1022-7954/05/4109- © 2005 Pleiades Publishing, Inc.
Russian Journal of Genetics, Vol. 41, No. 9, 2005, pp. 945–956. Translated from Genetika, Vol. 41, No. 9, 2005, pp. 1157–1169.
Original Russian Text Copyright © 2005 by Shidlovskii, Kopytova, Kurshakova, Nabirochkina.
STAGES OF TRANSCRIPTION. MODEL
OF SEQUENTIAL PIC ASSEMBLY
The process of transcription may be conventionally
divided into the following main stages: preinitiation
(assembly of the preinitiation complex, PIC), initiation,
promoter escape, elongation, and termination. RNA
polymerase II (Pol II) is incapable to recognize the
basal promoter and initiate transcription. For this, the
main transcription factors TFIIA, B, D, E, F, and H are
required. These factors are needed for positioning the
polymerase molecule on the promoter and for tran-
scription initiation itself. They are essential for tran-
scription of virtually all structural genes [1, 2].
The assembly of the preinitiation complex (PIC) on
the promoter from the above factors is the key stage of
transcription. Of the general transcription factors, only
the TFIIA, B, and D complexes can directly bind to the
promoter region. The remaining factors are recruited
and kept in the PIC by protein–protein interactions.
Based on in vitro experiments, a model of sequential
PIC assembly was designed. According to this model,
the TFIID protein complex consisting of factors TBP
and TAFs (TBP-associated factors) is the ﬁrst to inter-
act with the promoter. TBP binds to a TATA sequence;
TAFs also are involved in promoter binding. It has been
shown in vitro that the PIC may be assembled in the
absence of TAFs, which suggests the central role of
TBP in DNA binding. In binding, TBP bends DNA, so
that a BRE promoter element opens to interact with
TFIIB. The latter is recruited to PIC through interaction
with TFIID and BRE. In vivo, the TFIID–TATA com-
plex also binds TFIIA to form the metastable, pro-
moter-bound DAB complex (TFIID–TFIIA–BRE).
Then, the preformed Pol II–TFIIF complex binds to
TFIIB, which positions the polymerase molecule rela-
tive to the promoter. One of the TFIIF subunits, which
is homologous to the prokaryotic
nonspeciﬁc Pol II–DNA binding. In addition, TFIIF
stabilizes the DNA–TBP–Pol II complex. The so-called
closed PIC is thus formed, in which Pol II is not acti-
vated to start transcription. A part of promoter DNA
involved in this complex largely preserves its secondary
structure: both DNA strands are linked by hydrogen
bonds. This complex, whose structure is similar in all
eukaryotes, is relatively stable. It is thought that the
TFIIB complex, which interacts with TBP, Pol II,
TFIIF, and DNA, plays a central role in the PIC forma-
The last stages of the PIC formation involve TFIIE
and TFIIH. TFIIE binds to TFIIF and is thought to sta-
bilize the Pol II–DNA bond. In addition, TFIIE partici-
pates in binding and regulating the function of TFIIH.
Apart from TFII factors, the PIC was shown to include
The transcription initiation starts from the ATP-
dependent local melting of PIC DNA and its entering in
the active polymerase center. This process involves
helicases that are members of TFIIH. At the same time,
isomerization of the total complex occurs, after which
it is referred to as open. The key role in the transition to
the open state is played by factors TFIIH, E, and F. The
open PIC is unstable. RNA polymerase together with
TFIIB starts scanning the DNA template searching for
the transcription initiation point, after which mRNA
synthesis begins [1, 4, 5].
The early stages of RNA synthesis are characterized
by unstable RNA polymerase–DNA association and a
strong tendency to terminate synthesis prematurely.
Consequently, after the initiation, synthesis of short
(about 10-mer) oligoribonucleotides may be observed.
This stage was termed abortive transcription. Breaking
bonds between RNA polymerase, promoter, and tran-
scription initiation factors with simultaneous formation
of a stable elongation complex (TEC) occurs after syn-
Principles of Functioning of the Machinery
of Transcription Initiation by RNA Polymerase II
Yu. V. Shidlovskii
, D. V. Kopytova
M. M. Kurshakova
, and E. N. Nabirochkina
Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia;
fax: (095)135-41-05; e-mail: firstname.lastname@example.org
Center for Medical Research of Oslo University, Moscow, 119334 Russia
Received January 28, 2005
—This ﬁnal review describes the general principle and mechanisms that underlie functioning of the
machinery of transcription initiation by polymerase II in eukaryotes. The main models of transcription initia-
tion, the module principle underlying the structure of the transcription complex, the regulation of transcription
initiation, and the association between the nuclear architecture and transcription are discussed.