Biowulf Seminar: Precise genome-wide mapping of single nucleosomes and linkers in vivo
Biowulf Seminar Series
We developed a chemical cleavage method that allows us to precisely map
both single nucleosomes and linkers with very high accuracy genome-wide
in budding yeast. We confirm that /S. cerevisiae/ promoters are sites of
strong nucleosome depletion, but attribute the putative nucleosome
depletion seen at termination sites to MNase bias. Our nucleosome
mapping data has the highest resolution among the currently available
techniques, and this accuracy allows us to distinguish alternative
rotational positions that nucleosomes occupy in different cells.
Furthermore, we show that linker DNA has quantized lengths for
individual genes. By comparing our nucleosome dyad positioning maps to
existing genomic and transcriptomic data, we evaluate the contributions
of sequence, transcription, histone H1 and the H2A.Z variant in defining
the chromatin landscape. We show that DNA sequence has a very limited
effect on establishing the nucleosome organization as observed /in
vivo/. Moreover, we find that the degree of gene compaction, measured by
the spacing between neighboring nucleosomes, correlates with the
transcription level, amount of histone H1 bound to the gene, and the
amount of H2A.Z variant that is incorporated in the nucleosomes closest
to the gene promoter ( “ +1 nucleosomes ” ). Furthermore, we present a
biophysical model based on simple physical principles, which shows that
steric exclusion between neighboring nucleosomes suffices to ex...
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