ORIGINAL RESEARCH
published: 21 April 2016
doi: 10.3389/fpls.2016.00523
P1 Epigenetic Regulation in Leaves
of High Altitude Maize Landraces:
Effect of UV-B Radiation
Sebastián P. Rius, Julia Emiliani and Paula Casati *
Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET),
Universidad Nacional de Rosario, Rosario, Argentina
Edited by:
Anne Bagg Britt,
University of California, Davis, USA
Reviewed by:
Gabriela Carolina Pagnussat,
Universidad Nacional de Mar del
Plata, Argentina
Tzvetanka D. Dinkova,
Universidad Nacional Autónoma de
México, Mexico
*Correspondence:
Paula Casati
casati@cefobi-conicet.gov.ar
P1 is a R2R3-MYB transcription factor that regulates the accumulation of a specific
group of flavonoids in maize floral tissues, such as flavones and phlobaphenes. P1 is
also highly expressed in leaves of maize landraces adapted to high altitudes and higher
levels of UV-B radiation. In this work, we analyzed the epigenetic regulation of the P1
gene by UV-B in leaves of different maize landraces. Our results demonstrate that DNA
methylation in the P1 proximal promoter, intron1 and intron2 is decreased by UV-B in
all lines analyzed; however, the basal DNA methylation levels are lower in the landraces
than in B73, a low altitude inbred line. DNA demethylation by UV-B is accompanied by
a decrease in H3 methylation at Lys 9 and 27, and by an increase in H3 acetylation.
smRNAs complementary to specific regions of the proximal promoter and of intron 2
3′ end are also decreased by UV-B; interestingly, P1 smRNA levels are lower in the
landraces than in B73 both under control conditions and after UV-B exposure, suggesting
that smRNAs regulate P1 expression by UV-B in maize leaves. Finally, we investigated
if different P1 targets in flower tissues are also regulated by this transcription factor in
response to UV-B. Some targets analyzed show an induction in maize landraces in
response to UV-B, with higher basal expression levels in the landraces than in B73;
however, not all the transcripts analyzed were found to be regulated by UV-B in leaves.
Keywords: epigenetic regulation, flavonoids, maize, P1 transcription factor, UV-B
INTRODUCTION
Specialty section:
This article was submitted to
Plant Genetics and Genomics,
a section of the journal
Frontiers in Plant Science
Received: 05 February 2016
Accepted: 04 April 2016
Published: 21 April 2016
Citation:
Rius SP, Emiliani J and Casati P (2016)
P1 Epigenetic Regulation in Leaves of
High Altitude Maize Landraces: Effect
of UV-B Radiation.
Front. Plant Sci. 7:523.
doi: 10.3389/fpls.2016.00523
Due to its sessile condition, plants continually adjust their growth and physiology to the changing
environmental situations. In this context, epigenetic regulation seems to have a crucial role as
a linker between the environment and the genome. Unlike genetic inheritance, the epigenetic
modifications are unstable and are influenced by the environment (Baulcombe and Dean, 2014).
Epigenetic mechanisms, such as methylation of DNA cytosine residues, covalent modifications
of histones, ATP-dependent reorganization and positioning of DNA-histones and small RNAs
(smRNAs), can modify chromatin structure and as a consequence, gene expression (Verbsky and
Richards, 2001; Eberharter and Becker, 2002; Pfluger and Wagner, 2007; Vaillant and Paszkowski,
2007). DNA methylation and H3 methylation at K9 and K27 are generally associated with silent
chromatin, while histone acetylation is usually linked to euchromatin (Vaillant and Paszkowski,
2007). Environmental stresses can modify epigenetic marks; these marks can be inherited as a
preadaptation by subsequent generations (Pascual et al., 2014). For example, in Nicotiana tabacum,
salt stress induces a significant DNA demethylation in genes encoding enzymes of the flavonoid
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P1 Epigenetic Regulation by UV-B
support for the hypothesis that the organ-specific expression
pattern of P1-wr is epigenetically regulated (Cocciolone et al.,
2001); and studies have shown a correlation between H3K9me2
and DNA methylation in different P1 alleles (Chopra et al.,
2003; Sekhon et al., 2007, 2012). Interestingly, a particular
epigenetic state of the P1-rr allele is characterized by increased
methylation of the P1-rr flanking regions and presents decreased
levels of the P1-rr transcript (Sidorenko and Peterson, 2001).
Also, plants with an spontaneous loss-of-function epimutation
of the P1-wr allele shows a P1-ww phenotype (white kernel
pericarps and white cob glumes); in these plants the level of
cob pigmentation directly correlates with the degree of DNA
demethylation in P1 intron 2. Thus, distinct regulatory sequences
in the P1-wr promoter and intron 2 regions can undergo
independent epigenetic modifications to generate tissue-specific
expression patterns (Sekhon et al., 2007).
In this work, we have analyzed the epigenetic regulation of
the P1 gene by UV-B in leaf tissues of two different high-altitude
maize landraces and a low-altitude inbred line (B73), by
analyzing changes in DNA methylation, histone modifications
and smRNA levels after UV-B exposure. In addition, we
investigated if different P1 targets in flower tissues are also
regulated by this transcription factor in response to UV-B. Our
results provide evidence suggesting that changes in the epigenetic
state at specific P1 regions are important in the regulation of
flavonoid synthesis in maize leaves.
pathway (Bharti et al., 2015). The expression of genes during
different stress conditions was also reported to be under the
regulation of chromatin-associated modifications (Henderson
and Jacobsen, 2007). Moreover, epigenetic silencing can be an
adaptation of plants to climates with different UV-B incidence
levels (Questa et al., 2010).
