Inter-individual variation in DNA methylation is largely restricted to tissue-specific differentially methylated regions in maize
- Massimiliano Lauria†1,
- Rodrigo Antonio Echegoyen-Nava†2,
- Dalia Rodríguez-Ríos2,
- Silvio Zaina3 and
- Gertrud Lund2Email author
© The Author(s). 2017
Received: 16 November 2016
Accepted: 8 February 2017
Published: 23 February 2017
Variation in DNA methylation across distinct genetic populations, or in response to specific biotic or abiotic stimuli, has typically been studied in leaf DNA from pooled individuals using either reduced representation bisulfite sequencing, whole genome bisulfite sequencing (WGBS) or methylation sensitive amplified polymorphism (MSAP). The latter represents a useful alterative when sample size is large, or when analysing methylation changes in genomes that have yet to be sequenced. In this study we compared variation in methylation across ten individual leaf and endosperm samples from maize hybrid and inbred lines using MSAP. We also addressed the methodological implications of analysing methylation variation using pooled versus individual DNA samples, in addition to the validity of MSAP compared to WGBS. Finally, we analysed a subset of variable and non-variable fragments with respect to genomic location, vicinity to repetitive elements and expression patterns across leaf and endosperm tissues.
On average, 30% of individuals showed inter-individual methylation variation, mostly of leaf and endosperm-specific differentially methylated DNA regions. With the exception of low frequency demethylation events, the bulk of inter-individual methylation variation (84 and 80% in leaf and endosperm, respectively) was effectively captured in DNA from pooled individuals. Furthermore, available genome-wide methylation data largely confirmed MSAP leaf methylation profiles. Most variable methylation that mapped within genes was associated with CG methylation, and many of such genes showed tissue-specific expression profiles. Finally, we found that the hAT DNA transposon was the most common class II transposable element found in close proximity to variable DNA regions.
The relevance of our results with respect to future studies of methylation variation is the following: firstly, the finding that inter-individual methylation variation is largely restricted to tissue-specific differentially methylated DNA regions, underlines the importance of tissue-type when analysing the methylation response to a defined stimulus. Secondly, we show that pooled sample-based MSAP studies are methodologically appropriate to study methylation variation. Thirdly, we confirm that MSAP is a powerful tool when WGBS is not required or feasible, for example in plant species that have yet to be sequenced.
KeywordsInter-individual variation in methylation Tissue-specific CG and non-CG methylation Class II transposable elements Endosperm
In plants cytosine methylation occurs at symmetric 5′-CpG-3′ dyads (CG) and 5′-CpHpG-3′ (CHG; H is A, C or T) triads, in addition to asymmetric 5′-CpHpH-3′ (CHH) triads [1–3]. In each case, methylation is controlled by distinct DNA methyltransferases. In Arabidopsis thaliana, the main CG, CHG and CHH methylases are METHYLTRANSFERASE1 (MET1), CHROMOMETHYLASE 3 (CMT3) and CHROMOMETHYLASE 2 (CMT2) or DOMAINS-REARRANGED METHYLTRANSFERASE 2 (DRM2), respectively. In maize, the corresponding homologs are ZMET1 and ZMET2 or 5, CMT2 is absent and ZMET3 [4–10]. In addition, the DOMAINS-REARRANGED METHYLTRANSFERASE 2 (or ZMET3 in maize) plays an important role in the RNA-directed DNA methylation pathway [4, 9, 11], first discovered in tobacco plants , which culminates with de novo methylation of cytosine in CG, CHG and CHH contexts in response to small RNA signals (reviewed in ).
The genome-wide distribution of DNA methylation has been detailed both in arabidopsis [14, 15] and agronomically important plants such as rice, maize, soybean, cassava, soybean, common bean, wheat and cotton [16–23]. Collectively, these studies show that the bulk of DNA methylation is located within transposable elements (TEs), underlining its important and well-characterized function - proposed several years ago - in regulating TE activity [24, 25]. In addition, those data also uncovered the prevalence of CG methylation within the gene-body.
