INTRODUCTION -Transcription -Transcription Factors CLASSES OF TFs GENERAL TRANSCRIPTION FACTORS MEDIATOR FUNCTIONS -Formation of preinitiation complex -Elongation -Termination -Differential enhancement of transcription -Developmental REFERENCES

1. TRANSCRIPTION FACTOR IN EUKARYOTES
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

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CONTENTS
INTRODUCTION
-Transcription
-Transcription Factors
CLASSES OF TFs
GENERAL TRANSCRIPTION FACTORS
MEDIATOR
FUNCTIONS
-Formation of preinitiation complex
-Elongation
-Termination
-Differential enhancement of transcription
-Developmental
REFERENCES

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INTRODUCTION
Transcription- The process of making messenger RNA (mRNA) from a DNA template by
RNA polymerase.
Involves three steps:-
1) INITIATION-
A group of proteins called transcription factors mediate the binding of RNA polymerase and the
initiation of transcription.
2) ELONGATION-
RNA polymerase moves along the template strand, synthesising an mRNA molecule.
3) TERMINATION-
Termination is the final step of transcription. Termination results in the release of the newly
synthesized mRNA from the elongation complex.

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Transcription factor- A protein that binds to DNA and regulates gene expression
by promoting or suprresing transcription.
It is protein that regulates the transcription of genetic information from DNA to mRNA, by
binding to a specific DNA sequence.
The function of transcription factor is to regulate - turn on and off - genes in order to make
sure that they are expressing in right place and in right time.
Transcription factors are required for RNA polymerase II to initiate transcription.
There are upto 2600TFs (about 10% of the whole gene) in the human genome.

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TFs works alone or with other proteins in a comlex, by promoting (as an activator) or blocking
(as a repressor) the recruitment of RNA polymerase to specific genes.
A defining features of TFs is that they contain at least one DNA-binding domain (DBD), which
attaches to a specific sequence of DNA adjacent to the genes that they regulate.
The no. of transcription factors found within an organism increases with genome size, and larger
genomes tends to have more transcription factors per gene.
Other proteins such as coactivators, chromatin remodelers, histone acetyltransferases, histone
deacetylases, kinases and methylases are also essential to gene regulation but lack DBD and
therefore are not TFs.

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CLASSES OF TRANSCRIPTION FACTOR
Transcription factors may be classified into three classes:
1) Mechanism of action:
There are two mechanistic classes of transcription factors:
a) General transcription factors are involve in the formation of preinitiation complex.
The most common are TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.
b) Upstream transcription factors are proteins that bind somewhere upstream of the initiation site
to stimulate or repress transcription.

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2) Functional:
Classified according to their regulatory function.
a) Constitutively active- present in all cells at all time- general transcription factors, Sp1, NF1.
b) Conditionally active- requires activation.
HNF, PIT-1.
3) Structural:
Classified based on the sequence similarily and hence the tertiary structure of their DNA
binding domain.

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General Transcription Factors (GTFs)
In eukaryotes, an important class of transcription factors called general transcription factors
(GTFs) are necessary for transcription to occur.
Also known as basal transcriptional factors.
Many of these GTFs do not actually bind DNA, but rather are part of the large transcription pre-
initiation complex that interacts with RNA polymerase directly.
General transcription factors are required for initiation of transcription by RNA
polymerase II.
1) TFIIB
2) TFIID
3) TFIIE
4) TFIIF
5) TFIIH
6) TFIIA

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1)TFIIB-
It involved in the formation of RNA polymerase preinitiation complex (PIC).
Provides a platform for PIC formation by binding and stabilising the DNA-TBP (TATA-binding
protein) complex and by recruiting RNA polymerase II and other transcription factors.
TFIIB is a single 33kDa polypeptide consisting of 316 amino acids.

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2) TFIID-
Before the start of transcription , the TFIID complex binds to the TATA box in the core promoter
of the gene to position the polymerase properly.
Serves as the scaffolds for assembly of the remainder of the transcription complex.
Composed of two subunits- TBP and more than eight TAFs.

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3) TFIIE-
Makes up the RNA polymerase II preinitiation complex.
Tetramer of two alpha and two beta chains.
It recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal
domain kinase and DNA-dependent ATPase activities of TFIIH.
Required for promotor clearance by RNA polymerase.