In maize, P1 encodes an R2R3-MYB transcription factor that
regulates the accumulation of a specific group of flavonoids
in maize floral tissues, the flavones and the phlobaphenes
(Grotewold et al., 1994). P1 controls the accumulation of these
pigments by activating the expression of a subset of maize
flavonoid biosynthetic genes (Grotewold et al., 1994, 1998;
Quattrocchio et al., 2006) and it is primarily expressed in
floral tissues, including pericarps, cob glumes, silks and husks.
Among the compounds controlled by P1 are the flavones,
important phytochemicals that protect against a number of maize
pathogens, provide plants with UV shield and are significant
nutraceutical components of the human diet (Quattrocchio
et al., 2006). High-altitude maize landraces grown from 2000
to 3400 m naturally receive higher UV-B than plants at lower
altitudes and similar latitudes (McKenzie et al., 2007). Previously,
we demonstrated that some maize landraces adapted to high
altitudes accumulate flavones and express P1 in leaves and other
green tissues in the presence of UV-B, in sharp departure to the
floral-organ specific expression domain of P1 found in most other
maize inbred lines (Casati and Walbot, 2005; Rius et al., 2012).
These results suggest that a large P1 allelic diversity may exist as
a consequence of plants growing in diverse environments.
The P1 gene is in general present in tandem repeats
with different copy number depending on the genotype. The
expansion of the P1 expression domain in specific maize
landraces that have adapted to high altitude (and hence to
higher UV-B levels) could also be associated to changes in
the molecular structure of the corresponding P1 alleles. The
number of P1 copies varies depending on the maize genotype.
The P1-rr (red pericarp and red cob) allele has been well
characterized at the molecular level (Lechelt et al., 1989; Athma
et al., 1992; Chinnusamy and Zhu, 2009) and contains a single
coding sequence, which when expressed, confers pigmentation
to both the kernel pericarp and the cob (Grotewold et al., 1991).
Other allelic variants contain different P1 copy numbers within
their genomes. For example, the P1-wr (white pericarp and
red cob) allele is composed of eleven gene copies arranged in
a tandem head-to-tail array, and the B73 inbred line present
a multiple copy P1 cluster (Goettel and Messing, 2009). Also,
landraces adapted to different altitudes have different P1 copies
(Rius et al., 2012). Comparison of the expression properties
of the P1-wr and the P1-rr alleles has suggested that P1-wr
is regulated both transcriptionally and post-transcriptionally
in floral tissues (Chopra et al., 1996). The P1-wr gene has a
tandemly amplified structure, and is hypermethylated compared
to the single-copy P-rr allele. These results support a model
of tissue-specific gene silencing that may be responsible for
differences in expression between a single-copy and multicopy
allele (Chopra et al., 1996). Functional analysis of the P1-wr
promoter and coding sequences in transgenic maize plants, as
well as studies of natural P1 variants, have provided further
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MATERIALS AND METHODS
Plant Material and Radiation Treatments
Zea mays inbred line B73 and two high-altitude landraces
Arrocillo Amarillo (Mexico), and Mishca (South American
Andes) from altitudes between 2200 and 2800 m.a.s.l. were
used. For the analysis of P1 targets, high altitude landraces
Cacahuacintle (Mexico), Cónico Norteño (Mexico), and Confite
Puneño (South American Andes) were also used. High altitude
landraces were obtained from the Maize Genetics Cooperation
Stock Center, University of Illinois, Urbana/Champaign National
Plant Germplasm System (NPGS) (http://maizecoop.cropsci.
uiuc.edu/USDA/ARS) and from the International Maize and
Wheat Improvement Center (CIMMYT), D.F. Mexico, Mexico.
The Instituto Nacional de Tecnología Agropecuaria (INTA,
http://www.inta.gov.ar/) provided B73 seeds.
Plants were grown during 5 weeks in a greenhouse with a 16h-light/8-h-dark photoperiod. UV-B was provided once for 8 h,
starting 3 h after the beginning of the light period, using fixtures
mounted 30 cm above the plants (Philips, F40UVB 40 W and
TL 20 W/12) at a UV-B intensity of 2 W m−2 , UV-A: 0.65 W
m−2 . The bulbs were covered with cellulose acetate to exclude
wavelengths <280 nm. As a control, plants were exposed for 8 h
under the same lamps covered with polyester film (no UV-B
treatment, UV-B: 0.04 W m−2 , UV-A: 0.4 W m−2 ). Both groups
of plants looked healthy after the treatments. Samples were pools
of leaf pieces collected at the top of the canopy from multiple
plants, to avoid plant-to-plant variability. Leaf samples were
collected immediately after irradiation.
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P1 Epigenetic Regulation by UV-B
Lamp output was recorded using a UV-B/UV-A radiometer
(UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston,
UK) to insure that both the bulbs and filters provided the
designated UV dosage in all treatments.
TABLE 1 | Primers and probe sequences used.
EP5-8-F
ACGCGCGACCAGCTGCTAACCGTG
Chromatin Immunoprecipitation (ChIP)
Experiments
P1007ATG-R
TCGCAGCACGGCGCCCTCCCCAT
Primer/Probe name
For ChIP experiments, mature leaves from B73, Arrocillo and
Mishca from plants irradiated with UV-B or kept under control
conditions in the absence of UV-B were used. ChIP experiments
were carried out as described in Casati et al. (2008). For each
reaction, 4 µL of the following commercial antibodies were used:
anti-H3 (dimethylated K9) (ab1220), anti-H3 (trimethylated
K27) (ab6002), anti-H3 (ab1791) (Abcam, Cambridge, MA); and
anti-N-terminal acetylated H3 (06-599, Upstate Biotechnology,
Lake Placid, NY). All these antibodies were previously tested
for cross reactivity against maize proteins (Casati et al., 2008;
Questa et al., 2010). Three biological replicates from each
genotype/treatment sample type were performed, and three
qPCR experiments were done with each sample.
