Nucleosome Repeat Length Relates to the Gene Expression Level in Yeast

Abstract

We are investigating correlation between the DNA folding in 30-nm chromatin fiber and the level of gene expression. The 30-nm fiber is generally characterized by the nucleosome repeat length (NRL) - that is, the length of the core DNA, 147 bp, plus the linker DNA length, L. We found previously that there are two families of the two-start chromatin fiber structures characterized by different DNA topology and flexibility. (Depending on the NRL value, the energetically optimal fiber structure belongs to one of the two families.) Here we analyze the high resolution nucleosome positioning data to find whether there is any correlation between the NRL and the gene expression level in yeast. We calculate the NRL values for the two groups of genes - 25% highly expressed and 25% lowly expressed genes (out of ∼3,500 yeast genes that are at least 1,000 bp long). Our results show that the average NRL=161-162 bp for the highly active genes (i.e., linker L=14-15 bp), whereas NRL=167-168 bp (i.e., linker L= 20-21 bp) for the lowly transcribed genes. Based on these findings, we conclude that the highly and lowly active gene sets have distinct nucleosome fiber organization with the linker L≈10n+5 and 10n, respectively. We hypothesize that organization of the most active genes in fibers with L≈10n+5 (which are more flexible than the fibers with L≈10n) facilitates formation of gene loops, thereby inducing transcription of these genes.