RNA Polymerase II Transcription Elongation Control

Regulation of gene expression is critical in determining cell identity, development and responses to the cellular environment. DNA is the inherited source of genetic information and regulation of gene expression starts with the selection of which genes will undergo transcription. RNA, the product of transcription, is then utilized to generate functional products, including being translated into protein or processed into functional RNA. In eukaryotes, protein coding genes are transcribed by RNA polymerase II (Pol II) into messenger RNAs (mRNA). These short-lived RNA species have a variety of characteristics and are extensively regulated from production to degradation.1 With the assistance of methods such as those using microarrays and high-throughput sequencing, the scale and depth of Pol II transcription studies have exploded. The sheer volume and complexity of data from many sources have even triggered a call for careful rethinking of the methods used for analysis and interpretation.2 It is doubtless, though, that regulation of transcription critically affects gene expression and thus cell state and cellular identity.3 Pol II transcription starts with the assembly of a pre-initiation complex (PIC) with general transcription factors (GTFs) that recognize DNA sequence elements around the promoter and recruit Pol II.4 This process also requires the multi-subunit Mediator complex that could be viewed as a platform for transcription.5 In the PIC, the two strands of DNA are separated and the template strand migrates into the active center of Pol II, thereby allowing the synthesis of RNA from the transcription start site (TSS).6 Although initiation could be viewed as the “on” switch for Pol II, much of mRNA production is regulated at the elongation phase.7 Pioneering studies on MYC8, HIV9, and HSP7010 transcription have indicated that Pol II can be transcriptionally engaged in the 5′ end of genes without generating full-length mRNA prior to induction. Genome wide analyses showed that a large fraction of human and Drosophila genes have poised Pol II about 50 nt downstream of the transcription start site (TSS).11 Under various activation conditions, Pol II is released from promoter proximal positions to produce full length transcripts and subsequently increase mRNA level.12 The factor required to trigger Pol II to enter productive elongation is P-TEFb.13 Productive elongation has a high elongation rate that ranges from 1.1 to 4.3 kb/min as measured by many different methods.14 During productive elongation the RNA is co-transcriptionally spliced and polyadenylated to generate mature mRNAs.15 Mirroring the dramatic differences in properties, productive elongation complexes have significantly different protein compositions than early elongation complexes.16 Transcription termination is crucial for recycling Pol II after a round of transcription and globally releasing Pol II from chromatin prior to cell division.17 It also helps to prevent interference of promoter function by transcription from neighboring genes.18 In metazoans, Pol II termination downstream of the 3′ end of almost all protein coding genes requires a functional Poly(A) signal and is always coupled with 3′ end processing.19 Because termination is the end of transcription elongation and by definition is a very transient state, it has been notoriously difficult to study, especially in vivo.20 The steps in transcription have been traditionally studied individually in great depth using specific genes. The development of new technologies has allowed transcription to be viewed and studied on a global scale. This review discusses the bird’s eye view of Pol II transcription in the genome as well as insights provided by detailed mechanistic studies. Recent studies are emphasized, but initial discoveries are also described to provide a historical perspective. We mostly focus on metazoan systems, although some studies from yeast are also described for comparative purposes. Our goal is to cover topics in multiple levels so that beginning scientists as well as experienced researchers will find the review useful.