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  1. The ABCs of DNA & Chromatin FoldingTom Connor BishopAssociate Professor of Chemistry & PhysicsLouisiana Tech University

  2. A picture is worth a 1000 words

  3. ... or maybe a lot of arguments.

  4. The Human Genome is 3,000,000,000 basepairs long. That's one meter long. It is stored as 23 pairs of chromosomes... so there is actually 2m of DNA in every cell of your body! Chem. & Eng. News; July 17, 2006

  5. DNA Folding Felsenfeld, Nat. 2003 Luger Nat. 1997

  6. DNA Maker andInteractive Chromatin Folding www.latech.edu/~bishop

  7. Goal of Modeling • DNA sequencing  nucleosome positioning  chromatin folding  computational karyotyping If you know the nucleosome positions, then you can fold nucleosome arrays into chromatin. The Interactive Chromatin Modeling (ICM) web server at LA Tech allows users to do this in near real time for segments of DNA containing up to 20,000 base pairs. http://www.latech.edu/~bishop

  8. Goal of Modeling • DNA sequencing  nucleosome positioning  chromatin folding  computational karyotyping If you know the nucleosome positions, then you can fold nucleosome arrays into chromatin. The Interactive Chromatin Modeling (ICM) web server at LA Tech allows users to do this in near real time for segments of DNA containing up to 20,000 base pairs. http://www.latech.edu/~bishop

  9. BigJob Task Management • Typical BigJob Run • 210 simulations (5 x 21 x 2) • 2400 cores on Lonestar for ~21 hrs • 10 sub-queues, 240 cores each • Steady flow of sub-jobs thru pilot • ~1hr/simulation • ~50,000 SUs • ~750 GB of output • Total • 10+ BigJob runs (2100 sims) • 4 Restarts • ~500,000+ SUs • ~7.5 TB of output

  10. Kink Frequency vs. Sequence The 21 nucleosomes to the left are arranged in “reading” order. The second nucleosome represents a sequence shift of 1bp relative to the first. The third nucleosome is a shift of 2bp, etc. The first clip shows the 20ns dynamics of each individual nucleosome with red surface renderings highlighting where kinking occurs. The second clip displays only the frequency at which kinking occurs during the individual 20ns simulations. The assumption is that kinks are indicative of a stress release mechanism for sequences that do not favor nucleosome formation. Sequences that can form the superhelix without kinking should be more stable than kinked sequences, i.e. the stress is less. http://dna.engr.latech.edu/~bishop/Movies/chr15-kink-hp6-std1-frequency-rotate.mpg

  11. Computational Biology + Bioinformatics is Genome Browsing in 3D