RNA Isolation, Reverse Transcription
Reaction and qRT-PCR
RNA samples were isolated using Trizol (Invitrogen, Carlsbad,
CA) as described by Casati and Walbot (2003). RNA was isolated
from a pool of top leaves (which received the greatest UVB exposure) from six plants. Five micro gram of total RNA
from each genotype/treatment combination were used for cDNA
synthesis using Superscript II reverse transcriptase (Invitrogen).
cDNA was used as a template for quantitative PCR
amplification in a MiniOPTICON2 apparatus (Bio-Rad), using
the intercalation dye SYBRGreen I (Invitrogen) as a fluorescent
reporter and Platinum Taq Polymerase (Invitrogen). Primers
were designed to generate unique 150–250 bp-fragments using
the PRIMER3 software (Rozen and Skaletsky, 2000). Three
replicates were performed for each sample plus a negative control
(reaction without reverse transcriptase). To normalize the data,
primers for a thioredoxin-like transcript (AW927774) were used;
this transcript is not regulated by UV-B. Primers used are
listed in Table 1. Amplification conditions were as follows: 2 min
denaturation at 94◦ C 40–45 cycles at94◦ C for 15 s, 57◦ C for
20 s, and 72◦ C for 20 s, followed by 10 min at 72◦ C. Melting
curves for each PCR were determined by measuring the decrease
of fluorescence with increasing temperature (from 65 to 98◦ C).
To confirm the size of the PCR products and to check that
they corresponded to a unique and expected product, the final
products were separated on a 2% (w/v) agarose gel.
Enzyme Digestion and Quantitative PCR
The isolation of DNA templates for DNA methylation analysis
by qPCR, and the analysis of the percentage of methylation was
done as previously described (Oakes et al., 2006). One micro
gram of DNA was used for each DNA digestion reaction. DNA
was diluted to 50 ng µl−1 and digested overnight in a volume of
50 µl with 5 units of HpaII or MspI, or no enzyme as a control.
After digestion, each PCR template was diluted 8-fold in water
and incubated at 65◦ C for 30 min to inactivate the enzyme prior
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Sequence 5′ – 3′
Ex1end-F
GTCGCTGCCCAAGAATGCAG
EP3-13-R
TCCGCCCGAAGGTAGTTGATCC
10908-F
GTCCTGTCCATTTCGCTTTG
11202 R
CGGCGTGTGTTTATATATGG
U6 probe
TCATCCTTGCGCAGGGGCCA
smRNA-P1 probe4 R
GCGTGGCGTCGACGTGGAACCGAGCTCGGC
smRNA-P1 probe5 R
TGCAGTTTTGGACCCTTTGCTCGGCGCCATAGGCTAT
smRNA-P1 probe6 R
CCTCTCACCGTCCGCAGTGTCAACGTTAAG
GCGGGGGAAATCATTAGGGAGGGCCGGC
Thioredoxin-like F
GGACCAGAAGATTGCAGAAG
Thioredoxin-like R
CAGCATAGACAGGAGCAATG
EP3-13
TGGAGGTCGCTGCCCAAGAAT
P1-L010
TCCGCCCGAAGGTAGTTGATCC
STRS1-F
CAGGTGCTTGACATCTTGGA
STRS1-R
AGCTTCCCGTCTTTCTCCTC
JAC1-F
CCTGCTCTAAAACCGACGAC
JAC1-R
GCCTTCCCATTCTGTTGATG
WHP-F
GACCCGACCTACGAATAATG
WHP-R
AACTTGAGCTGGTGCACTG
MATE-F
CTCTGCCTCGAGACCTGGTA
MATE-R
GACAGAGAGTGAGGCCAAGG
LAC10-F
GGTAGCCGTTTTCATCGTAGAG
LAC10-R
AGGCCTCCTTTGTTAGATCCAC
F2H-F
CGGTCCATCCAAATTCAG
F2H-R
ACCAACATCGAACGGGTA
RHM-F
ACTTTACTTTTGGGCTGTCG
RHM-R
TCGACCTCCTCTGCTGTTC
CCR-F
CTCCTGCTCCTGTCCTACCAG
CCR-R
CCTCCTCTCACCTTGTTCAG
PAL1-F
GTCTCGACTCTCCACACCAC
PAL1-R
GGAGAGAACCAGCAGCAGTG
PAL2-F
GCCTCAGTGCCTCACCTAAG
PAL2-R
GGGCGAGGCGGTTATATAGG
PAL3-F
GGCTGCCATCCTATCCTATCC
PAL3-R
CCACCACTCACCTTGCTACAG
UGT1-F
GAGGAGCAGATTCGGTGAGC
UGT1-R
CGACTGACGACAGTGTCTGG
UGT3-F
ACTGGGCCTAGGCTAGACTGC
UGT3-R
GACCACCACAGTGGGGTATG
UGT4-F
AGTACGGCCATCCTCTGGTC
UGT4-R
CACCTTGACTCCGACCTTCC
UGT5-F
TGATTTCTGCGAGCCTGT
UGT5-R
AAGAAACGAGTGCGTGGA
to the reaction assay. Three biological replicates were performed
for each sample, and three qPCR experiments were done with
each sample using specific primers flanking regions of interest
(see Table 2). HpaII digest the sequence CCGG but it does not
cut the methylated form of this sequence, C5m CGG. If the CpG
island does not contain C5m CGG, DNA is digested and no PCR
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P1 Epigenetic Regulation by UV-B
2012). Figure S1 shows a qRT-PCR analysis of P1 expression in
leaves of B73 and two high altitude landraces, Arrocillo Amarillo
and Mishca, under control and UV-B conditions. The results
again demonstrate that P1 in expressed in maize leaves and
that its expression is highly induced by UV-B radiation in the
landraces.
