Transcription from the perspective of the DNA: twists and bumps in the road

Abstract

Although nature's design of the DNA double helix is ingenious for the storage of information, this design creates topological problems for the processes that occur on the DNA. Cellular processes, such as transcription, replication, chromosomal segregation, and chromosomal condensation, are all complicated by the double helix. The problem is compounded in cells since the DNA is in chromatin. Topoisomerases relax positive and negative superhelical turns in DNA, and thereby topoisomerases have long been recognized as key components of the DNA replication and chromosome segregation and condensation machinery. A role for topoisomerases in the transcription process has also been noted in living cells, but only recently has such a role been recapitulated in the test tube for transcription reactions. New data are discussed that demonstrate that for in vitro transcription reactions, topoisomerases are dispensable when the template is naked DNA, but when the template is reconstituted into chromatin, topoisomerases are required for transcription to proceed efficiently.