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Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2.

Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H - Acta Crystallogr. D Biol. Crystallogr. (2013)

Bottom Line: The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical.It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2.These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

ABSTRACT
The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A.Z.1 and H2A.Z.2 have been reported. In the present study, the crystal structures of nucleosomes containing human H2A.Z.1 and H2A.Z.2 were determined. The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical. This structural polymorphism may have been induced by a substitution that evolutionally occurred at the position of amino acid 38 and by the flexible nature of the L1 loops of H2A.Z.1 and H2A.Z.2. It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the distinctive dynamics of H2A.Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.

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Crystal structures of human nucleosomes containing histone H2A.Z.1 or H2A.Z.2. (a) Alignment of the human H2A, H2A.Z.1 and H2A.Z.2 amino-acid sequences. The secondary structure of H2A.Z in the nucleosome is shown at the top of the panel. Amino-acid residues that differ among H2A.Z.1, H2A.Z.2 and H2A are represented with a white background. (b) Purified nucleosomes containing either H2A.Z.1 or H2A.Z.2 were analyzed by 6% nondenaturing PAGE. DNA was visualized by EtBr staining. (c) The histone composition of the purified nucleosomes was analyzed by 18% SDS–PAGE. Histones were visualized by Coomassie Brilliant Blue staining. (d) Crystal structure of the nucleosome containing human histone H2A.Z.1. Two views are presented and the H2A.Z.1 molecules are coloured blue. The L1 loop region of H2A.Z.1 is enlarged and presented at the top of the right panel. (e) Crystal structure of the nucleosome containing human histone H2A.Z.2. Two views are presented and the H2A.Z.2 molecules are coloured magenta. The L1 loop region of H2A.Z.2 is enlarged and presented at the top of the right panel.
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fig1: Crystal structures of human nucleosomes containing histone H2A.Z.1 or H2A.Z.2. (a) Alignment of the human H2A, H2A.Z.1 and H2A.Z.2 amino-acid sequences. The secondary structure of H2A.Z in the nucleosome is shown at the top of the panel. Amino-acid residues that differ among H2A.Z.1, H2A.Z.2 and H2A are represented with a white background. (b) Purified nucleosomes containing either H2A.Z.1 or H2A.Z.2 were analyzed by 6% nondenaturing PAGE. DNA was visualized by EtBr staining. (c) The histone composition of the purified nucleosomes was analyzed by 18% SDS–PAGE. Histones were visualized by Coomassie Brilliant Blue staining. (d) Crystal structure of the nucleosome containing human histone H2A.Z.1. Two views are presented and the H2A.Z.1 molecules are coloured blue. The L1 loop region of H2A.Z.1 is enlarged and presented at the top of the right panel. (e) Crystal structure of the nucleosome containing human histone H2A.Z.2. Two views are presented and the H2A.Z.2 molecules are coloured magenta. The L1 loop region of H2A.Z.2 is enlarged and presented at the top of the right panel.

Mentions: Three amino-acid differences exist between human histones H2A.Z.1 and H2A.Z.2: at amino-acid residues 14 (Thr in H2A.Z.1 and Ala in H2A.Z.2), 38 (Ser in H2A.Z.1 and Thr in H2A.Z.2) and 127 (Val in H2A.Z.1 and Ala in H2A.Z.2) (Fig. 1 ▶a). Amino-acid residues 14 and 127 of H2A.Z are located in the unstructured N-terminal and C-terminal tails, respectively. On the other hand, amino-acid residue 38 is located within the histone-fold domain (Luger et al., 1997 ▶; Suto et al., 2000 ▶).


Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2.

Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H - Acta Crystallogr. D Biol. Crystallogr. (2013)

Crystal structures of human nucleosomes containing histone H2A.Z.1 or H2A.Z.2. (a) Alignment of the human H2A, H2A.Z.1 and H2A.Z.2 amino-acid sequences. The secondary structure of H2A.Z in the nucleosome is shown at the top of the panel. Amino-acid residues that differ among H2A.Z.1, H2A.Z.2 and H2A are represented with a white background. (b) Purified nucleosomes containing either H2A.Z.1 or H2A.Z.2 were analyzed by 6% nondenaturing PAGE. DNA was visualized by EtBr staining. (c) The histone composition of the purified nucleosomes was analyzed by 18% SDS–PAGE. Histones were visualized by Coomassie Brilliant Blue staining. (d) Crystal structure of the nucleosome containing human histone H2A.Z.1. Two views are presented and the H2A.Z.1 molecules are coloured blue. The L1 loop region of H2A.Z.1 is enlarged and presented at the top of the right panel. (e) Crystal structure of the nucleosome containing human histone H2A.Z.2. Two views are presented and the H2A.Z.2 molecules are coloured magenta. The L1 loop region of H2A.Z.2 is enlarged and presented at the top of the right panel.
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fig1: Crystal structures of human nucleosomes containing histone H2A.Z.1 or H2A.Z.2. (a) Alignment of the human H2A, H2A.Z.1 and H2A.Z.2 amino-acid sequences. The secondary structure of H2A.Z in the nucleosome is shown at the top of the panel. Amino-acid residues that differ among H2A.Z.1, H2A.Z.2 and H2A are represented with a white background. (b) Purified nucleosomes containing either H2A.Z.1 or H2A.Z.2 were analyzed by 6% nondenaturing PAGE. DNA was visualized by EtBr staining. (c) The histone composition of the purified nucleosomes was analyzed by 18% SDS–PAGE. Histones were visualized by Coomassie Brilliant Blue staining. (d) Crystal structure of the nucleosome containing human histone H2A.Z.1. Two views are presented and the H2A.Z.1 molecules are coloured blue. The L1 loop region of H2A.Z.1 is enlarged and presented at the top of the right panel. (e) Crystal structure of the nucleosome containing human histone H2A.Z.2. Two views are presented and the H2A.Z.2 molecules are coloured magenta. The L1 loop region of H2A.Z.2 is enlarged and presented at the top of the right panel.
Mentions: Three amino-acid differences exist between human histones H2A.Z.1 and H2A.Z.2: at amino-acid residues 14 (Thr in H2A.Z.1 and Ala in H2A.Z.2), 38 (Ser in H2A.Z.1 and Thr in H2A.Z.2) and 127 (Val in H2A.Z.1 and Ala in H2A.Z.2) (Fig. 1 ▶a). Amino-acid residues 14 and 127 of H2A.Z are located in the unstructured N-terminal and C-terminal tails, respectively. On the other hand, amino-acid residue 38 is located within the histone-fold domain (Luger et al., 1997 ▶; Suto et al., 2000 ▶).

Bottom Line: The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical.It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2.These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

ABSTRACT
The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A.Z.1 and H2A.Z.2 have been reported. In the present study, the crystal structures of nucleosomes containing human H2A.Z.1 and H2A.Z.2 were determined. The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical. This structural polymorphism may have been induced by a substitution that evolutionally occurred at the position of amino acid 38 and by the flexible nature of the L1 loops of H2A.Z.1 and H2A.Z.2. It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the distinctive dynamics of H2A.Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.

Show MeSH