Thus, and because P1 expression pattern was previously
correlated with epigenetic changes in the gene (Chopra et al.,
2003; Sekhon et al., 2007, 2012); the first aim of this study was to
determine if P1 DNA methylation is changed by UV-B radiation,
and whether this is true in a low altitude inbred, B73, and/or
the two high altitude landraces, Arrocillo Amarillo and Mishca.
To quantify methylation changes, a sensitive PCR protocol was
used to detect both methylated and unmethylated sequences.
Methylation levels from different P1 sequences corresponding
to the proximal promoter, intron 1 and intron 2 regions were
quantified using qPCR with HpaII and MspI -digested DNA
from control and UV-B treated plants. HpaII and MspI are
isoschizomers that recognize the C/CGG site. However, HpaII is
unable to digest DNA when the internal cytosine is methylated,
while MspI digests DNA independently of cytosine methylation
(see Materials and Methods). Table 1 and Figure S2 show the
number of restriction sites recognized by these enzymes in each
P1 region.
In all lines, the UV-B treatment induced a decrease in the
percentage of DNA methylation in the three different regions
analyzed. However, both under control conditions and after
UV-B exposure, the P1 promoter from the B73 inbred line
presented a higher degree of methylation than that from the
landraces. This was also true only under control conditions for
intron 2. After UV-B exposure, DNA methylation in the P1
promoter of the B73 line was similar to levels in the DNA of
the landraces under control conditions in the absence of UVB (Figure 1A). Interestingly, the demethylation in the promoter
region and in intron 2 is significantly higher in Arrocillo than
in the other two lines (Figure 1B). This could be associated
to the different P1 copy number in their genomes. Arrocillo
contains only one P1 copy, while B73 and Mishca have 13 and
8 copies, respectively (Table 2). However, methylation changes
by UV-B were similar for the 3 lines analyzed for intron 1;
with a small although still significant lower decrease measured
in Mishca (Figure 1B). Thus, if there is any effect of P1 copy
number in DNA demethylation after UV-B exposure, this is only
true for the promoter region. For both intron regions, UV-B
radiation induced a decrease in DNA methylation of about 20%
after 8 h of exposure, independently of the maize line. Under
control conditions, intron 1 was partially methylated (between
40 and 50% methylation) in the three lines; while intron 2 was
almost fully methylated in B73 but only around 60% in the
landraces.
TABLE 2 | HpaII/MspI restriction sites number and P1 copy number.
Proximal promoter
Intron 1
Intron 2
P1 copy number
B73
7
4
3
14
ARR
7
4
3
1
MIS
7
4
3
8
The sequences corresponding to the P1 proximal promoter, introns 1 and 2 are detailed
in Figure S2.
product can be detected after amplification. As individual sample
controls, PCR amplification was done on undigested DNA and
DNA digested with the restriction enzyme MspI using the above
protocol. MspI cuts both the unmethylated and methylated
sequence; thus, no PCR product should be detected. The total
amount of DNA from each sample was calculated using the
standard curve derived from the non–restriction enzyme treated
control. The methylation index was calculated as: (amount of
HpaII digested DNA/amount of input DNA)—(amount of MspI
digested DNA / amount of input DNA) multiplied by 100 [i.e.,
(methylated DNA—nonspecifically amplified DNA) × 100] to
adjust for incomplete digestion (Bastian et al., 2005; Hashimoto
et al., 2007).
Statistical Analysis
Data presented were analyzed using one-way analysis of variance
(ANOVA). Minimum significant differences were calculated by
the Bonferroni, Tukey, Dunett, and Duncan tests (P < 0.05)
using the SigmaStat Package.
Northern Blotting for smRNA Detection
Northern blot assays were performed with 30 µg of RNA. For
smRNA detection, total RNA was separated by electrophoresis
in 15% polyacrylamide gels containing 7 M urea in Tris-borateEDTA buffer (pH 8.0). Gels were transferred to a HybondNX membrane (Amersham) and were then UV cross-linked
(1.200 µJ; Stratalinker; Stratagene). All probes were labeled at
their 5′ end with the T4 Polynucleotide Kinase (Fermentas) in
the presence of [γ-32 P]ATP, and 32 P-labeled oligonucleotides
were separated from unreacted [γ-32 P]ATP by chromatography
through a small Sephadex R G-50 column in 10 mM Tris-HCl
(pH 7.5) and 0.1% SDS. Mixed probes were hybridized to one
piece of membrane. The specific radioactivity of the 32 P-labeled
oligonucleotides was 3 × 106 cpm/pmol. Probes are listed in
Table 1. U6 mRNA was used as a control for equal loading of
RNA in each lane.
RESULTS
UV-B Induces Changes in P1 DNA
Methylation
Changes in H3 Methylation by UV-B Are
Associated with Specific P1 Regions
Previously, we reported that P1, a transcription factor that
regulates the expression of several genes that encode enzymes in
the flavonoid pathway in maize, is highly expressed in leaves of
high altitude maize landraces; and it is also regulated by UV-B
radiation in these tissues (Casati and Walbot, 2005; Rius et al.,
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Histone methylation in H3K9me2 and H3K27me3 is an
epigenetic mark that mediates gene silencing and usually occurs
in association with DNA methylation. Thus, we next investigated
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FIGURE 1 | DNA methylation changes in three regions of the P1 gene in the B73 inbred line and Arrocillo (ARR) and Mishca (MIS) landraces after 8 h of
UV-B exposure. Methylation percentage measured by qPCR of digested DNA from the P1 proximal promoter, introns 1 and 2 under control conditions and after
UV-B exposure with HpaII/MspI restriction enzymes (A). Ratio of DNA methylation in UV-B exposed plants vs. DNA methylation in control plants (B). Primers were
designed to amplify across the restriction sites (Table 1); therefore, amplification is expected if DNA is methylated and not digested. Three biological replicates were
performed for each sample, and three qPCR experiments were done with each sample. Error bars are standard errors. Statistical significance was analyzed using
ANOVA, Tukey test with P < 0.05; differences from the control are marked with different letters.
