31 research outputs found
Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory
Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions
SS18 Together with Animal-Specific Factors Defines Human BAF-Type SWI/SNF Complexes
Contains fulltext :
94049.pdf (publisher's version ) (Open Access
Nucleosomes in gene regulation: theoretical approaches
This work reviews current theoretical approaches of biophysics and
bioinformatics for the description of nucleosome arrangements in chromatin and
transcription factor binding to nucleosomal organized DNA. The role of
nucleosomes in gene regulation is discussed from molecular-mechanistic and
biological point of view. In addition to classical problems of this field,
actual questions of epigenetic regulation are discussed. The authors selected
for discussion what seem to be the most interesting concepts and hypotheses.
Mathematical approaches are described in a simplified language to attract
attention to the most important directions of this field
Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler
PMC3561990Chromatin remodelers can either organize or disrupt
nucleosomal arrays, yet the mechanisms specifying
these opposing actions are not clear. Here, we show
that the outcome of nucleosome sliding by Chd1
changes dramatically depending on how the chromatin
remodeler is targeted to nucleosomes. Using a
Chd1–streptavidin fusion remodeler, we found that
targeting via biotinylated DNA resulted in directional
sliding towards the recruitment site, whereas targeting
via biotinylated histones produced a distribution of
nucleosome positions. Remarkably, the fusion remodeler
shifted nucleosomes with biotinylated
histones up to 50bp off the ends of DNA and was
capable of reducing negative supercoiling of
plasmids containing biotinylated chromatin, similar
to remodelling characteristics observed for SWI/
SNF-type remodelers. These data suggest that
forming a stable attachment to nucleosomes via
histones, and thus lacking sensitivity to extranucleosomal
DNA, seems to be sufficient for allowing
a chromatin remodeler to possess SWI/SNF-like disruptive
properties.JH Libraries Open Access Fun
Structural basis of nucleosome transcription mediated by Chd1 and FACT
Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II−Spt4/5−nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A−H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA