Why most of the in vivo experiments do not find the 30-nm chromatin fiber, well studied in vitro, is a puzzle. Two basic physical inputs that are crucial for understanding the structure of the 30-nm fiber are the stiffness of the linker DNA and the relative orientations of the DNA entering/exiting nucleosomes. Based on these inputs we simulate chromatin structure and show that the presence of non-histone proteins, which bind and locally bend linker DNA, destroys any regular higher order structures (e.g., zig-zag). Accounting for the bending geometry of proteins like nhp6 and HMG-B, our theory predicts phase-diagram for the chromatin structure as a function of DNA-bending non-histone protein density and mean linker DNA length. For a wide range of linker lengths, we show that as we vary one parameter, that is, the fraction of bent linker region due to non-histone proteins, the steady-state structure will show a transition from zig-zag to an irregular structure-a structure that is reminiscent of what is observed in experiments recently. Our theory can explain the recent in vivo observation of irregular chromatin having co-existence of finite fraction of the next-neighbor (i + 2) and neighbor (i + 1) nucleosome interactions.
机构:
UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143
GIESE, K
;
COX, J
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机构:
UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143
COX, J
;
GROSSCHEDL, R
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机构:
UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143
机构:
Penn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Grigoryev, Sergei A.
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Arya, Gaurav
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机构:
Univ Calif San Diego, Dept Nanoengn, La Jolla, CA 92093 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Arya, Gaurav
;
Correll, Sarah
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Correll, Sarah
;
Woodcock, Christopher L.
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h-index: 0
机构:
Univ Massachusetts, Dept Biol, Amherst, MA 01003 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Woodcock, Christopher L.
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Schlick, Tamar
论文数: 0引用数: 0
h-index: 0
机构:
NYU, Dept Chem, New York, NY 10012 USA
NYU, Courant Inst Math Sci, New York, NY 10012 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
机构:
UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143
GIESE, K
;
COX, J
论文数: 0引用数: 0
h-index: 0
机构:
UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143
COX, J
;
GROSSCHEDL, R
论文数: 0引用数: 0
h-index: 0
机构:
UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143UNIV CALIF SAN FRANCISCO,HOWARD HUGHES MED INST,DEPT BIOCHEM,SAN FRANCISCO,CA 94143
机构:
Penn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Grigoryev, Sergei A.
;
Arya, Gaurav
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Diego, Dept Nanoengn, La Jolla, CA 92093 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Arya, Gaurav
;
Correll, Sarah
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Correll, Sarah
;
Woodcock, Christopher L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Massachusetts, Dept Biol, Amherst, MA 01003 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA
Woodcock, Christopher L.
;
Schlick, Tamar
论文数: 0引用数: 0
h-index: 0
机构:
NYU, Dept Chem, New York, NY 10012 USA
NYU, Courant Inst Math Sci, New York, NY 10012 USAPenn State Univ, Milton S Hershey Med Ctr, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA