Abstract
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).
Highlights
Eukaryotic 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
We have analyzed sequence determinants of nucleosome positioning and occupancy using two large-scale maps of in vitro nucleosomes reconstituted on genomic DNA from the nematode worm C. elegans, a complex metazoan organism
Intrinsic histone-DNA sequence specificity explored in these experiments was first studied using biophysical models in which the effective free energy of nucleosome formation depends on the total number of mono- and dinucleotides in nucleosomal sequences and not on their position with respect to the nucleosomal dyad (N = 2 position-independent models, see Methods) [22,35,51]
Summary
Eukaryotic 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. The fundamental unit of chromatin is the nucleosome core particle – 147 base pairs (bps) of DNA wrapped in a left-handed superhelix around each histone various factors that define nucleosome positions in living cells is a challenging task. One of these factors is DNA itself – direct measurements of histone-DNA binding affinities have established that changes to DNA sequence can vary the energy of nucleosome formation by as much as 2–3 kcal/mol, typical differences in energy between two randomly picked genomic nucleosomal sequences are expected to be smaller [13,14,15,16,17,18,19]. There is a reason to believe that G/C mono- and di-nucleotides do promote nucleosome formation and are not an artifact of the experimental setup [29]
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