DNA accessibility is not the primary determinant of chromatin mediated gene regulation

CHEREJI, RAZVAN V.; PETER R ERIKSSON; JOSEFINA OCAMPO; CLARK, DAVID J.

Cold Spring Harbor

Congreso; Nuclear organization and function; 2018

Cold Spring Harbor

Genomic DNA is packaged into chromatin, which is composed of regularly spaced nucleosomes and folded into higher order structures, limiting DNA accessibility. DNA accessibility is thought to be of major importance in regulating gene expression. Here we test the hypothesis that chromatin compaction decreases DNA accessibility, using a restriction enzyme as a sequence-specific probe of chromatin structure in nuclei and as a proxy for transcription factors. We measured the rate of digestion and the final fraction of accessible DNA at all genomic AluI sites in haploid budding yeast and mouse liver nuclei. At essentially all AluI sites in all genomic regions, digestion eventually reaches a plateau, beyond which it is completely blocked. The plateau value represents the fraction of cells in which a given AluI site is accessible. The average value for AluI sites in yeast genes is ~25%, indicating that they are accessible in about one in four cells. This value can be explained by an average nucleosome spacing of 165 bp (the yeast repeat length), if digestion is limited to AluI sites located in the linker and just inside the nucleosome, and if the inner core of the nucleosome is completely resistant. Although yeast promoters are strongly nucleosome-depleted, promoter AluI sites are accessible in only about half of the cells, implying the presence of protective non-histone complexes. Mouse hepatocytes exhibit the same features, except that genes are ~32% accessible, consistent with longer nucleosome spacing. Mouse genes are therefore generally more accessible than yeast genes. Surprisingly, the accessibility of mouse genes is largely independent of transcriptional activity, such that active and poised genes have similar average accessibility to inactive genes. Heterochromatin is digested more slowly, but its accessibility is similar to that of active genes, indicating that extreme compaction increases the time required to penetrate the structure, but does not affect the fraction of accessible sites. We conclude that DNA accessibility is determined primarily by the average nucleosome spacing, except at active promoters, where other factors are also important. Cell-to-cell heterogeneity in accessibility has major implications for chromatin models of gene regulation: a transcription factor binding site is likely to be blocked in most cells, but not in all cells, in a population, guaranteeing neither activation nor repression.