Histone-histone interactions as revealed by formaldehyde treatment of chromatin

Identification and characterization of nucleoplasmin 3 as a histone-binding protein in embryonic stem cells

Embryonic stem (ES) cells are thought to have unique chromatin structures responsible for their capacity for self-renewal and pluripotency. To examine this possibility, we sought nuclear proteins in mouse ES cells that specifically bind to histones using a pull-down assay with synthetic peptides of histone H3 and H4 tail domain as baits. Nuclear proteins preferentially bound to the latter. We identified 45 proteins associated with the histone H4 tail and grouped them into four categories: 10 chromatin remodeling proteins, five histone chaperones, two histone modification-related proteins, and 28 other proteins. mRNA expression levels of 20 proteins selected from these 45 proteins were compared between undifferentiated and retinoic acid (RA)-induced differentiated ES cells. All of the genes were similarly expressed in both states of ES cells, except nucleoplasmin 3 (NPM3) that was expressed at a higher level in the undifferentiated cells. NPM3 proteins were localized in the nucleoli and nuclei of the cells and expression was decreased during RA-induced differentiation. When transfected with NPM3 gene, ES cells significantly increased their proliferation compared with control cells. The present study strongly suggests that NPM3 is a chromatin remodeling protein responsible for the unique chromatin structure and replicative capacity of ES cells.

Studies on structure and function of chromatin

This article covers research work in this laboratory on the structure and function of chromatin. Early studies have led to discovery of skeletal fibrils (nucleonemas) within the nuclei and showed the specific role of histone H1 in chromatin condensation and in restriction of transcription. More recently with the aid of a novel DNP electrophoresis technique the relation of histone H1 and non-histone proteins to nucleosomes was studied. Three types of mononucleosomes and a number of subnucleosomes were identified in chromatin digests. The complexes of certain HMG proteins with short DNA segments were isolated and found to originate frm transcriptionally active chromatin. Different forms of SV40 minichromosome were characterized. A method for the analysis of nucleosome distribution along the DNA sequence was elaborated and used to show non-random (phased) location of nucleosomes on SV40 DNA. The attachment of DNA to skeletal elements of interphase nuclei and metaphase chromosomes was shown to be a non-random, probably sequence-specific process.

Studies on protein organization of nucleosomes using cross-linking

When chromosomal proteins in chromatin or in mononucleosomes were extensively cross-linked with an imido ester, the H1-containing nonameric histone complex was revealed. In this complex, histone H1 is connected with the octamer of core histones. The cross-linking of H1 of the octamer is realized preferentially through H2a and H3 histones. Some HMG (high mortality group) proteins located presumably in the linker regions of a nucleosome fiber also take part in the formation of dimers, possibly with the histones of a nucleosomal core. The results suggest mutant interactions between some linker-associated proteins and intranucleosomal histones. Experiments involving extensive cross-linking of proteins in the purified mononucleosome subfractions demonstrated differences in the organization of core histones between 'complete' nucleosomes and nucleosomes lacking H1.

Studies on chromatin. V. A model for the structure of chromatin subunit

A new model for the fine structure of the chromatin subunit (or 'nucleosome') is proposed. The model is based on previous experimental findings [1-14] and on two new suggestions, namely: (1) Eight histones form a toroidal-shaped histone coe of nucleosome and are arranged in the following ciruclar sequence: (see article). (2) DNA is 'kinked' around a toroidal-shaped histone core in a 'solenoid-like' mode, each kink occurring every 10 base pairs along DNA. The electron microscopic evidence for a toroidal shape of the nucleosome is described in the preceding paper [13]. The possibility of the existence of kinks in the DNA double helix was considered recently by Crick and Klug [14]. The proposed model of the nucleosome, being more detailed than earlier models permits us to explain in direct structural terms the yet unordered set of data bearing on the pattern of histone-histone interactions in chromatin, the results of a mild deoxyribonuclease digestion of DNA within the nucleosomal particle and also the quantitative data on the unwinding of the DNA duplex upon formation of the nucleosome.