To date, nearly all genome-wide methylation studies of natural variation in DNA methylation, either within a genetically identical population following several generations, or across distinct genetic populations or tissue-types, compare average DNA methylation states of pooled individuals or less than 2 individuals per generation [18, 25–36]. However, the few studies that take inter-individual variation into account, show that both natural and stress-induced methylation responses are heterogeneous across individuals and can vary between developmental stages [37–42]. All the aforementioned studies were performed using the methylation sensitive amplified polymorphism (MSAP) technique. Although this technique only surveys the methylation state of a defined restriction enzyme site that is sensitive to DNA methylation (e.g. HpaII), it does give a reliable readout of the genome-wide methylation state. As an example, we demonstrated that the 13% reduction in DNA methylation in maize endosperm relative to leaf and embryo tissues largely resulted from maternal hypomethylation , results that were subsequently confirmed by high-throughput bisulfite sequencing of arabidopsis, rice, sorghum, maize and castor bean genomes [34, 43–47].
Currently scarce information is available regarding inter-individual methylation variation (ii-MV) across genetically identical progeny and whether such variation differs across plant tissues. Given the lack of such studies, we analysed methylation profiles of ten individual leaf and endosperm tissues derived from single cobs of two hybrid and one inbred line by MSAP. Furthermore, since pooled samples have been used in the majority of DNA methylation variation studies, we addressed the important methodological issue of whether individual samples better reflect methylation variation compared to pooled samples. Our data reveal that ii-MV is readily detected in both leaf and endosperm tissue, but largely restricted to tissue-specific differentially methylated regions (tDMRs). We find that the majority of such variation is detectable by analysis of pooled samples and show that MSAP represents a reliable alternative to WGBS for analysing methylation variation.
Characterization of inter-individual methylation variation (ii-MV) in maize endosperm and leaf using MSAP
MSAP was employed to characterize ii-MV. This technique is a modification of AFLP (Amplified Fragment Length Polymorphism), which is based on random amplification of restriction fragments typically generated by digestion of genomic DNA with EcoRI and MseI restriction enzymes . In MSAP, MseI is replaced by HpaII, which cleaves CCGG sites, unless one or both cytosines are methylated on both strands . Adaptors are ligated to digested restriction sites and resulting fragments are subsequently amplified in two consecutive PCR reactions with primers complementary to core sequence of adaptors and recognition sites of restriction enzymes. Typically, the number of selective nucleotides added to the primers at 3′ ends is increased in the second amplification reaction. In addition, one primer is radioactively labelled to enable visualization of restriction fragments by autoradiography.
Inter-individual variation in methylation of common and tissue-specific MSAP fragments
Next, we assessed whether ii-MV occurred preferentially of cytosines in a CG or CHG context by comparing MSAP profiles of individual endosperms from the W23/A69Y hybrid using either HpaII or its isoschizomer MspI in the initial restriction digest. These restriction enzymes differ in their sensitivity to methylation of the CCGG recognition site: HpaII is sensitive to methylation of either cytosine residues, but is insensitive to hemi-methylation of the external cytosine residue, whereas MspI is sensitive to hemi- or complete methylation of the external cytosine. We found that 89% of ii-MV occurred in a CG context; i.e. variation was only detected following HpaII, but not MspI digestion (Fig. 1b, panels i and ii). In 37% (28/75) of such cases, no fragment was detected with MspI (panel ii). This suggested either that the external cytosine residue of the CCGG recognition site was hemi-methylated, or the presence of an internal HpaII site that was methylated in a CG context only. The latter explanation is likely given that ~20% of MSAP fragments have internal CCGG sites . In contrast, only 11% (8/75) of ii-MV occurred exclusively in a CHG context, or in both a CG and CHG context; i.e. band absence following both HpaII and MspI digestion (Fig. 1b, panel iii).
