1. long-range allosteric effect in gene transcriptional regulation
International Symposium on the Recent Progress in Quantitative and Systems Biology , Dec 9-11, The Chinese University of Hong Kong
long-range allosteric effect in gene transcriptional regulation
Ming Li
Graduate School, CAS
Zhong-can Ou-yang
Institute of Theoretical Physics, CAS

2. Outline Stressed state of DNA in vivo
Model of topologically constrained DNA
and duplex separation
Long-range Allosteric Effect and Database investigation: a case study

3. Part I Stressed state of DNA in vivo

4. 4 types of nucleotides:
Adenine, Thymine
Guanine, Cytosine
Waston-Crick base pair:
A-T, G-C
Intrinsic right-handed
helix, stiff polymer
B-DNA:
uniform,
sequence-independent

5. DNA Mechanics Plays a Role ?
DNA: ~ centimeters
Nucleus: ~ microns
compaction ratio: ~1/8000
Twisting dsDNA is a highly efficient way for compaction !
Is the elastic response vital for DNA functioning ?
eukaryote
prokaryote

6. bases of chromatin loops S/MAR (Scaffold/Matrix Attachment Region)
Chromosome Assembly
Chromatin Loop Model
bases of chromatin loops S/MAR
(Scaffold/Matrix Attachment Region)
Hierarchical architecture
DNA Stressed
S/MARs:
Boundaries of topologically-independent domains ?

7. Genomic DNA is potentially under unwinding stress
DNA segment per nucleosome: ~167 bp
The segment is actually undertwisted :
one helical turn unwound per nucleosome.
torsional stress generated

8. Sequence Heterogeneity ? Structure Heterogeneity
Unstacking
Chirality Variable
bubble
cruciform

9. Unwinding can promote local strand-separation (bubble) as well as global axis-supercoiling

10. Unwinding stress in vivo Plays the Key Role
In summary:
Unwinding stress in vivo Plays the Key Role
in Bubble formation !
Standard B-DNA
Local bubble

11. Part II Benham Model of topologically constrained DNA && sequence-dependent duplex separation

12. Characterizing the degree of unwinding …
Lk : linking number, number of helical turns
Lk0 : ‘linking number’ of relaxed DNA
(uniform B-DNA) Lk0= N/10.5
σ : superhelical density. (Lk – Lk0)/ Lk0
σ< 0, negative supercoiling
σ> 0, positive supercoiling
For eukaryotes, DNA is always
unwound to a degree σ~ (1/167)

13. Supercoiling free energy ( when σ << 1 )
: bp number per helical turn of B-DNA
q is determined by the bending and twisting stiffness of dsDNA,
as well as the topological constraints imposed on dsDNA
Circular DNA
Fully-stretched linear
DNA with fixed ends
For more details on related DNA mechanics, see Ming Li, AAPPS Bulletin, Vol.16, No.3, 34-39

14. Bubble Formation is Sequence Dependent !
2N configurations
{… …}
local bubble
a : initiation energy of bubble formation =
0 … base paried
1 … base unparied
: rewinding angle of the denatured region
: base unparing energy

15. total change in twisting turns upon bubble formation
When there are small fraction of unwound region, the supercoiling energy form slightly changes as:
total change in twisting turns upon bubble formation
Bauer WR, Benham CJ., J Mol Biol. 1993, 234(4):

16. Benham Model long-range coupling between any two sites ! total energy
Topological constraint
long-range coupling between any two sites !
twisting energy of the two strands in bubble regions
unpairing energy in bubble
(sequence dependent )
nucleation (initiation) energy
for bubble formation (there can be multiple bubbles on a single DNA)

17. Parameter (illustrative) values under physiological condition
(the qualitative results shown later are actually quite insensitive to those values )

18. Unwounding Probability Profile
for any DNA sequence
Pi and Pj are tightly correlated due to the global topological constraints ( H1 !) imposed on the dsDNA, i.e., bubbles can be competitive in releasing the imposed twisting stress.

19. Can there be anything new (besides the individual denaturing events) introduced by topological constraints ? Long-range Allosteric Effect : the tele-communication between site A and B (protein binding onto the denatured site A may re-close the bubble and induce a new bubble at site B) A B
(DNA)
(protein)

20. Beginning with everything , ending with nothing !
It’s difficult to detect such a phenomenon in vivo by experiments, and it’s also almost impossible to directly ‘calculate’ such an effect quantitatively for real cases by taking account of every molecular detail (one can be drown in the details).
Anyway, How can one do anything meaningful ?
--- Bioinformatics to rescue !
Bioinformatics offers an alternative approach:
exploring the biological data to find the statistically significant patterns which may cast some light on the understanding of the underlying molecular mechanism

21. Part III Long-range Allosteric Effect and Database investigation: a (bioinformatic) case study on SMAR function

22. D. menalongaster Histone gene cluster
—H3—H4—H2A—H2B—H1—
MAR H3 H4
H2A
H2B H1
SMAR
Convergently transcribed gene pairs: H4/H2A, H2B/H1
Coordinate transcription
relation between these two aspects?

23. Bubble position coincides with annotated SMAR location
S/MAR is detected between H1 and H3 by biochemical experiments
(S/MARt-DB: SM )
Some SMARs are observed as stress-induced unwound elements ( necessary but insufficient for chromatin loop formation? )
goettingen.de/
SMARtDB/browse/index.html

24. Competition Between Bubbles : Long Range Allosteric Effect (LRAE)
SMAR binding to matrix:
recovering the supercoiling stress on the intervening dsDNA
New unwound regions
downstream to convergently- transcribed gene pairs
relation to gene transcription , or even to the coordinate transcription of the whole gene cluster ?
5—H3—H4—H2A—H2B—H1—3

25. SMAR: retaining the negative supercoils around the unwound regions
?? Buffer of the generated positive supercoils ??
Twin-model of supercoiling domain in gene transcription
Adapted from: Wang, J.C DNA topoisomerases: why so many? Journal of Biological Chemistry 266:

26. Homologous gene locus:
D.hydei Histone gene cluster
Further support is given when doing the homology analysis: the intergenic sequences differ, but the LRAE is similar
No record in SMARt DB; a prediction

27. The results are insensitive to parameter perturbation

28. More examples supporting the existence of LRAE :
Sorghum v.s. Rice :
Sh2/A1 (homologous locus)
SM SM SM SM SM SM SM SM SM
SM SM
Sorghum v.s. Maize :
Adh1 (homologous locus)
SM SM
hsIFNA
SM SM SM
IGF2
IFNA2
SM SM
SM SM
cspB
S/MARt-DB is still under construction. Meaningful statistics should be given when there are enough records available.

29. Summary
It’s possible to reveal LRAE by sequence analysis combined with mechanics investigation in a bioinformatic way
LRAE is hopefully an effective regulatory mechanism in gene transcription
(e.g. SMAR can function via LRAE)

30. Thanks For Your Attention !