Soon after the surprising announcement that the human genome had far fewer genes than most had expected, researchers began to realize that there were still a great many unexplored transcriptional start sites. Tom Gingeras' team at Affymetrix, along with Kevin Struhl of Harvard University and colleagues, confirmed some of these findings in a 2004 Hot Paper by mapping the binding sites for three DNA transcription factors: Sp1, cMyc, and p53. Using a combination of high-density oligonucleotide tiling arrays (in which every region of the genome is represented, thus eliminating bias toward promoter regions) and chromatin immunoprecipitation, they found that roughly 80% of the binding regions were not located at the 5' ends of protein-coding genes, and that many of these binding sites were associated with the noncoding RNAs found in earlier research.1

Struhl says that the results were at first controversial; the paper was originally rejected by Science. "I...


1. S. Cawley et al., "Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs," Cell, 116:499-509, 2004. (Cited in 163 papers)

Interested in reading more?

Magaizne Cover

Become a Member of

Receive full access to digital editions of The Scientist, as well as TS Digest, feature stories, more than 35 years of archives, and much more!
Already a member?