When genes are transcribed into RNA, the complexes of RNA polymerase (and factors), DNA and RNA should undergo multiple conformational changes. We have been elucidating molecular and sub-molecular level interactions between the macromolecules and their changes from initiation, elongation to termination, especially in the interactions between polymerase and DNA or RNA. The interaction changes are complex, multiple and sequential in each stage of transcription. Single-subunit RNA polymerases are excellent models for elucidating universal fundamental mechanisms underlying all classes of transcription.
(1) Elongation and Termination by Phage RNA Polymerase: Macromolecular interactions between phage T7, SP6 and K11 RNA polymerases and their promoters have been studied in the lab. Now, sub-molecular level interactions between the single-subunit polymerase and transcript RNA or template DNA are being elucidated during elongation and termination as monitored by cross-linking especially when they approach a sequence-specific terminator.
(2) Global Search for Factors Binding to Promoters in Vivo. Our current interests are to characterize all the transcription factors that bind to a
particular promoter in vivo. We develop a platform technology for isolating promoter-binding protein complexes in vivo. High-throughput proteomic
identification for a particular promoter would reveal all the factors involved in its transcriptional regulation and their changes.
(3) Human Mitochondria RNA Polymerase and Factors: Human mitochondrial transcription initiation complexes have been only recently characterized
and reconstituted. The single-subunit RNA polymerase and initiation factors are characterized as their genes were cloned and expressed in E. coli, and
the macromolecular interactions are elucidated with reconstituted initiation complexes.