Structural studies of short nucleosome arrays containing linker histone H1

Abstract

The DNA inside the eukaryotic nucleus is bound by octamers of histone proteins to form the nucleosome as the basic repeating unit of chromatin. Along the genome, nucleosomes locally form regularly spaced arrays. The relative position of nucleosomes along the DNA can be described by the nucleosome repeat length (NRL) as the sum of nucleosomal DNA and linker DNA connecting neighboring nucleosomes. Whereas short NRL are prevalent near active promoter and enhancer regions, long NRL can be found in transcriptionally repressed heterochromatin. Linker histone H1 is one of the most abundant nucleosome binding proteins and serves to repress transcription. In vivo, long NRL are associated with higher H1 content while regions with short NRL are H1 depleted. While well documented in the literature, the underlying mechanisms for the preferential H1 occupancy in long NRL arrays remain elusive. Here, we present the cryo-electron microscopy structures of H1-bound tetranucleosome arrays with four physiologically relevant NRL. These NRL are characteristic for active promoter and enhancer regions, gene bodies with active transcription and transcriptionally repressed heterochromatin. The structures reveal an overall similar architecture of local nucleosome organization with zig-zagging linker DNA connecting neighboring nucleosomes. Nucleosomes 1 and 3 form a stack while nucleosome 2 and 4 do not stack. Nucleosomes that do not stack have H1 bound whereas H1 binding to the stacked nucleosomes changes with NRL. Exit and entry DNA trajectories in stacked nucleosomes deviate in short NRL arrays and likely preclude H1 binding, but DNA trajectories successively relax with increasing NRL and approach optimal conditions for both stacked nucleosomes in long NRL arrays. The structures presented here have important implications for understanding transcription in the context of nucleosome arrays. Our findings indicate that H1 binding may be destabilized in short NRL and suggest an alternative mechanism that contributes to H1 depletion or maintenance of H1 depletion. Further, the stable binding of H1 to long NRL arrays can explain the repressive nature of heterochromatin. The data presented here provide a basis for understanding how higher-order chromatin structure influences binding of chromatin factors to shape chromatin function.