Global remodeling of nucleosome positions in C. elegans

BMC Genomics

Research Article

Devorah Haberman¹  Steven M Johnson²  Alexandre V Morozov³  George Locke³ 

[1] Department of Chemistry, Princeton University, 08544, Princeton, NJ, USA;Department of Microbiology and Molecular Biology, Brigham Young University, 84602, Provo, UT, USA;Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, 08854, Piscataway, NJ, USA;

关键词: Nucleosome;    Histone-DNA interactions;    Chromatin domains;    Nucleosome positioning;   

DOI  :  10.1186/1471-2164-14-284

 received in 2012-10-01, accepted in 2013-04-17,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundEukaryotic chromatin architecture is affected by intrinsic histone-DNA sequence preferences, steric exclusion between nucleosome particles, formation of higher-order structures, and in vivo activity of chromatin remodeling enzymes.ResultsTo disentangle sequence-dependent nucleosome positioning from the other factors, we have created two high-throughput maps of nucleosomes assembled in vitro on genomic DNA from the nematode worm Caenorhabditis elegans. A comparison of in vitro nucleosome positions with those observed in a mixed-stage, mixed-tissue population of C. elegans cells reveals that in vivo sequence preferences are modified on the genomic scale. Indeed, G/C dinucleotides are predicted to be most favorable for nucleosome formation in vitro but not in vivo. Nucleosome sequence read coverage in vivo is distinctly lower in chromosome arms than in central regions; the observed changes in apparent nucleosome sequence specificity, likely due to genome-wide chromatin remodeler activity, contribute to the formation of these megabase-scale chromatin domains. We also observe that the majority of well-positioned in vivo nucleosomes do not occupy thermodynamically favorable sequences observed in vitro. Finally, we find that exons are intrinsically more amenable to nucleosome formation compared to introns. Nucleosome occupancy of introns and exons consistently increases with G/C content in vitro but not in vivo, in agreement with our observation that G/C dinucleotide enrichment does not strongly promote in vivo nucleosome formation.ConclusionsOur findings highlight the importance of both sequence specificity and active nucleosome repositioning in creating large-scale chromatin domains, and the antagonistic roles of intrinsic sequence preferences and chromatin remodelers in C. elegans.Sequence read data has been deposited into Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; accession number SRA050182). Additional data, software and computational predictions are available on the Nucleosome Explorer website (http://nucleosome.rutgers.edu).

【 授权许可】

Unknown   
© Locke et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.