The human embryonic stem cells (hESC) have the remarkable potential to replicate themselves indefinitely and differentiate into virtually any cell type under appropriate environmental conditions. They accomplish this through regulating the production of a unique set of proteins in the cells, a process known as gene regulation. While the genes encoding these stem cell proteins have been largely identified over the years, the mechanisms of gene regulation are not yet understood. This gap in our knowledge has seriously limited our ability to manipulate hESC for therapeutic purposes.

In Eukaryotic cells, gene regulation depends on specific sequences in the DNA known as transcriptional regulatory elements. These regulatory DNA consists of promoters, enhancers, insulators and other regulatory sequences. As a key step towards understanding the gene regulatory mechanisms in hESC, we have determined the transcriptional regulatory sequences throughout the genome of human ES cells. Our strategy involves identifying the DNA sequences that are associated with the specific transcription factors or chromatin modification signatures known to be present at each type of regulatory elements inside the hESC. We focused our analysis on undifferentiated hESC, and revealed a large number of novel promoters, enhancers and insulator elements. Function of the majority of these elements is supported by independent evidence.