Published online 14 December 2004
Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved
Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications
Life Science Core Curriculum and 1 Molecular, Cell and Developmental Biology Department and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA, 2 Department of Chemistry and 3 Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22904-4319, USA
* To whom correspondence should be addressed. Tel: +1 310 825 0182; Fax: +1 310 206 3987; Email: jacobsen{at}ucla.edu
Correspondence may also be addressed to Donald F. Hunt. Email: dhf{at}virginia.edu
Present address: Sahana Mollah, Applied Biosystems, Foster City, CA 94404, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received September 28, 2004; Revised November 12, 2004; Accepted November 22, 2004
Chromatin is regulated at many different levels, from higher-order packing to individual nucleosome placement. Recent studies have shown that individual histone modifications, and combinations thereof, play a key role in modulating chromatin structure and gene activity. Reported here is an analysis of Arabidopsis histone H3 modifications by nanoflow-HPLC coupled to electrospray ionization on a hybrid linear ion trap-Fourier transform mass spectrometer (LTQ/FTMS). We find that the sites of acetylation and methylation, in general, correlate well with other plants and animals. Two well-studied modifications, dimethylation of Lys-9 (correlated with silencing) and acetylation of Lys-14 (correlated with active chromatin) while abundant by themselves were rarely found on the same histone H3 tail. In contrast, dimethylation at Lys-27 and monomethylation at Lys-36 were commonly found together. Interestingly, acetylation at Lys-9 was found only in a low percentage of histones while acetylation of Lys-14 was very abundant. The two histone H3 variants, H3.1 and H3.2, also differ in the abundance of silencing and activating marks confirming other studies showing that the replication-independent histone H3 is enriched in active chromatin.
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