The results presented in Figure 2A show that there is
a decreased association of H3K9me2 with the P1 proximal
promoter of B73 and Arrocillo after UV-B exposure; in contrast,
no significant changes in the enrichment of H3K9me2 are
observed in Mishca samples after UV-B exposure.
On the other hand, when H3K27me3 associated to the P1
proximal promoter region was analyzed, a significant decrease in
enrichment was measured after the UV-B treatment in all three
maize lines, which was of more than 50% in all lines (Figure 3A).
In this case, H3K27me3 association to the B73 P1 promoter was
higher than that to Arrocillo and Mishca promoters, both under
control conditions and after UV-B exposure (2-fold higher than
Arrocillo and 8-fold higher than Mishca, Figure 2A). The 3 lines
showed a similar decrease in H3K27me3 association with the
proximal promoter after UV-B exposure (Figure 3A).
As a control, immunoprecipitation was also done using
antibodies against total H3. No difference in enrichment was
detected between control and UV-B treated samples for either
B73 or landraces samples, although enrichment levels were
different between lines (Figure 2A).
When a similar analysis was done for intron 1, a significant
decrease in the enrichment of H3K9me2 associated to this
if the differences in DNA methylation observed in the different
maize lines and after UV-B exposure were also accompanied
by changes in the H3 methylation associated to the same DNA
regions.
ChIP (chromatin immunoprecipitation) analyses were done
using commercial antibodies against H3K9me2, H3K27me3,
and total H3. B73 and the two landraces under control and
after UV-B exposure were sampled, and the enrichment after
immunoprecipitation was analyzed by qPCR using specific
primers that amplify the P1 proximal promoter, intron 1
and intron 2 (Table 1 and Figure 2). The coding region of a
constitutive thioredoxin-like gene was used as an internal control
to show that there were no significant changes in the enriched
fractions for the control gene with either antibody (Figure S3).
To evaluate nonspecific binding, a qPCR reaction was done
with samples incubated without any antibody as a control; all
ChIPed samples were also analyzed in parallel with total DNA
from sonicated nuclei to evaluate the selective recovery of gene
segments. The percentage of DNA recovered relative to the DNA
input when experiments were done in the absence of antibodies
was always lower than five percent of the DNA recovered when
antibodies were used.
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FIGURE 2 | Methylation state of H3 K9 and K27 associated with the P1 proximal promoter, introns 1 and 2 of B73, Arrocillo (ARR), and Mishca (MIS).
ChIP assays were done using antibodies specific for H3K9me2, H3K27me3, or total H3 in nuclei from leaves after an 8-h-UV-B treatment (UV-B) or kept under control
conditions in the absence of UV-B (control). The immunoprecipitates were analyzed for the presence of the P1 proximal promoter (A), intron 1 (B), and intron2
(C) sequences by qPCR. Enriched fractions from UV-B treated vs. control plants were compared. ChIP data were normalized to input DNA before
immunoprecipitation. The signal detected in samples incubated in the absence of any antibody as a control was less than 5% of the signal when antibodies were
used. Error bars are standard errors. Statistical significance was analyzed using ANOVA, Tukey test with P < 0.05; differences from the control are marked with
different letters. Three biological replicates of chromatin immunoprecipitation (ChIP) were performed from each genotype/treatment sample type, and three qPCR
experiments were done with each sample.
H3K9me2 enrichment than B73 plants after UV-B exposure
(Figure 3B).
For H3K27me3, there was also a decreased association with
intron 1 after UV-B exposure in all lines, although H3K27me3
intron was measured after the UV-B treatment in all lines.
Despite this, H3K9me2 association to intron 1 was higher in
Mishca than in B73 and Arrocillo (Figure 2B); however, both
Mishca and Arrocillo showed a significant higher decrease in
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FIGURE 3 | Methylation state ratio of H3 K9 and K27 associated with the P1 proximal promoter, introns 1 and 2 of B73, Arrocillo (ARR) and Mishca
(MIS) enriched fractions from UV-B treated vs. control conditions plants. P1 proximal promoter (A), intron 1 (B), and intron 2 (C) sequences were analyzed.
ChIP data were normalized to input DNA before immunoprecipitation. Absolute values correspond to data shown in Figure 2. The signal detected in samples
incubated in the absence of any antibody as a control was less than 5% of the signal when antibodies were used. Error bars are standard errors. Statistical
significance was analyzed using ANOVA, Tukey test with P < 0.05; differences from the control are marked with different letters. Three biological replicates of
chromatin immunoprecipitation (ChIP) were performed from each genotype/treatment sample type, and three qPCR experiments were done with each sample.
treated samples for either B73 or landraces samples, although
enrichment levels were different between lines (Figure 2B).
Finally, when intron 2 was analyzed, both H3K9me2 and
H3K27me3 enrichments were significantly decreased after the
UV-B treatment in the 3 lines studied (Figure 4). For H3K9me2,
association to intron 1 was higher in Mishca than in B73 and
Arrocillo, similarly as measured for H3K9me2 (Figure 2B). In
all lines, the relative decrease in H3K27me3 after the treatment
was similar (Figure 3B). No difference in enrichment was
detected in H3 binding to intron 1 between control and UV-B
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FIGURE 4 | Acetylation state of H3 associated with P1 regions of B73, Arrocillo (ARR) and Mishca (MIS). ChIP assays were done using antibodies specific
for N-terminal acetylated H3, in nuclei from leaves after an 8-h-UVB treatment (UV-B) or kept under control conditions in the absence of UV-B (control). The
immunoprecipitates were analyzed for the presence of P1 sequences of the proximal promoter, introns 1 and 2. Enriched fractions from UV-B treated vs. control
plants were compared. ChIP data were normalized to input DNA before immunoprecipitation. The signal detected in samples incubated in the absence of any
antibody as a control was less than 5% of the signal when antibodies were used. Error bars are standard errors. Statistical significance was analyzed using ANOVA,
Tukey test with P < 0.05; differences from the control are marked with different letters. Three biological replicates of chromatin immunoprecipitation (ChIP) were
performed from each genotype/treatment sample type, and three qPCR experiments were done with each sample.
