Lecture notes BIOL3015 Transcriptional Regulation

Transcriptional Regulation
Example regulatory circuits
 Simple negative feedback – homeostasis
 Toggle switch – choice and commitment
 Cycle – alternation of multiple states
Simple negative feedback
 An activity leads to inhibition of said activity
 Gene produces activator that activates promotor of repressor which activates
promotor that stops the activator – maintains balance
 Steady state created
 External influence can change balance
 Chaperone proteins assist in folding of proteins
 A stress can cause an unfolding protein response
 Chaperone recognises protein with hydrophobic surfaces facing outwards
 Chaperones bind to correct unfolding
 Hsp70 normally binds to Hsf1 transcription factor
which keeps Hsp70 inactive as the transcription
factor cannot bind to activation site
 In presence of unfolded protein, transcription
factor releases Hsp70
 More Hsf1 which activates the gene to produce
Hsp70
 Once the cell is oversaturated with Hsp70, it
begins to bind to Hsf1 again which reduces the
production of Hsp70 bringing the ratio back to
balanced
 In healthy neurones, HSF1 is important in
multiple proteins which are for cell survival and
maintenance
 In certain diseases, unfolded protein responses
can be mimicked so the system cannot return
to equilibrium
 Huntington's disease, develops sequences that
act on proteins which are important for HSF1 –
capacity to deal with stress responses is reduced
Toggle switch circuit
 Two possible mutually exclusive outcomes
 Two genes each encode proteins that enhance the
function of the gene but reduce the function of the other
gene
 Whichever gene gains advantage will have the function
amplified
 If b inhibits c and c inhibits b, if you have more b then c is
inhibited, and more b is produced or vice versa
 Two steady states the system can be in
 Bacteriophage lambda – can lysogeny (co-existence) or lysis (murder) the cell

,  The bacteriophage can stay in the cell and merge DNA and the switch to lysis state
and releases bacteriophages killing the cell
 Both advantages in certain scenarios – if lots of host bacteria cells available then lysis
more effective, however, if fewer host cells available then lysogeny is more effective
 Bidirectional promoter (lambda switch region) – transcription proceeds via Prm
(producing C1) or Pr region (producing cro)
 If cro is produced then a homeodimer of 2
cro which promotes expression of cro and
inhibits the expression of c1
 If c1 produced a homeodimer of c1 promotes
the expression of c1 and inhibition of cro
 Both act on PL promotor locus, if more cro
then C3 inhibited, if more c1 then c3
expressed
 C3 degradation reaction inhibits c2
degradation
 Cro produces C2 and C2 activates a promotor
that is in the same orientation as C1
 However, C2 is unstable so does not affect reaction unless C3 is present to stabilise it
 Cro promotes lysis state and c1 promotes lysogeny state
 Whichever produces more, in the beginning, gains the switch and maintains
production
Cycles of transcription
 Data encoded using biological cycles
 Repressilator – 3 bacterial repressors which
each activator by repressor sensitive
promotors
 If one repressor is made then promotor of
another repressor is activated, which in turn
activates the promotor of the next repressor
forming a cycle as each is toggled on and off
Real examples of transcriptional cycles
 Somitogenesis
 Circadian clock
 Cell cycle
Properties of Somitogenesis Oscillator
 Rhythm in Presomitic mesoderm (PSM) cells
 Fixed number of cycles
 Rhythm across cells
 Fixed periodicity – 6 hours humans, 2 hours mouse, 30 min zebrafish
 Somites emerge from tail end
 Clock and wavefront model – assumes there is a gradient and a clock periodic signal
– slower level of oscillation causes slower bigger fewer somites, increased speed of
oscillation causes smaller and more somites
 Hes6 mutant in zebrafish causes slower somite clock oscillation and hence fewer
somites form
 Her1 marks somites