Key Concepts of Section 9.3

• RNA polymerase II initiates transcription of genes at the nucleotide in the DNA template that corresponds to the 5′ nucleotide that is capped in the encoded mRNA.

• Three principal types of promoter sequences have been identified in eukaryotic DNA. The TATA box is prevalent in highly transcribed genes. Initiator promoters are found in some genes, and CpG islands, the promoters for about 70 percent of protein-coding genes in vertebrates, are characteristic of genes transcribed at a low rate.

• Transcription of protein-coding genes by Pol II is initiated by sequential binding of the following in the indicated order: TFIID, which contains the TBP subunit that binds to TATA box DNA; TFIIA and TFIIB; a complex of Pol II and TFIIF; TFIIE; and finally, TFIIH (see Figure 9-19).

• The helicase activity of a TFIIH subunit helps to separate the DNA strands at the transcription start site in most promoters, a process that requires hydrolysis of ATP. As Pol II begins transcribing away from the start site, its CTD is phosphorylated on serine 5 by the TFIIH kinase domain.

• In metazoans, NELF and DSIF associate with Pol II after initiation, inhibiting elongation fewer than 100 bp from the transcription start site. Inhibition of elongation is relieved when cyclin T–CDK9 (also called P-TEFb) associates with the elongation complex and CDK9 phosphorylates subunits of NELF, DSIF, and serine 2 of the Pol II CTD.