- Research article
- Open Access
Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice
- Ningning Wang†1, 2, 5,
- Di Zhang†1,
- Zhenhui Wang1,
- Hongwei Xun1,
- Jian Ma2,
- Hui Wang1,
- Wei Huang1,
- Ying Liu1,
- Xiuyun Lin3,
- Ning Li1,
- Xiufang Ou1,
- Chunyu Zhang1, 4,
- Ming-Bo Wang5 and
- Bao Liu1Email author
© Wang et al.; licensee BioMed Central Ltd. 2014
Received: 24 January 2014
Accepted: 3 June 2014
Published: 30 June 2014
Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown.
We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions.
Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response.
RNA silencing is an evolutionally conserved gene regulation mechanism in eukaryotes mediated by 20–25 nt non-coding small (sm)RNAs. These smRNAs are processed from double-stranded (ds) or hairpin RNA molecules by Dicer-like (DCL) proteins, and guide RNA-induced silencing complexes to cognate single-stranded RNAs based on sequence complementarity, and result in degradation of the targeted RNAs [1–3]. In plants, there are several different classes of smRNAs, including 20–24 nt micro RNAs (miRNAs) processed by DCL1, 21–22 nt small interfering RNAs (siRNAs) by DCL4 and DCL2, and the 24 nt heterochromatin-associated siRNAs by DCL3. miRNAs play an important role in plant development by directing posttranscriptional gene silencing (PTGS) of regulatory genes such as those encoding transcription factors. Similarly, 21–22 nt siRNAs guide the degradation of viral RNAs as well as some endogenous mRNAs and are important for plant defense against viruses and for some aspects of plant development [4–6]. Unlike these PTGS-associated smRNAs, the 24 nt siRNAs are associated with RNA-directed DNA methylation (RdDM), a plant-specific de novo DNA methylation pathway required for transcriptional silencing of transposable elements and other DNA repeats to maintain genome stability [7–10].
The biogenesis of siRNAs in plants requires the activity of RNA-dependent RNA polymerase (RDR), which converts single-stranded RNAs to dsRNA precursors of siRNAs. The dicot model plant Arabidopsis thaliana has six RDR genes, i.e., RDR1, RDR2, RDR3a, RDR3b, RDR3c and RDR6, of which three RDRs (RDR1, RDR2 and RDR6) are shown to play roles in the RNA silencing pathways. RDR2 is required for 24 nt siRNA biogenesis and therefore involved in the canonical RdDM pathway [7–9]. RDR6 is involved in the production of the endogenous 21 nt trans-acting siRNAs and also essential for sense transgene-induced PTGS [12, 13]. Both RDR6 and RDR2 are also involved in viral siRNA accumulation in infected Arabidopsis plants[14–16]. The function of RDR1 in RNA silencing is less understood, but recent studies have shown that it is involved in siRNA biogenesis from a subset of RNA viruses [17–19]. Furthermore, rdr1 mutant of Arabidopsis showed loss of DNA methylation in a subset of genomic loci in comparison to wild-type Arabidopsis plants [20, 21], suggesting that RDR1 plays a role in the recently identified non-canonical, 21 nt siRNA-directed RdDM pathway [20, 21]. However, the function of RDR1 in gene regulation from a genome-wide perspective has not been investigated in any plant.
In contrast to Arabidopsis that has six RDR genes, the RDR family of rice (Oryza sativa L.), a model plant for monocots, contains only three members, namely OsRDR1, OsRDR2 and OsRDR6[11, 22, 23]. A previous study showed that OsRDR1 has a similar function to its counterparts in Arabidopsis and tobacco (Nicotiana tabacum) in PTGS-based silencing of certain RNA viruses, such as Bromovirus [6, 19, 24]. To investigate if OsRDR1 plays a role in regulation of endogenous genes in rice, we characterized a loss-of-function mutant of OsRDR1 derived from a disruptive LTR retrotransposon (Tos17) insertion into the 2nd exon of the gene. We investigated genome-wide changes in gene expression and smRNA profiles, localized changes in DNA methylation, and phenotypes under normal and several abiotic stress conditions in this rice rdr1 mutant.
