Transcription in four dimensions: nuclear receptor-directed initiation of gene expression

Abstract

Regulated gene expression, achieved through the coordinated assembly of transcription factors, co-regulators and the basal transcription machinery on promoters, is an initial step in accomplishing cell specificity and homeostasis. Traditional models of transcriptional regulation tend to be static, although gene expression profiles change with time to adapt to developmental and environmental cues. Furthermore, biochemical and structural studies have determined that initiation of transcription progresses through a series of ordered events. By integrating time into the analysis of transcription, chromatin immunoprecipitation assays and live-cell imaging techniques have revealed the dynamic, cooperative, functionally redundant and cyclical nature of gene expression. In this review, we present a dynamic model of gene transcription that integrates data obtained by these two techniques.

Figure 1

Cyclical recruitment of transcription factors to the pS2 promoter. The recruitment of cofactors (top) and the dynamics of the nucleosome (bottom) mediated by oestrogen receptor-α (ER-α) on the pS2 promoter in MCF-7 cells in the presence of oestrogen. The periodic association of HATs, HDACs, HMTs and SWI/SNF (Brg/Brm), as well as other important complexes that contribute to ER-α dynamics and promoter clearance are shown with arrows. The association phase of each productive cycle is shown by grey bars. Location of the modified histones in nucleosome E (NucE) and nucleosome T (NucT) are shown, with increased accessibility of either the TATA box or the ERE shown by dashed lines. Schemes are based on Métivier et al (2003) and Reid et al (2003) and our unpublished data. Specific recruitment of NuRD at the end of the second transcriptionally productive cycle corresponds to NucT remodelling, displacement of TBP and demethylation of dimethylated H4 R3 (either complete or with only one CH₃ group). This step, which provokes the promoter to return to the basal state, delineates the two transcriptionally productive cycles. Ac-H3, acetylated histone 3 (K14); Ac-H4, acetylated histone 4 (K16); APIS, AAA ATPase proteins independent of 20S; ERE, oestrogen response element; HAT, histone acetyltransferase; HDAC, histone deacetylase; HMT, histone methyltransferase; Met-H3, dimethylated histone 3 (R17); Met-H4, dimethylated histone 4 (R3); NucE, nucleosome including the ERE; NucT, nucleosome including the TATA box; NuRD, nucleosome remodelling and deacetylating complex; p68, p68 RNA helicase; TBP, TATA-binding protein.

Figure 2

Proposed allosteric, stochastic and dynamic model. This model integrates the general concepts that have emerged from detecting oestrogen receptor-α (ER-α) in live-cell imaging experiments such as fluorescence recovery after photobleaching (FRAP) and those from chromatin immunoprecipitation (ChIP) assays. This model incorporates both stochastic and deterministic concepts into transcriptional attainment. We postulate that transcriptionally productive complexes, which have slower mobility, are rarely formed on promoters. Transcription initiation requires a specific sequence of events to occur, defining a transcriptional ratchet that orientates progression through the cycles. Before that one deterministic event takes place, many rapid stochastic and transient associations of factors occur that are unproductive. It is only when a specific required factor is recruited at the appropriate time that progress is made. Allostery is instrumental in these transitions, as functional, three-dimensional changes are anticipated to occur on all participating partners (namely, proteins, DNA and RNA). Whereas FRAP experiments mainly detect the rapid, unproductive binding of factors, ChIP assays allow the determination of the precise kinetics of the productive associations and of the time required for the transition from one step to another.