title: Novel nucleosomal particles containing core histones and linker DNA but no histone H1.
abstract: Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp of DNA wrapped ∼1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ∼160 bp, and then converts it to a core particle, containing ∼147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these 'proto-chromatosomes' are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Hope A
authors.initials: HA
authors.lastname: Cole
authors.affiliation: Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Cui
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Josefina
authors.initials: J
authors.lastname: Ocampo
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Tara L
authors.initials: TL
authors.lastname: Burke
authors.affiliation: National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Nikitina
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: V
authors.initials: V
authors.lastname: Nagarajavel
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Naoe
authors.initials: N
authors.lastname: Kotomura
authors.affiliation: National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA zhurkin@nih.gov.
authors.forename: Victor B
authors.initials: VB
authors.lastname: Zhurkin
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA clarkda@mail.nih.gov.
authors.forename: David J
authors.initials: DJ
authors.lastname: Clark
mesh_terms: D000818:Animals; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005090:Exodeoxyribonucleases / Q000235:genetics / Q000378:metabolism; D005260:Female; D015870:Gene Expression; D006657:Histones / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D008099:Liver / Q000378:metabolism; D051379:Mice; D008836:Micrococcal Nuclease / Q000737:chemistry; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism
chemical_list: D006657:Histones; D009707:Nucleosomes; D011994:Recombinant Proteins; D004247:DNA; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III; D008836:Micrococcal Nuclease