Methyl-accepting assay of endosperm and leaf DNA
Target/haploid genome (x106)a
0.34 ± 0.12
0.071 ± 0.016
0.64 ± 0.24
0.16 ± 0.024
1.94 ± 0.51
0.41 ± 0.25
The methylation state of pooled samples largely reflects the predominant methylation profile across individual samples
Validation of MSAP data
We excised a total of 106 MSAP fragments that either lacked or showed ii-MV in the Mo17/B73 hybrid. Following sequence analysis, 26 non-variable and 28 variable fragments reached our stringent criteria for further analysis (see methods). We also identified six variable and eight non-variable previously isolated MSAP fragments  that showed ii-MV in the W23/A69Y hybrid. Using selected fragments as probes in Southern blot analysis we confirmed that endosperm-specific variable MSAP fragments showed reduced levels of both CG and CHG methylation in endosperm relative to leaf tissue, while these profiles were largely identical of a non-variable fragment (Additional file 2: Figure S1a, compare tissue-specific HpaII and MspI profiles). In addition, we compared ii-MV in CG and CHG context of two variable fragments and one non-variable MSAP fragment using the methylation-sensitive restriction enzymes HpaII and MspI, respectively (Additional file 2: Figure S1b). Both variable MSAP fragments showed ii-MV in a CG context, while variation in CHG context was restricted to the variable PMP2 band. Conversely, no evidence of inter-individual variation was observed following digestion with the EcoRI and EcoRV restriction enzymes that are generally considered methylation-insensitive (Additional file 2: Figure S1b). Likewise, no inter-individual variation was detected of the non-variable fragment, neither with methylation-sensitive nor methylation-insensitive restriction enzymes.
We also validated the methylation states of variable and non-variable HpaII sites predicted by MSAP using the publicly available WGBS data from leaf tissue of B73 and Mo17 inbred lines . To this end, we successfully mapped 17/26 non-variable and 24/28 variable MSAP fragments to unique regions of the B73 inbred line genome (B73 RefGen_V4) (Additional file 3) and recovered the methylation state of each HpaII sites. The remaining MSAP fragments, showed partial or ambiguous overlap to the reference genome and/or lacked methylation data. Next, we predicted the methylation state of mapped variable and non-variable HpaII sites in leaf based on the presence or absence of MSAP fragments across endosperm and leaf individuals (Additional file 4: Figure S2a). Most non-variable fragments (94%) were detected in both tissues - and in all individuals - and were thus predicted to be unmethylated in both leaf and endosperm. Conversely, the non-variable fragment that was specifically detected in endosperm samples was considered methylated in leaf. Using similar arguments, 79% of variable fragments (i.e. 67 + 8 + 4%) were expected to show some degree of methylation in leaf, while the remaining 21% were predicted to lack methylation in this tissue (Additional file 4: Figure S2a). Overall, 85% of the predicted methylation states of individual HpaII sites were confirmed in WGBS data of cytosine methylation in a CG context (Additional file 4: Figure S2b). In particular, the predicted unmethylated state was confirmed - in at least one of the two inbred lines- of 88 (15/17) and 100% (5/5) of non-variable and variable fragments, respectively; the corresponding percentages for the predicted methylated state were 100 (1/1) and 79% (15/19), respectively. With respect to CHG methylation, we found that fewer non-variable and variable HpaII sites were associated with CHG methylation. In addition, CHG methylation levels were significantly lower that CG methylation levels in both the B73 and Mo17 inbred line (p < 0.0028 and 0.0003, respectively) (Additional file 4: Figure S2c).
Collectively, these data confirmed that ii-MV was largely restricted to tDMRs and preferentially associated with CG methylation. Conversely the analysed non-variable regions were largely unmethylated in either tissue.
Characteristics of isolated variable and non-variable fragments
We also assessed whether HpaII sites that showed ii-MV tended to map closer to a repetitive DNA region. As a control group, we included non-variable HpaII sites. In each case, we scored the distance to the closest repeat region and annotated both its size and classification. We found that 88% of variable HpaII sites were closest to class I or II transposable elements (TEs), while the majority of non-variable HpaII sites (53%) were closer to a tandem repeat (Additional file 7: Figure S4a). With respect to TE, we found that the hAT superfamily was the most frequent class II TE found in close proximity to - and exclusively of - variable HpaII sites (Additional file 7: Figure S4b). However, neither the average distance to a repeat region, nor its size, differed significantly between variable and non-variable HpaII sites (p < 0.82 and p < 0.11, respectively).
