Orientation and spacing of HRE halfsites

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Orientation and spacing of HRE half-sites

• Ivanda Pavlovska

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HRE

• A specific DNA sequence--normally contains two
  consensus hexameric half-sites (6 bpAGAACA,
  steroid class III rec., or AGGTCA, the rest of
  rec.). Found on gene promoters, sometimes
  enhancer regions.
• Palindromes, inverted palindromes or direct
  repeats, half sites separated by 0-4 (or more) bp
  (sequence irrelevant).
• 2. Hexamer
• N-terminal variable region ---DNA-binding domain
  ---variable linker domain ---ligand-binding
  domain ---variable C-terminal domain

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Cont.

• 3. Identity of a HRE- three features
• a. base pair sequence in the half-site
• b. number of base pairs between the
  half-sites
• c. orientation of the two half-sites/
  polarity
• Nature of HRE determined by combinations of a,
  b, c. Each receptor dimer binding to DNA has to
  recognize all 3.
• 4. Configuration- polarity and spacing

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Recent studies show that

• Receptor binding efficiency depends on spacing
  as well as differences in the half-site sequence
  and HRE flanking sequence extensions.

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Sequences and spacing

• Optimal nuclear receptor binding siteREs that
  are formed by a direct repeat spaced by 4
  nucleotides both DBDs face the same side of DNA
  for better binding.
• Variations of 5 flanking sequence of the
  upstream motif (where HREs are
  present)influence on the complex formation,
  heterodimer functional activity.

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Examples of arrangement and spacing differences

• GR, AR, MR, PRform homodimers (half site
  sequence TGTTCT). Palindromic half-site
  arrangement.
• The estrogen (ER)same (sequence TGACCT).
• The thyroid, vitamin D, retinoic acid and
  9-cis-retinoic acid recsheterodimers (TGACCT).
  The half sites are direct repeats.
• Recognition
• 1bp-RXR,  3 bp-VDR, 4 bp-T3R, 5 bp- RAR

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HREs for RXR-heterodimers

• Receptor demands a particular spacing steric
  requirements in order to achieve high affinity
  and dimer formation on the HRE

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Some examples of HREs
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Estrogen receptor interaction with DNA
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A couple more facts

• HREs
• Varying only the spacing between the repeats
  creates different HREs5 different possible
  HREs with one given repeat
• Receptor can bind HRE when there is no
  hormonerepress gene activity

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References

• Quack, Frank, Carlberg. Differential Receptor
  Signalling from DR4-Type Response Elements.
  Journal of Cellular Biochemistry, Dusseldorf,
  Germany, 2002, 86601-612
• http//www.ks.uiuc.edu/Research/pro_DNA/ster_horm_
  rec/. Nuclear Hormone Receptors
• http//pps98.cryst.bbk.ac.uk/assignment/projects/s
  cotti/claudia/pps9798/progpps/part4.htmalpha-heli
  x. Interactions with DNA
• http//pharmacology.cwru.edu/Downloads/Classes/PHR
  M515/nrrev.pdf. Nuclear hormone receptors and
  gene expression
• 5. Cooper, Krauss, Schouml, Brunner.
  Biochemistry of Signal Transduction and
  Regulation, 2001