both landraces was higher than that of B73. A similar result
was observed when AcH3 association to the intron 1 region
was analyzed. However, for intron 2, B73 showed higher H3
acetylation levels than the landraces under control conditions,
while after the UV-B treatment H3 acetylation was similar in the
three lines (Figure 4).
although enrichment under control conditions was similar for
the 3 lines, after UV-B exposure there was a higher decrease in
histone methylation in the landraces than in B73 (Figure 3C).
On the contrary, the decrease in H3K27me3 enrichment by UV-B
was similar in the three lines (Figure 3C); although basal levels of
enrichment in Mishca were significantly lower than in B73 and
Arrocillo (Figure 2C). Again, no difference in enrichment was
detected in H3 binding to intron 2 in control and UV-B treated
samples from either B73 or the landraces, although enrichment
levels were different between lines (Figure 2C).
Together, a decrease in the degree of association to H3K9me2
and H3K27me3 by UV-B occurs in the three P1 regions analyzed
in the lines under study. For H3K9me2, both intron regions
showed a higher decrease in enrichment in the landraces than in
B73 after the UV-B treatment; while the decrease in association
to H3K27me3 was similar for the three lines. On the contrary, for
the proximal promoter region, H3K27me3 association was lower
in the landraces than in B73, both under control conditions and
after UV-B exposure.
Small RNAs Could Guide P1 Methylation
after UV-B Exposure
Tandem repeat sequences are frequently associated with gene
silencing. The P1 gene is in general present in tandem repeats
with different copy number depending of the genotype, with
some exceptions like Arrocillo, with only one P1 copy in its
genome. Tandem repeats throughout the genome can produce
smRNAs, suggesting that repeat acquisition may be a general
mechanism for the evolution of gene silencing. Interestingly,
smRNAs play important roles in plants under stress conditions
(Lin et al., 2013). To investigate whether changes in DNA
methylation and histone methylation in P1 regions by UVB are correlated with smRNA production, smRNA levels that
correspond to different regions of the P1 gene (Rius et al., 2012)
were measured by northern blot assays as shown in Figure 5
and Figure S4 in leaves of the different maize lines after UV-B
exposure and in control conditions in the absence of UV-B.
While all the leaf samples expressed the population of
smRNAs analyzed, the expression levels differed between control
and treated plants, and also between B73 and the landraces at
same treatment condition (Figure 5). Under control conditions,
P1 smRNAs in B73 leaves were twice as high as in the landraces.
After 8 h of UV-B exposure, smRNAs complementary to discrete
P1 sequences were decreased in all lines; however, smRNA levels
were lower in the two landraces (Figure 5 and Figure S4).
H3 Acetylation in P1 Regulatory Regions Is
Increased after UV-B Exposure
Increases in transcript abundances often correlate with increased
histone acetylation (Eberharter and Becker, 2002; Li et al., 2007).
Thus, ChIP analysis was also performed using antibodies specific
for acetylated Lys residues in the N-terminal tail of histone H3
(AcH3) to investigate if histone acetylation is also involved in the
regulation of P1 expression in maize leaves in response to UV-B.
P1 proximal promoter, intron 1 and intron 2 regions
were enriched in immunoprecipitated fractions using antiAcH3 antibodies in control samples and after UV-B irradiation
(Figure 4). Both under control conditions and after UV-B
exposure, enrichment of AcH3 to the P1 proximal promoter of
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Interestingly, P1 copy number seems not to be related with
expression levels of the selected smRNAs. While B73 and Mishca
have high P1 copy number, Arrocillo has only one copy. Thus, the
smRNA levels seem to be independent of P1 gene copy number
but related to the genome background.
Some but Not All P1 Target Genes in
Pericarps and Silks Are Regulated by UV-B
in Leaves
Finally, by RT-qPCR, we analyzed if a subset of genes previously
identified as direct P1 targets in silks and pericarps (Morohashi
et al., 2012) were also expressed in leaves of B73 and high altitude
landraces, and were regulated by UV-B in correlation to P1
expression patterns and epigenetic regulation in leaves.
Interestingly, transcript levels of some P1 target genes showed
higher expression under control conditions in the absence of UVB in the landraces than in B73, for example PHENYLALANINE
AMMONIA LYASE 2 (PAL2, GRMZM2G441347) and 3
(PAL3, GRMZM2G170692), UDP-GLUCOSYL TRANSFERASE
1 (UGT1, GRMZM2G162755), and LACCASE 10 (LAC10;
GRMZM2G140527; Figure 6). In addition, some P1 targets
were also highly induced by UV-B in at least one of the
landraces, for example PAL3, FLAVONE SYNTHASE 1 (FNS1,
GRMZM2G167336), UGT1, and LAC10. In general, transcript
levels of the targets analyzed were higher both before and after
the UV-B treatment in the landraces than in B73, with the
exception of FNS1 under control conditions.
This analysis was also carried out simultaneously using RNA
samples from other landraces from high altitudes: Cacahuacintle,
Conico and Confite Puneño; the results obtained for the
expression analysis of these 5 genes were similar to those obtained
using samples from Arrocillo and Mishca (Figure S5).