Overall, we found that v-genes were expressed at higher levels in leaf - but not in endosperm tissue - relative to n-genes (p < 0.008 and p < 0.123, respectively). Furthermore, the majority of v-genes (77%) showed significant (or borderline-significant) differences in expression between tissues compared to only 22% of n-genes (Fig. 4a). However, across tissue-types, we found no specific trend between methylation and expression. For example, of the seven v-genes that were more methylated within the gene-body in leaf compared to endosperm, two (v71 and v9) showed increased levels of transcription in leaf relative to endosperm tissue, while four (v39, v85, v103 and v80) showed the opposite profile (Fig. 4a). The same was true of variable HpaII sites located either within 2 kb of TSS and TTS, or within gene-bodies that were more methylated in endosperm relative to leaf. To validate those database-deduced transcriptional profiles by direct expression, we designed primers pairs that spanned the variable HpaII sites of MSAP fragments v71, v9 and v59 that were located within GRMZM2G068392, GRMZM2G097109 and GRMZM5G817886 (Fig. 4b). We confirmed the expression profile of the two former - i.e. their increased levels of transcription in leaf relative to endosperm tissue in the B73 inbred line. However, v59 transcription differed from the expected expression profile, since this gene showed increased levels of transcription in endosperm relative to leaf (Fig. 4b). In addition to the B73 inbred line, we also analysed RNA from Mo17, A69Y and W23 inbred lines and found that gene-specific expression profiles were largely conserved across inbred lines (Fig. 4b). The only exception was GRMZM2G068392 that showed higher levels of expression in endosperm tissue from the A69Y inbred line.
Our results reveal that the bulk of methylation at HpaII sites (CCGG) in leaf is conserved across maize individuals germinated from single-cob seeds of either inbred or hybrid maize lines. In leaves, only ~3% of MSAP fragments showed ii-MV, which is comparable – albeit slightly higher – to the less than 1% reported of individual arabidopsis seedling leaf tissue analysed by MSAP . Although we found no significant differences in the frequency of ii-MV between leaf and endosperm, the total number of variable MSAP fragments was increased four to fivefold of the latter. This finding is largely explained by the tight association between ii-MV and tDMRs and the fact that the latter are much more abundant in endosperm relative to leaf . Interestingly, a study of ii-MV across genetically identical mice also found that more than 50% of variable regions overlapped with tDMRs .
As a consequence of the above, the bulk of variable MSAP fragments were more methylated in leaf relative to endosperm tissue. By contrast, most non-variable fragments were unmethylated; i.e. detected in both tissues. Using publicly available WGBS data of maize leaf tissue , we confirmed that non-variable HpaII sites lacked DNA methylation, while most variable HpaII sites showed varying levels of CG methylation in genic regions, or CG and CHG methylation in intergenic regions. Furthermore, these particular methylation states were generally representative of extended genomic regions ranging from ~1–10 kb in size. Taken together, the data suggest that ii-MV is preferentially associated with methylated DNA regions. In accordance, a recent analysis of single-cell methylation variation in liver tissue from the Japanese rice fish Oryzias latipes found that methylation-variation was increased of hyper rather than hypomethylated DNA regions . Importantly, the convergence between our MSAP methylation and previously generated WGBS from leaf tissue , indicates that MSAP represents a reliable and representative read-out of methylation states. This suggests that MSAP represents a valuable alternative for analysing DNA methylation states, either in plant species with incomplete or no genome information, or when the optimal sample size renders WGBS (or any other next generation sequencing technique) not practical.
