Transcriptional elongation complex

RNA polymerase (4) ATP Multisubunit polymerase within transcription elongation complex Nucleus Translocation along DNA during transcription... 

Kainz M., Roberts J. (1992) Structure of transcription elongation complexes in vivo. Science 255 838. 

Figure 26.9 Protein-nucleic acid interactions in the transcription elongation complex. 

Wooddell, C. I., and Burgess, R. R. (2000). Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity crosslinking [in process citation]. Biochemistry 39(44), 13405-13421. 

The most incisive studies of the problem at the molecular level are those from the Felsenfeld laboratory (see, for example. Refs. [75,76]). They have shown that at least under some circumstances, a polymerase can step around a nucleo-some, displacing it in cis, but not causing dissociation. It is not yet clear, however, if this mechanism is physiologically relevant and/or whether it is the only mechanism. There exist results in apparent conflict with this model (i.e.. Ref. [77]). That the in vivo process is certainly more complex than the in vitro models used to date is further indicated by the discovery of elongation factors that markedly increase transcriptional rates and suppress pausing (see, for example, Conaway and Conaway [78]). Thus, the question as to how transcription elongation occurs in a chromatin template remains at least partially unresolved. For a further discussion, see Jackson, this volume, p. 467. 

S. cerevisiae 1000 molecules/cell. Chdlp is partially redundant with SWI/SNF complex, ISWlp and ISW2p [94,98]. Chdlp may function during transcript elongation [255]. 

RNA Strand Initiation and Promoter Clearance TFIIH has an additional function during the initiation phase. A kinase activity in one of its subunits phosphorylates Pol II at many places in the CTD (Fig. 26-9). Several other protein kinases, including CDK9 (cyclin-dependent kinase 9), which is part of the complex pTEFb (positive transcription elongation/actor b), also phosphorylate the... 

Fig. 1 Molecular and biochemical basis of Friedreich s ataxia (FRDA). (a) A GAA-repeat expansion in the first intron of the FRDA gene results in decreased levels of frataxin as a result of inhibition of transcriptional elongation, (b) Alterations in mitochondrial biochemistry that are associated with reduced frataxin levels. Proposed functions for frataxin include iron binding, protection and synthesis of Fe-S clusters, providing a binding partner for ferrochetalase in heme (haem) metabolism, and providing a metabolic switch between heme metabolism and Fe-S cluster biosynthesis. In FRDA, reduction of firataxin results in lowered levels of aconitase and respiratory complexes 1,11, and 111. Cytosolic proteins that contain Fe-S clusters may also be affected. Inability to form Fe-S clusters leads to an accumulation of iron, which leads to increased free radical formation (Fenton chemistry) in these organelles. Increased free radical formation may feed back to further decrease levels of Fe-S clusters, which are known to be sensitive to oxidative stress.

Cyclin T-CDK9 (review Simone and Girodano, 2001) functions as a positive transcription factor during transcription elongation of RNA polymerase II by phosphor-ylating the CTD. The HIV regulatory protein Tat binds to and specifically activates the cyclin T-CDK9 complex. 

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