On the other hand, other P1 targets were also analyzed
for their expression in high altitude landraces and after
UV-B exposure. CINNAMOYL-COA REDUCTASE (CCR,
GRMZM2G068917); JACALINE 1 (JAC1, GRMZM2G314769);
RHAMNOSE SYNTHASE 1 (RHM1, GRMZM2G031311);
MULTI
ANTIMICROBIAL
EXTRUSION
PROTEIN
(MATE, GRMZM2G079554); WHITE POLLEN (WHP,
GRMZM2G151227); UDP-GLUCOSYL TRANSFERASE 2
(UGT2, GRMZM2G063550) and 4 (UGT4, GRMZM2G180283);
and PHENYLALANINE AMMONIA LYASE 1 (PAL1,
GRMZM2G334660), which were expressed at significantly
higher levels in P1-rr compared to P1-ww pericarps (Morohashi
et al., 2012), did not show a consistent up-regulation by UV-B
and higher expression levels in the landraces (Figure S5). Thus,
other transcription factors besides P1 may have a major role in
the regulation of the expression of this subset of genes in maize
leaves.
FIGURE 5 | Expression of smRNAs complementary to the P1 proximal
promoter and the 3′ end of intron 2 in leaves of B73, Arrocillo (ARR) and
Mishca (MIS). Plants were irradiated with UV-B for 8 h or kept under control
conditions in the absence of UV-B. (A) Northern blot analysis developed using
32 P-labeled smRNA probes complementary to the P1 proximal promoter
(probes 4 and 5) and the 3′ end of intron 2 (probe 6), described in Table 3, or
alternatively with an specific U6 probe. U6 mRNA was used as a control of
equal loading of RNA in each lane. Each blot is representative of three
individual experiments. (B) Densitometry analysis of replicated experiments
normalized to U6. Different letters indicate significant differences between
samples from control and UV-B irradiated plants (p < 0.05).
(Ballare et al., 2001). Although low levels of UV-B can initiate
photomorphogenic responses through the activation of the
UV-B photoreceptor UVR8 (Nawkar et al., 2013), high UV-B
intensities cause cellular damage to proteins, lipids, DNA
and RNA molecules (Hollosy, 2002; Gill et al., 2015; Manova
and Gruszka, 2015). Plants exposed to UV-B show increased
levels of flavonoids, as these compounds are effective UV-B
sunscreens and have antioxidant properties (Falcone Ferreyra
et al., 2010). On the other hand, chromatin remodeling has also
been previously implicated in plant responses to UV-B by several
lines of evidence. Transcriptome profiling of high-altitude,
UV-B-tolerant maize landraces showed constitutively higher
expression of genes predicted to encode chromatin remodeling
factors; these landraces also showed UV-B up-regulation of these
genes (Casati et al., 2006). Moreover, transgenic plants with
decreased expression of four UV-B regulated chromatin factors
were hypersensitive to UV-B at doses that do not cause visible
damage to normal maize (Casati et al., 2006, 2008; Campi et al.,
2012; Questa et al., 2013). In maize, the R2R3-MYB transcription
DISCUSSION
Solar radiation is an important environmental factor, as it is not
only a source of energy for photosynthesis and an informational
signal for growth and development, but also contains
potentially harmful UV-B radiation (UV-B, 280–315 nm)
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FIGURE 6 | Expression analysis of P1 target genes under control conditions and after UV-B exposure in leaves of B73, Arrocillo (ARR) and Mishca
(MIS). Transcript levels relative to the reference thr-like gene that is not regulated by UV-B are shown. Statistical significance was analyzed using ANOVA, for each
sample analyzed, different letters indicate significant differences with P < 0.05.
with the P1 promoter, may be important for higher P1 expression
in leaves in high altitude landraces, and its UV-B regulation.
The tissue-specific expression pattern generated by P1-wr
has previously been attributed to repeat-induced gene silencing
through a mechanism that may involve intrachromosomal
interactions among repeats (Chopra et al., 1998). However,
Sekhon et al. (2007) suggested that distinct regulatory sequences
in the P1-wr promoter and intron 2 regions could undergo
independent epigenetic modifications to generate tissue-specific
expression patterns (Sekhon et al., 2007). Although not
completely understood, the role of epigenetic mechanisms in
regulating the expression of tandem repeated endogenous genes
or genes with repeated sequences has been investigated in
many systems (Birchler et al., 2000; Chan et al., 2005). In
this case, in the presence of a trans-acting modifier Unstable
factor for orange1 (Ufo1), P1-wr becomes less methylated
and shows increased P1 transcription (Chopra et al., 2003).
The Ufo1-induced phenotypes show a range of pigmentation
that positively correlates with the degree of demethylation
of the P1-wr repeat complex. On the other hand, intron 1
contains two RY-like elements. Similar cis sequences have been
shown to play a role in the regulation of gene expression
(Bobb et al., 1997). Generally, regulatory elements are found
in the promoter; however, their occurrence in other genic
regions has also been documented (Sieburth and Meyerowitz,
1997; Deyholos and Sieburth, 2000; Sheldon et al., 2006).
DNA methylation and/or chromatin modifications of the
intronic sequences containing regulatory elements may cause
transcriptional silencing (Chan et al., 2005; Sheldon et al.,
2006). Intronic enhancers have been previously described to
regulate the genes they reside within (Mascarenhas et al.,
1990; Jeon et al., 2000; Rose, 2002). In particular, it has been
proposed that a region of 168-bp in P1 intron 2 could act as
an enhancer, alone or in combination with distal enhancers
for the other P1 copies located downstream (Sekhon et al.,
2007).
