Another important cellular process is transcription--the formation of a complementary strand of RNA based upon one of the two strands of DNA. But the in vivo study of DNA transcription is difficult because basal transcription factors are vital to cells' survival. Disruption of their function can lead to cell death, making experimentation difficult. Two Cold Spring Harbor scientists, Winship Herr and Nouria Hernandez, study the components of this vital process and their interactions. Some transcription factors, the proteins required to initiate or regulate transcription, recognize the promoter region of the DNA where transcription begins. A key regulatory element in the promoter region of the DNA is known as the TATA box.

Both Winship and Nouria study the TATA box-binding protein (TBP) and its interaction with other transcription factors. Winship's lab developed a new system to study the relationship between TBP and the transcription factor TFIIB in human cells by building on the work of Kevin Struhl of Harvard Medical School. Kevin developed an altered promoter (TGTA instead of TATA) and an altered TBP binding protein that was engineered to match it. In this system, transcription continued to occur, yet the potentially lethal consequences of disrupting the endogenous transcription machinery were circumvented. Bill Tansey in Winship's lab took this approach an important step forward: using this altered TGTA box/TBP pair, they developed a new altered pair of basal transcription factors--TBP and TFIIB--that works in concert with the original TGTA box/TBP pair. This "sequential altered specificity" has enabled Winship's group to study TFIIB in living cells, which was previously not possible in human cells.

Nouria reported interesting results in her work on the interaction between TBP and another group of transcription factors, the small nuclear RNA (snRNA)-activating protein complex (SNAPc), that binds to the U6 RNA polymerase III promoter. TBP consists of a conserved domain long thought to be the only functional region of the protein, while it also contains a non-conserved amino-terminal region long thought to be less, if at all, useful. Nouria has shown that upon truncating the TBP protein to eliminate the amino-terminal domain, the TBP bound much better to the TATA box. In addition, truncation of the amino-terminal domain resulted in strongly diminished binding of SNAPc to its binding site next to the TATA box on the DNA. Her results indicate two previously unknown roles for the non-conserved region of TBP: inhibiting TBP's binding to the DNA and interacting with another member of the transcription machinery (SNAPc) to promote its binding to the U6 promoter. Hence, the presence of this previously unrecognized component is essential to U6 transcription.