Published online 15 February 2010 Nucleic Acids Research, 2010, Vol. 38, No. 11 3533–3545 doi:10.1093/nar/gkq076 Histone H1 vertebrate cells exhibit altered nucleosome architecture Hideharu Hashimoto1,2, Yasunari Takami3, Eiichiro Sonoda 4 , Tomohito Iwasaki5, Hidetomo Iwano 6 , Makoto Tachibana1,2, Shunichi Takeda 4 , Tatsuo Nakayama3,7, Hiroshi Kimura8 and Yoichi Shinkai1,2,* 1Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, Shogoin Kawara-cho, 2Department of Molecular and Cellular Biology, Graduate School of Biostudies, Kyoto University, Shogoin Kawara-cho, Kyoto 606-8507, 3Section of Biochemistry and Molecular Biology, Department of Medical Sciences, Miyazaki Medical College, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, 4Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Yoshida Konoe, Kyoto, 606-8315, 5Department of Food Science, Rakuno Gakuen University, Ebetsu, 6Department of Veterinary Biochemistry, Graduate School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, 7Department of Life Science, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692 and 8Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka 565-0871, Japan Received February 21, 2009; Revised January 19, 2010; Accepted January 26, 2010 ABSTRACT In eukaryotic nuclei, DNA is wrapped around an octamer of core histones to form nucleosomes, and chromatin fibers are thought to be stabilized by linker histones of the H1 type. Higher eukaryotes express multiple variants of histone H1; chickens possess six H1 variants. Here, we generated and analyzed the phenotype of a complete deletion of histone H1 genes in chicken cells. The H1-null cells showed decreased global nucleosome spacing, expanded nuclear volumes, and increased chromosome aberration rates, although proper mitotic chromatin structure appeared to be main- tained. Expression array analysis revealed that the transcription of multiple genes was affected and was mostly downregulated in histone H1-deficient cells. This report describes the first histone H1 complete knockout cells in vertebrates and suggests that linker histone H1, while not required for mitotic chromatin condensation, plays important roles in nucleosome spacing and interphase chromatin compaction and acts as a global transcription regulator. INTRODUCTION The fundamental unit of chromatin is the nucleosome, which comprises an octamer of core histones, H2A, H2B, H3 and H4, wrapped around 146 or 147 bp of DNA (1,2). The linker histone H1 binds to the core particles and protects an additional 20 bp of DNA (linker DNA). Several lines of evidence suggest that H1 plays an important role in establishing and maintaining the structure of the chromatin ﬁber (3–5). However, linker histone H1 is not evolutionarily conserved as extensively as other core histones (6). In higher eukaryotes, histone H1 consists of a globular domain with N-terminal and C-terminal tails, but this domain structure is not conserved in unicellular organisms. Macronuclear histone H1 of Tetrahymena only has a C-terminal tail, and Saccharomyces cerevisiae Hho1 has two globular domains. In unicellular organisms such as Tetrahymena thermophila, S. cerevisiae and Aspergillus nidulans, deple- tion of histone H1 or the H1-like protein does not induce global transcriptional upregulation, but instead aﬀects only a small subset of genes, resulting in little eﬀect on cell growth and chromatin condensation and segregation (7–10). Tetrahymena strains deﬁcient in HHO (encoding macronuclear histone H1) and MLH (encoding micronuclear linker histone) exhibit enlarged macro- and *To whom correspondence should be addressed. Tel: +81 75 751 3990; Fax: +81 75 751 3991; Email: yshinkai@virus.kyoto-u.ac.jp Present address: Hideharu Hashimoto, Department of Biochemistry, Emory University, 1510 Clifton Rd Atlanta, GA 30322, USA. The authors wish it to be known that, in their opinion, the last two authors should be regarded as joint Last Authors. The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.