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4 C) gradually induce the
downregulation of FLC in a quantitative manner ( Fig. 6.1 A). Two long non-
coding RNAs (lncRNAs) and the activities of distinct PRC2 contribute to
the radical change in chromatin state at FLC . About 2 weeks after cold expo-
sure, FLC mRNA levels drop concomitantly with the transient upregulation
of a set of antisense noncoding transcripts, referred to as COOLAIR, which
initiate from the 3 0 end of the FLC gene ( Fig. 6.1 A and B) ( Swiezewski, Liu,
Magusin, & Dean, 2009 ). COOLAIR transcripts participate in the recruit-
ment of the H3K4me2/3 demethylase FLD ( Liu et al., 2007 ), which acts
in concert with the histone deacetylase HDA6, the MSI4 and MSI5 proteins
( Pazhouhandeh, Molinier, Berr, & Genschik, 2011 ), and PRC2-mediated
H3K27me3 deposition to repress FLC through the vernalization-
independent, autonomous pathway. Indeed, although COOLAIR accumu-
lation in response to cold leads to downregulation of FLC , it is, however,
neither sufficient nor required for vernalization ( Helliwell, Robertson,
Finnegan, Buzas, & Dennis, 2011 ). Nevertheless, COOLAIR-triggered
transcriptional repression of FLC might provide a bridge between the auton-
omous and vernalization pathways by promoting the transient expression of a
second lncRNA named COLDAIR ( Heo & Sung, 2011 ). Expression of this
sense RNA encoded in the first intron of FLC peaks about 3 weeks after the
start of vernalization ( Fig. 6.1 A and B). Contrary toCOOLAIR, COLDAIR
expression is required for the stable silencing of FLC after cold exposure,
and this has been proposed to be associated with an ability to recruit
PRC2 ( Heo & Sung, 2011 ). The gradual decrease of FLC mRNA during
the first 4 weeks of cold exposure is indeed paralleled by the progressive accu-
mulation of H3K27me3 catalyzed by a specific PRC2 that comprises CLF
and plant homeodomain (PHD) proteins ( De Lucia, Crevillen, Jones,
Greb, & Dean, 2008 ). H3K27me3 deposition by PHD-PRC2 first occurs
at a short nucleation region within the first intron of FLC ( Fig. 6.1 C), which
overlaps with a region necessary for stable silencing ( Sheldon, Conn,
Dennis, & Peacock, 2002; Sung et al., 2006 ).
Remarkably, polymorphism in sequences spanning the nucleation
region was shown to account for the different vernalization requirements
that characterize Arabidopsis strains growing under different latitudes, such
as Col (a laboratory strain) and Lov-1 (an accession from northern Sweden)
( Coustham et al., 2012 ). Indeed, fine-mapping of a quantitative trait locus
for vernalization in a segregating population between these two accessions
identified a combination of four single-nucleotide polymorphisms that
quantitatively affects H3K27me3 deposition. Thus, in comparison to Col,
During vernalization, cold temperatures (
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