Short nucleosome repeats impose rotational modulations on chromatin fibre folding

Abstract

In eukaryotic cells, DNA is organized into arrays of repeated nucleosomes where the shorter nucleosome repeat length (NRL) types are associated with transcriptionally active chromatin. Here, we tested a hypothesis that systematic variations in the NRL influence nucleosome array folding into higher-order structures. For NRLs with fixed rotational settings, we observed a negative correlation between NRL and chromatin folding. Rotational variations within a range of longer NRLs (188 bp and above) typical of repressed chromatin in differentiated cells did not reveal any changes in chromatin folding. In sharp contrast, for the shorter NRL range of 165-177 bp, we observed a strong periodic dependence of chromatin folding upon the changes in linker DNA lengths, with the 172 bp repeat found in highly transcribed yeast chromatin imposing an unfolded state of the chromatin fibre that could be reversed by linker histone. Our results suggest that the NRL may direct chromatin higher-order structure into either a nucleosome position-dependent folding for short NRLs typical of transcribed genes or an architectural factor-dependent folding typical of longer NRLs prevailing in eukaryotic heterochromatin.

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

“…The detached cells (>98% in metaphases) were collected by centrifugation for 3 min at 1,000 × g. Fresh chicken whole blood was obtained from Bell and Evans, and CEs were isolated as in ref. 27. HeLa S3 cells (ATCC no.…”

“…Next, we reconstituted and analyzed 12-unit and 22-unit arrays of strongly positioned nucleosomes (27) with NRL of 188 bp close to that of HeLa cells (28). The arrays were reassociated with increasing levels of linker histone H1 resulting in efficient compaction as seen by EM (Fig.…”

The proto-chromatosome: A fundamental subunit of chromatin?

“…This rule has crucial implications for the structure of the 30-nm fiber, because it determines the orientation of the second nucleosome relative to the first and therefore dictates the structure of the 30-nm fiber. [24][25][26] Assuming that proto-chromatosomes cannot overlap, then the minimum linker length is 15 bp, which fits the rule with n D 1 (n cannot be 0 unless they overlap). Consequently longer linkers would separate proto-chromatosomes in units of 10 bp (if n > 1), preserving their relative orientation because the B-DNA helix has 10.5 bp/turn.…”

“…This is an intriguing observation, but there is no evidence at this point for nucleosomes with 2 complete turns within the intact chromatin fiber. In fact, the crystal structure of a tetra-nucleosome does not support this idea, 23 although fibers with different linker lengths are predicted to form different 30-nm fiber structures [24][25][26] and so a tetra-nucleosome with a different linker length might form a structure that is quite different.…”

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

“…For example, they have been widely used to study the mechanism of chromatin fiber condensation in solution [30][31][32][33][34] , and made it possible to obtain an x-ray structure of a tetranucleosome 35 . More recently they have proven useful in deciphering the structural effects of specific core histone variants, mutants and posttranslational modifications [14][15][16]36 .…”