Similar to variation in methylation between Arabidopsis accessions and maize or soybean inbred lines [26–28, 30, 33], much ii-MV mapped within the gene-body and was largely restricted to CG methylation. A possible explanation for the absence and low levels of CHG ii-MV is that such methylation is only present transiently during transcription due to INCREASED IN BONSAI METHYLATION 1 (IBM1) activity, an H3K9 demethylase that actively prevents CMT3-mediated CHG methylation within gene bodies [55, 56]. Importantly, in this MSAP study CHG methylation was assayed in a CCG context and such methylation is largely MET1-dependent as opposed to CHG methylation in a CTG and CAG context . However, given that actively transcribed genes with a high density of CTG and CAG are preferentially targeted for gene body methylation , we cannot exclude that methylation in those sequence contexts may be more prone to CHG ii-MV. Akin to several other studies we found a complex relationship between gene-body methylation and expression across tissues [14, 15, 18, 43, 44, 59]. Indeed, a recent study shows that the lack of gene body methylation in the angiosperm Eutrema salsugineum seemingly has no functional consequences with respect to transcription regulation .
Interestingly, a previous study of ii-MV across leaf tissue by MSAP showed that only a minority (17%) of ii-MV was conserved between two leaf developmental stages . Such transient or stochastic ii-MV could have implications with regards to interpreting long-term effects of any particular stress on the epigenome or identifying epialleles generated across generations. Indeed, stress responses to phosphate starvation, heat, cold, UV or hyperosmosis have been shown to be transient or heterogeneous, both across individuals and generations [61–63]. It follows that differentially methylated regions (or differentially methylated cytosines) identified by studies performed on bulked tissues, or designed with a sub-optimal sample size, detect a combination of methylation variability that can be both transient and stable. This may be particularly relevant of low frequency demethylation events since such variation was less efficiently captured in a pooled sample by MSAP. At any rate, our data demonstrate that sample pooling can faithfully reflect at least a portion of methylation variation.
Several studies in both plants and mammals have shown that TEs exhibit both intra-individual and ii-MV [53, 64–67] and there is ample evidence of methylation variation between and within genotypes resulting from proximity to TEs [30, 32, 62–74]. In this study, we analysed whether variable HpaII sites were in closer proximity to a TE compared to non-variable sites. Overall, we found no differences between these two groups, neither with respect to distance, nor size of the TE. However, we did find that variable HpaII sites were preferentially located in vicinity of hAT superfamily of class II transposons. One obvious caveat of the present study is the comparatively small number of fragments yielded by the MSAP platform that showed ii-MV. Nonetheless, analysis of ii-MV in mice by whole genome bisulfite sequencing revealed only a total of 356 loci that showed ii-MV. In that study, ~15% of variable regions were associated with Endogenous retroviruses (ERV), a class I TE. Such data warrant further studies on the relevance of TE on ii-MV following specific environmental or developmental stimuli.
Our data suggest that ii-MV is largely restricted to tDMRs. Importantly, we show that sample pooling is a methodologically appropriate design to study methylation variation in response to a given stimulus. Additionally, comparative analyses to publicly available databases confirm that MSAP is an effective tool for DNA methylation profiling when WGBS is not feasible, either due to lack of genomics/epigenomic data, or because of a large optimal sample size.
A69Y, W23, B73 and Mo17 inbred lines were grown in the field where out-crosses were performed to produce W23/A69Y and Mo17/B73 F1 hybrids (the egg donor of the cross is underlined). B73 and Mo17 seeds were obtained from the Maize Genetics Cooperation Stock Center, while A69Y and W23 seeds were a kind gift from Dr. Angelo Viotti. For each genotype, seeds were harvested either at 15 days after pollination (DAP) or at maturity. Individual endosperms were dissected from immature seeds, whereas mature seeds were germinated for two weeks in the greenhouse to obtain leaf tissue. In both cases, tissue was derived from a single cob.
MSAP and AFLP analysis
MSAP restriction digests, ligations and pre- and selective PCR reactions were performed as previously described . For each sample, three independent MSAP reactions were performed; once reproducible, one sample was used for further analysis. EcoRI and HpaII preselective primers were: 5′-AGACTGCGTACCAATTC-3′ and 5′-TCATGAGTCCTGCTCGG-3′, respectively. Selective primers were identical to preselective primers including additional 3′ nucleotides. EcoRI selective primers were: EcoRI-01 AGT, EcoRI-02 ACA, EcoRI-03 AGA, EcoRI-04 ACC; HpaII selective primers were: HpaII-02 TAGC, HpaII03 CGAA, HpaII-03A CGTT, HpaII-04 AATT. An MSAP band was scored at variable if it showed variation between individual endosperms. Only well resolved MSAP bands were scored.
