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Lee et al. J Cancer Metastasis Treat 2021;7:27 https://dx.doi.org/10.20517/2394-4722.2021.58 Page 3 of 18

General transcriptional machinery and its main regulators
Transcription starts from the assembly of the pre-initiation complex (PIC), a complex of about 100 proteins
that binds to the transcription start sites of genes and promotes DNA entry to the active site of RNA
Polymerase II (RNA Pol II) for transcription initiation [Figure 1]. The PIC formation requires the
[32]
recruitment of several general transcription factors (GTFs), which include TFIIA, TFIIB, TFIID, TFIIE,
[33]
TFIIF, and TFIIH . Promoters typically have a TATA box [TATA(A/T)A(A/T)(A/G)] located 25 base
pairs upstream of the transcription start site .
[34]
TATA binding protein (TBP), which is a subunit of TFIID, binds to the TATA box in the promoter of
DNA. Subsequent recruitment of TFIIA and TFIIB stabilizes this TBP-promoter complex. TFIIB recruits
RNA polymerase II and TFIIF to the promoter complex. This binding further stabilizes the RNA Pol II
complex and other initiation factors on the promoter to confirm that the transcription initiation by the
RNA Pol II occurs at the appropriate location [32,35] .

The mediator complex, which is a 23-subunit assembly, cooperatively binds with RNA Pol II and a subset of
transcription factors (TFs) during the process of the PIC formation despite not binding directly to DNA
[36]
sequence-specifically . The mediator complex is recruited to promoter-enhancer regions by TFs and
functions to signal the messages from the TFs to RNA Pol II, thereby enabling TF-dependent regulation of
gene expression. Such communication is indispensable for transforming biological inputs from TFs to
physiological responses through changes in gene expression .
[37]

The final GTF to be recruited to the PIC is TFIIH, consisting of multiple subunits, including MAT1, cyclin-
dependent kinase 7 (CDK7), its paired cyclin H, and ATP-dependent helicases (XPB and XPD) .
[38]
[39]
Following recruitment, XPB enables promoter opening for transcription to occur , whereas CDK7-
mediated phosphorylation of C-terminal domain (CTD) of RPB1, which is the largest subunit of RNA Pol
II, at serine 5 induces dissociation of the mediator from the PIC, thereby leading to binding of mRNA
capping enzymes that catalyze addition of the methyl-guanosine cap structure to the 5` end of nascent
mRNA transcript . CDK7 also phosphorylates TFIIE that facilitates activities of TFIIH as an ATPase and a
[40]
kinase, and its phosphorylation drives the transition from transcription initiation to elongation .
[41]
Elongation of RNA Pol II pauses 30-50 nucleotides downstream of the transcription start site. This
transcriptional pause enables rapid and synchronous transcriptional activation upon release of RNA Pol II
[42]
from the paused state and also functions as a check point for mRNA quality control . The positive
transcription elongation factor b (P-TEFb)/CDK9 complex is then recruited to the paused RNA Pol II and
cooperates with bromodomain-containing protein 4 (BRD4) and the super elongation complex to release
RNA Pol II for active transcription. While CDK7 is important for driving the initial stages of RNA Pol II
elongation, CDK9 produces a fully matured elongation complex that can engage in mRNA slicing,
termination, and co-transcriptionally modifying the chromatin structure . In addition, the P-TEFb
[43]
promotes the CTD phosphorylation at serine 2, a conserved marker of elongating RNA Pol II in promoting
recruitment of the 3`-end processing and splicing factors for mRNA maturation . CDK12 and CDK13 also
[44]
directly contribute to the CTD phosphorylation at serine 2, transcription elongation , splicing of pre-
[45]
mRNA, and transcriptional termination .
[46]
Mechanisms of transcriptional dysregulation in cancer
In normal cells, cell identity is largely controlled by the action of TFs that interact with specific regions in
the genome to regulate gene expression. The TFs deregulated in cancer can be subdivided into three major
groups: (1) master/lineage TFs involved in organization of cell identity; (2) proliferation control TFs that
can amplify transcriptional output to meet cellular demands; and (3) signaling TFs that regulate a series of