Combinatorial patterns of histone acetylations and
methylations in the human genome
Zhibin Wang1,5, Chongzhi Zang2,5, Jeffrey A Rosenfeld3–5, Dustin E Schones1, Artem Barski1,
Suresh Cuddapah1, Kairong Cui1, Tae-Young Roh1, Weiqun Peng2, Michael Q Zhang3 & Keji Zhao1
Histones are characterized by numerous posttranslational
modifications that influence gene transcription1,2. However,
because of the lack of global distribution data in higher
eukaryotic systems3, the extent to which gene-specific
combinatorial patterns of histone modifications exist remains
to be determined. Here, we report the patterns derived from
the analysis of 39 histone modifications in human CD4+
T cells. Our data indicate that a large number of patterns
are associated with promoters and enhancers. In particular,
we identify a common modification module consisting of 17
modifications detected at 3,286 promoters. These modifications
tend to colocalize in the genome and correlate with each other
at an individual nucleosome level. Genes associated with this
module tend to have higher expression, and addition of more
modifications to this module is associated with further
increased expression. Our data suggest that these histone
modifications may act cooperatively to prepare chromatin
for transcriptional activation.
Histones are subject to numerous covalent modifications, including
methylation and acetylation, that occur mainly at their N-terminal
tails and that can affect transcription of genes1,2,4,5. Extensive studies
have established that histone acetylation is primarily associated with
gene activation, whereas methylation, depending on its position and
state, is associated with either repression or activation5–10. Various
models, including the histone code, the signaling network and the
charge neutralization model, have been proposed to account for the
function of histone modifications11–14. The histone code hypothesis
suggests that multiple histone modifications act in a combinatorial
fashion to specify distinct chromatin states. However, the extent to
which combinatorial patterns of histone modifications exist in
the genome is unknown. We have now produced genome-wide
maps of 18 histone acetylations (H2AK5ac, H2AK9ac, H2BK5ac,
H2BK12ac, H2BK20ac, H2BK120ac, H3K4ac, H3K9ac, H3K14ac,
H3K18ac, H3K23ac, H3K27ac, H3K36ac, H4K5ac, H4K8ac,
H4K12ac, H4K16ac and H4K91ac) at an individual nucleosome
level (see Methods section for data deposition), and analyzed these
together with the H2A.Z and 19 histone methylation maps we
generated previously15.
We first systematically evaluated the specificities of the acetylation
antibodies used in this study (Supplementary Methods, Supplemen-
tary Table 1 and Supplementary Fig. 1 online). Competition assays
using modified and unmodified peptides indicated that most anti-
bodies showed specificity for the desired acetylation (Supplementary
Fig. 1). The H4K5ac and H3K4ac antibodies demonstrated some
crossreactivity toward H4K12ac and H3K9ac, respectively, in a con-
dition with excess competitor peptides (Supplementary Fig. 1d,j),
and the H4K91ac antibody did not work in protein blotting. Thus, the
results for these modifications should be interpreted with caution. Of
note, H2AK9ac has not been reported previously, and H3K4ac has
only been identified by mass-spectrometry analysis and has not been
previously characterized functionally16. Protein blotting indicated that
these acetylations indeed exist in human CD4+ T cells (Supplemen-
tary Fig. 1j,o). We previously analyzed the genome-wide distribution
of H2BK5me1 (ref. 15), and protein blotting data in this study
indicated that this methylation exists in human cells and that the
H2BK5me1 antibody is specific (Supplementary Fig. 1p).
Next, we determined the genomic distribution patterns of these
histone acetylations using the ChIP-Seq technique15, which we pre-
viously confirmed yields H3K4me3 distribution patterns similar to
those generated by the ChIP-SAGE (GMAT) strategy15,17. To validate
the histone acetylation data, we compared the genomic distribution
patterns of the K9/K14-diacetylated histone H3 from ChIP-SAGE18
with the separately examined patterns of H3K9ac and H3K14ac in
this study (Supplementary Fig. 2 online). We found that the ChIP-
Seq acetylation data are reliable and that the previously observed
H3K9/K14 diacetylation patterns could be primarily attributed to
H3K9 acetylation.
To examine the distribution of the histone acetylations at different
functional regions, we generated composite profiles for the region
spanning the transcription start sites (TSSs; Fig. 1a–c and Supple-
mentary Fig. 3 online) or the entire gene bodies and extending 5 kb
Received 19 December 2007; accepted 1 April 2008; published online 15 June 2008; doi:10.1038/ng.154
1Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA. 2Department of
Physics, The George Washington University, Washington, D.C. 20052, USA. 3Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. 4Department
of Biology, New York University, New York, New York 10003, USA. 5These authors contributed equally to this work. Correspondence should be addressed to K.Z.
(zhaok@nhlbi.nih.gov).
NATURE GENETICS VOLUME 40 [ NUMBER 7 [ JULY 2008 897
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