The Dynamic Association of RNA Polymerase II with Initiation, Elongation, and RNA Processing Factors during the Transcription Cycle

Kristi L. Penheiter and Judith A. Jaehning

Department of Biochemistry and Molecular Genetics and Molecular Biology Program, University of Colorado Health Sciences Center, B121, 4200 East 9th Avenue, Denver, CO 80262

Key Words: transcription, RNA polymerase II, Pafl complex,initiation,elongation,RNA processing


The transcription of protein encoding genes by RNA polymerase II (RNAPII) is a complex and highly regulated process. RNAPII and several of its associated general transcription factors (GTFs), including TBP, TFIIB, TFIIF, and TFIIH are sufficient for recognition and low levels of accurate transcription from common core promoter elements in vitro (Roeder, 1996 and Orphanides et al., 1996). However, in addition to these factors necessary for basal transcription initiation, accurately regulated transcription requires additional cofactors which assemble into various complexes to mediate the communication between DNA-binding activators, as well as repressors, and RNAPII. The precise manner in which the RNAPII transcription machinery is assembled upon a region of DNA determines the ability of RNAPII to initiate the synthesis of mRNA at a specific location and with a defined frequency and processivity. The dynamic nature of the RNAPII holoenzyme and the ever-increasing number of RNAPII-associated factors being identified that regulate transcription at the levels of initiation, elongation, and processing will be discussed in this chapter.

RNA Polymerase II and Transcription Initiation

In order to properly initiate transcription of eukaryotic mRNAs, transcriptional activators recruit the RNAPII-containing machinery to promoters of protein-coding genes. The assembled apparatus, or "holoenzyme" consists of the 12-subunit RNAPII, a subset of GTFs, and one or more multisubunit complexes referred to as coactivators or mediators. How this assembly and recruitment occurs is a highly complex and variable process, and a growing number of holoenzyme complexes and subcomplexes are being identified.

A: The Core RNAPII

The yeast core RNAPII is a multi-subunit enzyme comprised of 12 proteins, Rpbl-Rpbl2, ranging in size from ~8kDa (RpblO and Rpbl2) to ~200kDa (Rpbl). Of the 12 subunits, 10 are encoded by genes essential for cell viability. The extreme importance of the enzyme to all eukaryotic cells is also reflected in the high degree of structural conservation among the subunits not only between eukaryotic species, but also between the three nuclear RNAPs and the prokaryotic core RNAP. For example, six subunits of the human RNAPII can functionally substitute for their yeast homologs (McKune et al., 1995). In addition, the Rpbl, Rpb2, Rpb3, and Rpbll subunits of RNAPII are homologous to subunits of RNAPI and RNAPIII, and Rpb5, Rpb6, Rpb8, RpblO, and Rpbl2 are shared among all three RNAPs. Only three subunits, Rpb4, Rpb7, and Rpb9 are

Corresponding Author: Judith A. Jaehning, Tel: (303) 315-3004, E-mail: [email protected]

unique to RNAPII (reviewed in Hampsey, 1998).

Extensive mutational analyses of RPB1 and RPB2 (reviewed in Archambault and Friesen, 1993) have revealed roles for Rpbl and Rpb2 in regulating the efficiency of transcription initiation and directing start site selection (Berroteran et al., 1994; Hekmatpanah and Young, 1991) as well as elongation (Archambault et al., 1992; Powell and Reines, 1996).

The X-ray crystallographic structure of the complete 12-subunit yeast RNAPII, which includes the reversibly-associating heterodimer of Rpb4 and Rpb7, has recently been determined (Bushnell and Kornberg, 2003; Armache et al., 2003; comment by Asturias and Craighead, 2003). The Rpb4/7 subunit was not present in previous structures of the "core" RNAPII, but it is known to be required for transcription initiation (Edwards et al., 1991), whereas the RNAPII 10-subunit core is sufficient for elongation. This structural determination reveals that the Rpb4/7 heterodimer maintains the polymerase in the conformation of a transcribing complex and is in a position to interact with general transcription factors and mediator components, thus rendering it a crucial factor for proper transcription initiation. A complete list of the RNAPII subunits and some of their features is shown in Table 3.1 (reviewed in Lee and Young, 2000; Cramer, 2002).

Table 3.1 Yeast RNA polymerase II subunit composition
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