Lecture 10 - Modular mechanisms of transcription activation and repression Flashcards
what is a zinc-figer motif
protein regions that fold around a central Zn2+ ion.
2 zinc finger motifs and their occurence
C2H2 zinc finger –> most common motif in humans
C4 zinc finger –> found in approx. 50 human TFs
What are C and H in C2H2 and C4 zinc fingers
a.a cystine and histidine
C2H2 zinc finger how it works, how many of this motif the domain contains, how domain/prot. bind
Binding of 2 C and 2 H to zinc compacts the domain and allows insertion of alpha helix in the major groove.
Usually domain contains 3 or more C2H2 motifs
Motifs bind as monomers
C4 zinc finger how many of this motif the domain contains, how domain/prot binds.
Domain contains only two motifs
Binds as homodimers. Note : like C2H2, fingers insert in DNA
Something particular about binding of domains that have C4 zinc finger motif
Domains have two-fold rotational symmetry and bind to consensus DNA sequences that are inverted repeats.
2 other DNA binding domains
leucine zipper. basic helix-loop-helix (bHLH)
Leucine zipper motif. Leucine characteristic. and consequence
Leucine residue at every seventh position. Leucine is hydrophobic so goes inwards and gives helical form to helices of zipper
How leucine zipper binds DNA
as dimers, often heterodimers
Proteins like leucine zipper principle and how you call them
'’Basic zipper (bZip)’’ is the name of the larger family. Prots in this family have a zipper with a different hydrophobic a.a at every seventh position
basic helix-loop-helix description (diff. w/ basic zipper)
similar to basic zipper but a nonhelical loop seperates two alpha-helical regions.
How bHLH containing proteins bind
Bind as heterodimers
Activation domain a.a usually found
usually high percentage of one or two a.a (Asp, Glu, Gln, Pro, Ser, Thr)
Acidic activation domain what it’s made of and something particular
high percentage of Asp or Glu and is active when bound by a coactivator
Ex. of acidic activation domains (2)
1) RARgamma has to bind retinoic acid to be in an active conformation
2) CREB must be phosphorylated to bind its coactivator CBP and become an active TF.
Activation domains before they bind co-activator
may be random coils/unstructured
Other exemple of act. domain w/ coactivator and how it works
Estrogen receptor ligand-binding activation domain When estrogen (grey) binds activation domain (brown), a green alpha helix interacts with the ligand (domain -> brown). Alpha helix of domain bends and can bind alpha helix subunit of another coactivator
Repressor of estrogen binding in estrogen receptor ligand binding activation domain
Tamoxifen. Blocks binding of estrogen. Domain can’t become active
Length of repression domains (and activation domains)
may be short (<15 a.a.)
Repression domains, 2 (obvious) things it does
Binds co-repressor proteins and mediates protein-protein interaction.
Repressors and activators DNA binding in common (2 things to note)
1) Certain repressors can block activators by binding to their DNA sequence
2) Repressors and activators can bind to common sequences or have their specific sequences
Exemple of repressor and how it interacts with DNA
Bacteriophage 434. Helix interacts with MAJOR groove
Why are TFs required
basal transcription is very low
3 things that can generate transcription factor regulatory diversity
Heterodimers, Inhibitory factors, Cooperative binding of unrelated TFs to nearby sites
Heterodimers : how they can generate TF regulatory diversity
In some heterodimers, each monomer has different DNA-binding and activation/repression domain specificity. Therefore, different combinations between monomers can create diversity.
Inhibitory factors how they work (what 2 known motifs they act on specifically)
block DNA binding by some bZip and bHLH monomers, (which bind as heterodimers)
What is necessary if you want to use inhibitory factors to create TF regulatory diversity ?
You have to express the inhibitory factors
How cooperative binding of unrelated TFs works
If they bind alone to DNA, their bining is weak. They bind together and then bind to DNA and their binding to DNA becomes strong
Why cooperative binding of unrelated TFs enhances their binding to DNA
prot-prot interaction stabilizes their binding
Exemple of 2 TFs that do cooperative binding
NFAT and AP1
What links activation domain of TFs to RNAP II at the promoter and how
mediator complex -> forms molecular bridge between activation domain and Pol II
What could we consider the mediator complex to be
A co-activator of transcription
How does the mediator complex acting as a bridge between activation domain and Pol II activate transcription
Activation-domain + mediator interactions STIMULATE assembly of pre-initiation complex at promoter.
Which part of mediator complex interact with Pol II and how and what other parts of mediator may interact with ?
Head and middle of mediator complex interact directly with RNAP II SUBUNITS. Other mediator domains interact w/ activation domains of activators that are bound to ENHANCERS OR PPEs
Steps of eukaryotic transcription initiation control
1) Pioneer TF binds to sequence in condensed chromatin and recruits chromatin modelling complexes
2) Chromatin is open so activators bind enhancers and PPEs interact with each other and with subunits of mediator complex to assemble preinitiation complex (recruit Pol II and GTFs)
How eukaryotic transcription activators/repressors affect gene expression (2 ways)
1) Interact with co-activators/co-repressors that modulate chromatin structure
2) Interact with Pol II and GTFs
What is required for assembly of PIC in vivo and how cell manages that
several activators. Cell produces specific set of activators required for transcription of a particular gene to express it.
