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

OCAMPO J.,; CHEREJI, RAZVAN V.; ERIKSSON, PETER R.; PRAJAPATI H; CLARK D J

Conferencia; Gordon Conference on Chromosome Dynamics; 2019

Gordon Conference

into higher order structures, limiting DNA accessibility. DNA accessibility is thought to be of majorimportance in regulating gene expression. Here we test this hypothesis, using a restriction enzyme as asequence-specific probe of chromatin structure 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 inbudding yeast and mouse liver nuclei. At essentially all AluI sites in all genomic regions, digestion eventuallyreaches a plateau, beyond which it is completely blocked. The plateau value represents the fraction of cells inwhich a given AluI site is accessible. The median value for AluI sites in yeast genes is ~20%, indicating that themedian site is accessible in about one in five cells. This value can be explained by an average nucleosomespacing of 165 bp (the yeast repeat length), if digestion is limited to AluI sites located in the linker and justinside the nucleosome. Although yeast promoters are strongly nucleosome-depleted, promoter AluI sites areaccessible in only about half of the cells, implying the presence of protective non-histone complexes.Mouse liver cells exhibit the same features, except that genes are ~32% accessible, consistent with longernucleosome spacing. As in yeast, active promoters have higher accessibility and are accessible in about halfof the chromosome copies. Surprisingly, inactive promoters are also accessible in about one in threechromosome copies, implying that transcription factors could bind without activating the gene. Furthermore,DNA accessibility does not depend strongly on epigenetic state; the accessibility of heterochromatin is verysimilar to that of euchromatin, indicating that extreme compaction does not prevent access.In conclusion, DNA accessibility is determined primarily by the average nucleosome spacing, except at activepromoters, where other factors are also important. Cell-to-cell heterogeneity in accessibility has majorimplications for chromatin models of gene regulation: a transcription factor binding site is likely to be blockedin some cells in a population, but not in all cells, guaranteeing neither activation nor repressio