AFLP was conducted as previously described . Pre-selective primers were complementary to core sequences of EcoRI and Mse1 adaptors including one selective nucleotide for both EcoRI (5′- GACTGCGTACCAATTCA) and MseI (5′-GATGAGTCCTGAGTAAC) primers. EcoRI selective primers were: E31 AAA and E32 AAC; selective MseI primers were M47 CAA, M48 CAC, M49 CAG, M50 CAT, M51 CCA.
Isolation and analysis of MSAP fragments
MSAP bands were isolated from acrylamide gels as previously reported . In maize, a total of 58 and 48 fragments that showed or lacked variation in methylation, respectively were isolated from B73 and Mo17 inbred lines. Following re-amplification, PCR products were cloned and sequenced in triplicate on both strands. Only fragments that were of the expected size, contained the appropriate selective primer sequences and represented a single DNA sequence were selected for further analysis. Blast analysis of variable and non-variable fragments was performed against the updated maize B73 RefGen_V4 (http://ensembl.gramene.org/Zea_mays/); methylation values of variable and non-variable HpaII sites were recovered from publicly available methylation data .
DNA extraction and Southern blot analysis
Extraction of genomic DNA, restriction enzyme digests and Southern blotting was performed as described previously .
Quantification of CG- and CHG methylation in maize endosperm
The in vitro methyl-accepting assay using S-adenosyl-L-[methyl-3H] methionine ([3H]SAM) was performed exactly as previously described . The rationale of the assay is that when using [3H]SAM as substrate, the amount of incorporated radioactivity is directly proportional to the extent of initial DNA hypomethylation. Reactions were carried out with 0.3–0.5 μg DNA for 3 h. In these conditions, incorporation of radioactivity is linearly proportional to DNA concentration and the reaction is carried out to completeness . Raw data were converted into copies of unmethylated target per haploid genome considering a haploid maize and mouse genome content of ~2.5 and 3.5 pgs, respectively  using the formula: 2.5(DN A)/AS where D is total incorporated radioactivity (dpm), N A is Avogadro’s number, A is specific activity (dpm/mole), S is the amount of substrate DNA (pg).
RNA extraction and RT-PCR analysis
RNA was extracted with TRIzol®Reagent (Cat. 15596-026 Life Technologies) according to the manufacturer’s instructions and treated with DNAseI (Turbo DNA-free kit, Ambion cat. AM1907). RNA quality was assessed by 1% agarose gel electrophoresis and quantified using a Nanodrop-1000 spectrophotometer. For RT-PCR analysis, cDNA was synthesized from 1 μg of total RNA (SuperScript III kit, Invitrogen). Subsequently, 1/20 reaction volume was used in a standard PCR reaction with gene-specific primers. Primer specificity was confirmed by sequence analysis.
Multiple comparisons of MSAP data across hybrid and inbred lines were performed with the Kruskal-Wallis test. A student T-test for two independent means was used for comparisons of expression profiles between leaf and endosperm tissues.
Amplified Fragment Length Polymorphism
Days after pollination
Inter-individual methylation variation
Methylation Sensitive Amplified Polymorphism
Tissue-specific differentially methylated regions
This work was funded by the Mexican Council for Science and Technology (CONACyT) “Ciencia Básica” grant no. 47633/A-1 to G.L. The funding body had no role in the design of the study, collection, analysis and interpretation of data nor the writing of the manuscript.
Availability of data and materials
All data generated or analysed during this study are included in this published article and its Additional files.
ML generated and analysed MSAP and AFLP data, RE-N and DR-R cloned variable and non-variable MSAP fragments and performed RT-PCR analysis. SZ performed the in-vitro methyl-accepting assay, RE-N and GL performed the bioinformatics analysis, GL designed and supervised the study and wrote the final manuscript version. All authors have read and approved this manuscript.
The authors declare that they have no competing interests.
Consent for publication
Ethics approval and consent to participate
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