Chromatin fiber polymorphism triggered by variations of DNA linker lengths

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 22; pp. 8061 - 8066
• Main Authors: Collepardo-Guevara, Rosana, Schlick, Tamar
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 03.06.2014; National Acad Sciences
• Subjects: Algorithms; Animals; Architecture; Bending; Biological Sciences; Cell cycle; Chromatin; Chromatin - chemistry; Chromatin - genetics; Chromosomes; Conformity; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; Fibers; Gene Expression Regulation; Genetic polymorphism; Histones; Histones - chemistry; interphase; Models, Chemical; Molecular Conformation; Monte Carlo method; Monte Carlo simulation; Nucleic Acid Conformation; Nucleosomes; Nucleosomes - chemistry; nucleotide sequences; Polymorphism; Polymorphism, Genetic; Protein Structure, Quaternary; Rats; Static Electricity; coarse-grained modeling; nonuniform NRL; chromatin polymorphism; chromatin bending and looping
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1315872111

Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin’s diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes.