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Chapter 13
11-11-05
Unlike prokaryotes, in which sigma factors are solely responsible for directing RNA Pol to
promoters, & txn is regulated by only a few other proteins (e.g., lac repressor, CAP,
etc.), eukaryotic txn initiation requires numerous proteins & many additional proteins
are involved in regulating txn.
These proteins are called transcription factors (TFs).
Two classes of TFs: (1) General TFs
 Required for txn.
(2) Gene-specific TFs
 Responsible for regulating txn.
Assembly of Txn Initiation Complex on promoter.
General TFs assist RNA Pol II binding to core promoter region.
TFIID binds to TATA box within proximal promoter.
= TBP + >8 TBP-Associated Factors ( TAFs)
Joined by TFIIA, then TFIIB.
Remainder of TFs bind along with RNA Pol II.
In vivo, Initiation Complex can't efficiently assemble on promoter without assistance from
Activator proteins that bind to Promoter-Proximal & Enhancer elements.
Tissue-specific & temporal regulation of txn by enhancers.
Either: Activators only expressed in certain tissues or at certain times.
Or
Tissue-specific Repressor may bind to silencer element and either interfere
with Activator binding, or Activator's ability to interact with basal TFs.
Steroid Hormone Receptors
A special class of Activators.
Their activities are regulated by binding to specific steroid hormone.
When hormone not present, receptor is in the cytoplasm & inactive.
When hormone enters cell, it binds to the receptor, changes its conformation & the
receptor-hormone complex enters the nucleus.
Receptor binds to specific enhancer elements & activates the txn of a specific subset of
genes.
Activator Protein Domains
Most Activators are composed of at least 2 functional domains:
DNA binding domain
A relatively few DNA binding motifs are found in many different Activators.
Two examples:
(1) Helix-turn helix motif
"Recognition" -helix fits into major groove of DNA.
Amino acids within recognition helix form H-bonds with bases in
major groove.
2nd -helix ("stabilization helix") is separated from recognition helix by a
short "turn of a few a.a.
Interactions between stabilization & recognition helices help stabilize
h-t-h teriary structure & help position recognition in major
groove.
(2) Zinc Finger motif
2 Cys's & 2 His's coordinate binding of Zn atom.
Zn-binding is necessary in order for formation of tertiary structure of
this DNA binding motif.
Left side of finger, -sheet
Right side of finger, -helix
Interactions between -sheet & -helix sides of finger
position helix in major groove.
Activation Domains
Physically interact with general TFs or other proteins.
These interactions facilitate assembly of Pol II Initiation Complex on promoter
& initiation of txn.
Summary:
In order to initiate txn, RNA Pol II Initiation Complex must assemble on the
promoter.
TFIID binding to TATA box within core promoter directs where Initiation
Complex will form and in which direction txn will proceed.
However, Initiation Complex needs the help of other proteins, Activators, in order
to assemble.
Some Activators bind to promoter-proximal elements, others bind to enhancer
elements, due to the sequence-specific DNA binding properties of their DNA
binding domains.
Activators' activation domains physically interact with general TFs to facilitate
assembly of Initiation Complex.
Tissue-specific &/or temporal regulation of txn of genes is controlled by when
Activators are expressed &/or they are able to bind to a gene's enhancer
element(s).
Some genes have multiple enhancer elements that regulate txn in different tissues
or at different times.
These contain binding sites for different Activators that may be present at different
times or in different tissues.