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4) TFIIF-
TFIIF binds to RNA polymerase II when the enzyme is already unbound to any other transcription
factors, thus avoiding it from contacting DNA outside the promoter.
TFIIF stabilizes the RNA polymerase II while it is contacting TBP and TFIIB.

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5) TFIIH-
Transcription factor II Human is an important protein complex, having roles in transcription of
various protein coding genes and DNA nucleotide excision repair (NER) pathways.
Consist of ten subunits.
Recruits RNA pol II to the promoter of genes.
Function as helicase that unwinds DNA.

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6) TFIIA-
TFIIA interacts with the TBP subunit of TFIID and aids in the binding of TBP to TATA-box containing
promoter DNA.
Interaction of TFIIA with TBP also results in the exclusion of negative (repressive) factors that
might otherwise bind to TBP and interfere with PIC formation.
Also acts as coactivator for some transcriptional activators, assisting with their ability to increase
or activate transcription.
it is a Heterodimer with two subunits.

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MEDIATOR
The sequential recruitment of all general transcription factors and RNA polymerase II
represents the minimal system required for transcription, some additional factors are also requir-
ed to stimulate transcription within the cell.
These factors include a large protein complex, called MEDIATOR.
Consists of more than 20 distinct subunits and interacts both with general transcription factors
to the gene-specific transcription factors that regulate gene expression.
The mediator proteins are released from the polymerase following assembly of the preinitiation
complex and phosphorylation of the polymerase C-terminal domain.
The phosphorylated CTD then binds to other proteins that facilitate transcriptional elongation
and function in mRNA processing.

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FUNCTIONS OF TFs
1) Formation of polymerase II preinitiation complex:
Sequence elements at polymerase II promoters include the TATA box, 25 to 30 nucleotides
upstream of the transcription start site, the TFIIB recognition element (BRE) approximately 35
nucleotides upstream of the transcription start site, the initiator (Inr) element, which spans the
transcription start site, and several elements downstream of the transcription start site (the DCE
, MTE and DPE).
Formation of a transcription complex is initiated by the binding of transcription factor TFIID to
the promoter.
One of subunit of TFIID called TBP binds specifically to the TATA box while other subunit of TFIID
(TAFs) bind to the Inr, DPE, DPC and MTE sequences.

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The binding of TFIID is followed by recruitment of a second general transcription factors (TFIIB),
which binds to TBP as well as to BRE sequences.
TFIIB serves as a bridge to RNA polymerase II, which binds to the TBP-TFIIB complex in associa-
tion with a third factor, TFIIF.
Following recruitment of RNA polymerase II to the promoter, the binding of two additional factors
(TFIIE and TFIIH) complete formation of the preinitiation complex.

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2) In the process of Elongation-
Transcription by RNA polymerase II initiates following phosphorylation of CTD serine-5 by the TFIIH
protein kinase .
Following initiation the polymerase synthesizes a short region of RNA and then pause near the
beginning of the gene, typically within about 50 nucleotide of the transcription start site.
The arrest of polymerase at this point results from the association of negative regulatory factors,
including NELF and DSIF that prevent further transcription.
Continuation of transcription is dependent on the action of another factor called P-TEFb, it
contains a protein kinase that phosphorylates NELF and DSIF as well as serine-2 of the RNA
polymerase CTD .

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3) In the process of Termination-
Protein coding genes have 2 regions;
i) AAUAAA sequence (upstream) which is recognise by the protein factor known as CPSF protein.
ii) GU rich sequence (downstream) which is recognise by protein Cstf .
After binding of these CPSF cleave the mRNA after 10-30 nucleotides of AAUAAA sequence.

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4) Diffrential enhancement of transcription:
Other transcription factors differentially regulate the expression of various genes by binding to
enhancer region of DNA adjacent to regulate genes.
These TFs are critical to make sure that genes are expressed in the right cell at the right time
and in right amount, depending on the changing requirements of the organism.
5)Development:
Many transcription factors in multicellular organisms are involved in development.
Responding to stimuli, these transcription factors turn on/off the transcription of the appropriate
genes.

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REFERENCES
THE CELL
A Molecular Approach (fifth edition)
Geoffrey M. Cooper
Robert E. Hausman
http://www.khanacademy.org>biolo
gy