1 / 30

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. Outline.

brone
Download Presentation

long-range allosteric effect in gene transcriptional regulation

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 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 IStressed 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 • Hierarchical architecture • DNA Stressed • S/MARs: Boundaries of topologically-independent domains ?

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

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

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

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

  11. Part IIBenham 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~ - 0.06 (1/167)

  13. Circular DNA Fully-stretched linear DNA with fixed ends 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 For more details on related DNA mechanics, see Ming Li, AAPPS Bulletin, Vol.16, No.3, 34-39

  14. 2N configurations {…10111111100…} = 0 … base paried = 1 … base unparied local bubble : base unparing energy : rewinding angle of the denatured region a: initiation energy of bubble formation Bubble Formation is Sequence Dependent !

  15. 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):1184-96.

  16. Benham Model • 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. A (DNA) B (protein) B A 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)

  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 IIILong-range Allosteric Effect and Database investigation: a (bioinformatic) case study on SMAR function

  22. H2A H4 H2B 5- —H3—H4—H2A—H2B—H1— -3 MAR MAR H3 H1 SMAR SMAR D. menalongaster Histone gene cluster • 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: SM0000037 ) • Some SMARs are observed as stress-induced unwound elements ( necessary but insufficient for chromatin loop formation? ) http://smartdb.bioinf.med.uni- goettingen.de/ SMARtDB/browse/index.html

  24. 5—H3—H4—H2A—H2B—H1—3 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 ?

  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. 1991. DNA topoisomerases: why so many? Journal of Biological Chemistry 266:6659-6662.

  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. SM0000063 SM0000064 SM0000065 SM0000066 SM0000067 SM0000068 SM0000069 SM0000070 SM0000071 Sorghum v.s. Rice : Sh2/A1 (homologous locus) Sorghum v.s. Maize : Adh1 (homologous locus) SM0000032 SM00000170 hsIFNA SM0000011 SM0000012 IGF2 SM0000023 SM0000028 SM0000029 IFNA2 SM0000074 SM0000075 cspB SM0000080 SM0000081 More examples supporting the existence ofLRAE: 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 !

More Related