Transcription is the first step of an essential multistep bioprocess and consists of three major steps: initiation, elongation and termination
[11][78]. In eukaryotes, the activity between transcription initiation and elongation can be further described in five major steps: (1) chromatin remodeling; (2) formation of the preinitiation complex (PIC); (3) formation of an open complex and abortive synthesis of short (2–8) nt RNAs; (4) promoter pausing and escaping by RNAPII; and (5) pause releasing and productive elongation (). In this section, we will describe these steps in detail.
Figure 1.
Transcriptionally Active Chromatin Structure and the Five Steps of Transcription Activation.
Step 1
. Chromatin remodeling;
Step 2
. Formation of transcription pre-initiation complex (PIC);
Step 3
. Unwinding of the DNA strands to form the open complex;
Step 4
. RNA polymerase II (RNAPII) pausing and escaping from the promoter;
Step 5
. Productive transcript elongation by RNAPII. Abbreviations: SWI-SNF, switch/Sucrose non-fermentable; TF, transcription factor; H, histone; PIC, preinitiation complex; GTFs, general transcription factors; TFIIA-F, transcription factor II A–F; TAF1, TATA-box binding protein associated factor 1; TBP, TATA-box binding protein; CDK7/TFIIH, cyclin-dependent kinase 7; TSS, transcription start Site; Spt5/4, suppressor of Ty 5 and 4 (transcription elongation factors 5 and 4); DSIF, DRB sensitivity-inducing factor; CDK9/p-TEFb, cyclin-dependent kinase 9.
Chromatin remodeling begins with the interaction between sequence-specific transcription factors (TFs) and chromatin modifiers to “open” condensed chromatin (heterochromatin)
[12][79] (, step 1), allowing RNAPII/Mediator complex to bind specific DNA sequences and form a PIC at the gene promoters and enhancers
[12][79] (, step 2). The mediator of RNAPII transcription (mediator) complex is critical in transcription activation and is assembled at the PIC. Interactions between RNAPII and mediator complex are facilitated by the C-terminal domain (CTD) of the largest unit, RPB1, of RNAPII, which contains a highly conserved region with up to 52 repeats of the heptad of Y
1S
2P
3T
4S
5P
6S
7 (YSPTSPS) largely unphosphorylated during initiation
[13][80] (, step 2). Open complex formation is initiated by the multiprotein complex TFIIH. TFIIH can not only unwind DNA to form the transcription “bubble” through its associated helicases (, step 3), but can also phosphorylate the YSPTSPS CTD serine 5 residue through its associated CDK7 and cyclin H kinases, stimulating mediator complex and PIC general TF dissociation and allowing RNAPII escape from the promoter
[14][15][81,82] (, step 3). Two other factors, DRB sensitivity inducing factor (DSIF) and negative elongation factor (NELF) contribute to the transition from transcriptional initiation to elongation and RNAPII promoter escape
[16][83]. DSIF is a heterodimer composed of Spt4 and Spt5, and NELF consists of four subunits (A, B, C/D, and E)
[17][18][84,85]. Spt5 interacts with the 5′ cap of nascent RNA (pre-mRNA), and then NELF recognizes the Spt5 interface
[19][86]. TFIIH interacts with DSIF and NELF, which then cooperatively induce RNAPII promoter escape and subsequent pausing (, step 4). Finally, transcription elongation is promoted by P-TEFb
[20][87], which consists of a kinase/cyclin pair of CDK9 and CCNT1 (or CCNT2). P-TEFb phosphorylates DSIF and RNAPII CTD serine 2, inducing NELF release from RNAPII
[21][88] and allowing RNAPII interaction with other elongation factors and chromatin modifying complexes to ensure productive transcription elongation, respectively
[22][23][24][89,90,91] (, step 5).