Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Mapping Transcription Factor Occupancy in Human Embryonic Stem Cells

• Growth Conditions
• Human ES Cell Quality Control
• Technology and Protocols

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• Data Analysis

DNA sequences occupied by Oct4 in human H9 ES cells (NIH code WA09) were identified in a replicate set of experiments using chromatin-immunoprecipitation (ChIP) combined with DNA microarrays (Figure 1A). For this purpose, DNA microarrays were designed that contain 60-mer oligonucleotide probes covering the region from -8kb to +2kb relative to the transcript start sites for 17,917 annotated human genes. Although some transcription factors are known to regulate genes from distances greater than 8kb, 98% of known binding sites for human transcription factors occur within 8kb of target genes (Supplemental Data Figure S1). The sites occupied by Oct4 were identified as peaks of ChIP-enriched DNA that span closely neighboring probes (Figure 1B). Oct4 was associated with 623 (3%) of the promoter regions for known protein-coding genes and 5 (3%) of the promoters for known miRNA genes in human ES cells (Supplemental Data Table S2).





Genome-wide ChIP-Chip in human embryonic stem cells. Examples of Oct4 bound regions. Plots display unprocessed ChIP-enrichment ratios for all probes within a genomic region. Genes are shown to scale below plots (exons and introns are represented by thick vertical and horizontal lines, respectively), and the genomic region represented is indicated beneath the plot. The transcription start site and transcript direction are denoted by arrows.

Regions of the Genome Bound By Oct4 (Table S1)
Known Genes bound by Oct4, Sox2, Nanog, and E2F4 in ES cells (Table S2)