The structure and composition of native human nucleosomes

Since the first high-resolution structures of recombinantly assembled nucleosomes, efforts have shifted towards understanding chromatin structure in a native context. Most of these efforts have focused on native-like, yet still recombinantly assembled, nucleosomes that contain native DNA sequences. To date, no high-resolution structures of native human nucleosomes have been reported. Here we report the high-resolution cryo-EM structure of native human nucleosomes isolated from HEK293 cells. The HEK293-NCP structure reveals that native human nucleosomes store 145 bp of DNA. Despite the DNA sequence diversity of native nucleosomes, we observe conserved nucleotides that support the idea of a nucleosome positioning code. In addition to these striking features of nucleosomal DNA, we note alternate conformations of several DNA contacting histone residues that hint at dynamics in the HEK293-NCP. To complement the HEK293-NCP structure, we provide a mass spectrometry analysis of histone modifications and variants present in the sample, which demonstrates that a typical HEK293-NCP is composed of canonical histones with N-terminal tails that are methylated at K9, K27 and/or K36 of histone H3. Altogether these findings have implications for biological processes such as chromatin remodelling and transcription and improve our understanding of nucleosome and chromatin structure in a native context.