There are numerous accounts of environmental stresses—
such as extreme temperature, drought or ultraviolet radiation—
reported to trigger epigenetic changes, thus affecting the
factor P1 controls the accumulation of several UV-B absorbing
phenolics by activating a subset of flavonoid biosynthetic genes
in leaves of maize landraces adapted to high altitudes. Thus, in
this work, we investigated the possible epigenetic mechanisms
that could participate in P1 regulation by UV-B radiation. We
here demonstrate that induction of P1 expression by UV-B
correlates with epigenetic changes in specific regions of the
gene. These changes occur at the level of DNA methylation
of specific sequences in the proximal promoter region, intron
1 and intron 2; as well as by changes in histone methylation
and acetylation; and in the levels of smRNAs complementary
to P1 sequences. These modifications take place in both the
high altitude landraces Arrocillo and Mishca but also in the low
altitude inbred B73. However, the chromatin changes at the P1
locus by UV-B differ between the lines under study. For example,
both under control conditions and after UV-B exposure, the P1
promoter from the B73 inbred line present a higher degree of
methylation than that from the landraces. Interestingly, after
UV-B exposure, DNA methylation of B73 P1 promoter is similar
to that of the landraces under control conditions in the absence
of UV-B. Thus, P1 transcription in response to UV-B could
be regulated by the DNA methylation state at the proximal
promoter. However, intron 1 and 2 methylation state would have
a minor role in P1 expression under UV-B conditions.
We here demostrate that H3K27me3 association to the B73 P1
promoter is higher than that to Arrocillo and Mishca promoters,
both under control conditions and after UV-B exposure. On
the other hand, both introns 1 and 2 show a lower H3K9me2
enrichment in the two landraces than in B73 after the UVB treatment. In addition, both under control conditions and
after UV-B exposure, AcH3 enrichment to the P1 proximal
promoter of both landraces is higher than that in B73; and B73
almost duplicates the levels of smRNAs in the landraces both
under control conditions and after UV-B exposure. Thus, specific
changes at the chromatin structure of the P1 gene, such as (1)
decreased DNA methylation and H3K27me3 at the proximal
promoter region, (2) decreased H3K9me2 associated to introns
1 and 2, and (3) decreased smRNA levels complementary to P1
regions, together with (4) increased H3 acetylation associated
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P1 Epigenetic Regulation by UV-B
transcription certain genes (Matzke and Mosher, 2014). A
number of studies have shown that these DNA and histone
modifications play a key role in gene expression and plant
development under stress conditions (Chinnusamy and Zhu,
2009); however, the precise role for individual chromatin
remodeling proteins in the regulation of gene expression
in plants is now only being established for a few specific
genes. Many of the chromatin-associated factors that have
now been characterized in plants mediate posttranslational
histone tail modifications or DNA methylation (Wagner, 2003).
On the other hand, smRNAs play important regulatory roles
in gene expression during development, stress response and
phytohormone signaling. In spite of the substantial amount
of experimental work with plant smRNAs, little is known
about their expression pattern and function during stresses
like UV-B. One example is the production of smRNAs by
Dicer-like 1 (DCL1) after mechanical wounding in sweet
potato. After wounding, DCL1 generates 22 and 24 nt mature
smRNAs, and these smRNAs target the first intron of IbMYB1
before RNA splicing, and mediate RNA cleavage triggering
the production of secondary smRNAs and DNA methylation
of IbMYB1 (Lin et al., 2013). This process finally represses
the expression of the IbMYB1 family genes and regulates
the phenylpropanoid pathway (Lin et al., 2013). Moreover,
studies evaluating the overexpression of REPRESSOR OF
SILENCING 1 (ROS1) from Arabidopsis in transgenic tobacco
(Nicotiana tabacum L.), provided evidence for the epigenetic
regulation of genes encoding enzymes of the flavonoid and
antioxidant pathways during salt-stress exposure (Bharti et al.,
2015).
We here also provide evidence that several P1 target genes in
silks and pericarps identified by RNAseq (Morohashi et al., 2012)
are also expressed in maize leaves and are UV-B regulated. In
particular, three transcripts encoding enzymes of the flavonoid
pathway, two PALs and one UGT, showed higher expression
under control conditions in the absence of UV-B in the landraces
than in B73. Moreover, some of P1 targets were also highly
induced by UV-B in at least one of the high altitude lines,
for example PAL3, FNS1, UGT1, and LAC10. For this set of
transcripts, in general expression levels were higher both before
and after a UV-B treatment in the landraces than in B73. Despite
this, other P1 target genes in silks and pericarps did not show
higher expression in leaves of high altitude landraces and/or in
response to UV-B. Thus, it is possible that for the expression of
this subset of genes in leaves, other transcription factors and/or
environmental conditions may have more important regulatory
effects.
Together, the results presented here demonstrate that changes
in the chromatin state of the P1 gene in maize leaves can provide
an important regulation mechanism for the expression of this
transcription factor under UV-B radiation. These changes in
P1 expression may be key to properly regulate the expression
of genes in the phenylpropanoid pathway in leaves, to be able
to confer plants with better shielding protection against UV-B.
The intelligent exploitation of maize resources for plant breeding
requires detailed knowledge and quantification of phenotypes
differentially represented among the lines. The alleles responsible
for these phenotypes could be bred into lower altitude inbred
lines as one route to improve UV-B tolerance.
AUTHOR CONTRIBUTIONS
SR and PC designed the experiments and wrote the paper. SR and
JE did the experiments.
FUNDING
This research was supported by FONCyT grants PICT 2012-1521
to SR and PICTs 2012-267 and 2013-268 to PC.
ACKNOWLEDGMENTS
Sebastián Rius and Paula Casati are members of the Researcher
Career of the Consejo Nacional de Investigaciones Científicas y
Técnicas (CONICET), and Julia Emiliani is a postdoctoral fellow
from the same Institution.
SUPPLEMENTARY MATERIAL
The Supplementary Material for this article can be found
online at: http://journal.frontiersin.org/article/10.3389/fpls.2016.
00523
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Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
Copyright © 2016 Rius, Emiliani and Casati. This is an open-access article
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