for three classes are illustrated on the right.