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in
Baker, 2011; van Steensel, 2011
). A first integrative view of the
Arabidopsis
epigenome, based on the combinatorial analysis of 12 major chromatin mod-
ifications, revealed a short-range organization around four predominant
chromatin states (CS1-4) with distinct biochemical, transcriptional, and
sequence properties (
Roudier et al., 2011
). CS1 corresponds to transcription-
ally active genes and is typically enriched in the trimethylated forms of H3K4,
H3K9, and H3K36 as well as H2Bub. Local distribution of these different
marks over genes suggests that CS1 could be subdivided into additional chro-
matin signatures. Thus, H3K4me3 and H3K56Ac peak around the transcrip-
tion start site of active genes and are possibly linked with the initiation of
transcription. On the other hand, H2Bub, H3K9me3, and H3K36me3 are
found over the transcribed region and are likely associated with transcrip-
tional elongation. Three other states, CS2-4, correspond to distinct types
of chromatin with very low transcriptional activity (
Roudier et al., 2011
).
H3K27me3-marked chromatin (CS2) is mainly associated with genes under
PRC2-mediated repression. H3K9me2- andH4K20me1-marked repressive
chromatin (CS3) corresponds to classical heterochromatin and is almost
exclusively located over silent repeated sequences. The fourth chromatin
state (CS4) is characterized by the absence of any prevalent mark among
the 12 studied, is preferentially associated with intergenic regions, and is also
found over
10% of genes showing weak expression levels.
The seemingly simple organization of
Arabidopsis
chromatin into four
main states shows similarities with that obtained in
Drosophila
, where five
principal chromatin types have been defined (
Filion et al., 2010; van
Steensel, 2011
).
Arabidopsis
CS2 and CS3 resemble
Drosophila
“BLUE” and
“GREEN” repressive chromatin types, which also have counterparts in other
metazoans (Reviewed in
Baker, 2011
). Conservation of the Pc pathway and
classical heterochromatin between plants and animals is remarkable, given the
mechanistic divergences associated with the absence of Pc and of the canon-
ical HP1a- and H3K9me3-based heterochromatin pathway in plants. CS4 is
reminiscent of
Drosophila
“BLACK” chromatin, which constitutes a repres-
sive environment distinct from heterochromatin. In contrast to the single
transcriptionally active chromatin state described in
Arabidopsis
(CS1), two
distinct types exist in
Drosophila
that differ in several ways, including the
enrichment of H3K36me3 in “YELLOW” but not in “RED” chromatin.
The organization of plant chromosomes into small and well-demarcated
chromatin domains that often coincide with single genes points to a
predominant role for transcription in shaping the chromatin landscape
(
Li et al., 2008; Wang et al., 2009
). Noticeably, the short-range distribution