Characterization of the rice RDR1 mutant (Osrdr1)
Genome-wide changes in gene expression in Osrdr1
The highly reproducible microarray profiles among three biological replicates for both Osrdr1 and its WT sibling plants testified reliability of the data and their analysis. All microarray data have been submitted to the GEO repository under the accession number of GSE58007. To further verify the quality of the microarray data and analysis, we analyzed 18 genes representing both up- and down-regulation in Osrdr1 vs. WT, as well as equal expression between the two lines using qRT-PCR assay on the same cDNAs as used for microarray. The qRT-PCR results were highly consistent with the microarray data for almost all the 18 tested genes in levels or at least in trends of expression changes (Figure 2d), confirming reliability of the microarray analysis.
Alteration in smRNA clusters in Osrdr1
Genome-wide overall similarity in smRNA abundance does not necessitates absence of smRNA fluctuations in localized smRNA clusters, because up- and down-regulated smRNA accumulation can be masked by reciprocal compensation. We thus investigated localized smRNA accumulation between Osrdr1 and its sibling WT by mapping the cleaned smRNA reads to 100 bp sliding windows (being reflected as smRNA clusters) across each of the 12 rice chromosomes, normalized the reads to Reads per Million (RPM), and then compared the RPM smRNA clusters between Osrdr1 and WT. Using 4-fold difference as a cut-off threshold, we identified many smRNA clusters with differential abundance between Osrdr1 and its sibling WT, which were uniformly distributed across the entire length of each chromosome (Figure 3c). Next, we extracted the differentially expressed smRNAs between Osrdr1 and WT (also based on a cut-off threshold of 4-fold difference) in the size range of 20-24 nt, which should parsimoniously contain all siRNAs, and mapped them to the same 100 bp windows across each chromosome. We found that this subset of differential smRNA clusters also distribute on both arms of each chromosome (Additional file 1), although due to their smaller numbers, we cannot rule out the possibility that the distribution might show “hot spots” within a given chromosome. Taken together, the smRNA sequencing data suggested that loss-of-function mutation in OsRDR1 caused extensive alterations in smRNA clusters across each chromosome and throughout the genome, but it did not result in marked fluctuations of overall smRNA profiles, probably due to more or less equally increased and decreased abundance of the smRNA clusters which offset each other.
Altered expression of miRNAs and their target genes in Osrdr1
In addition to the known miRNAs, we identified a total of 10 putative novel osa-miRNAs from the smRNA data of the mutant and WT plants based on prediction of pre-miRNA-like stem-loop structures in sequences surrounding the smRNA sequences in the rice genome (Additional file 3). Three of these novel miRNAs (Osr-miRNA-N5.1, −N5.2 and -N5.3) had an identical mature sequence but corresponded to three independent genomic loci, thereby forming a novel miRNA family. For the putative miRNA Osr-miRNA-N7, smRNA reads were detected from both the 5’ (5p) and the 3’ (3p) half of the predicted stem-loop structure, but the 5p smRNA showed a higher abundance than the 3p smRNA (Additional file 3), indicating that the 5p smRNA is the guide strand (miRNA) whereas the 3p smRNA is the passenger strand (miRNA*) . Like the known miRNAs, these novel miRNAs also showed expression variation between Osrdr1 and WT, with 3 showing expression only in Osrdr1, and 5 showing expression only in WT plants (Additional file 3). Taken together, our results suggest that OsRDR1 was likely involved in miRNA accumulation in rice.
To investigate if the altered miRNA accumulation in Osrdr1 relative to WT was associated with changes in miRNA target gene expression, we compared the miRNA expression profiles (abundance) derived from the smRNA sequencing data with the target gene expression levels based on the microarray data. We did not find a generalized relationship between the miRNA abundance and target gene expression levels (Additional file 4a). Instead, four types of relationships were recognized for a subset of miRNAs and their predicted targets (Additional file 4b), which included: (1) reduced miRNA abundance was correlated with up-regulated expression of target genes in Osrdr1 relative to WT (Additional file 4b-i); (2) increased miRNA abundance was correlated with down-regulated expression of target genes in Osrdr1 relative to WT (Additional file 4b-ii); (3) both miRNAs and their target genes were up-regulated in Osrdr1 relative to WT (Additional file 4b-iii); (4) both miRNAs and their target genes were down-regulated in Osrdr1 relative to WT (Additional file 4b-iv). The first two types of relationships supported a role of miRNAs in down-regulating expression of their predicted target genes. The last two types of relationships could be a result of concordant transcriptional regulation of the miRNAs and their target genes caused by another more upstream regulator(s) whose expression or activity was modified due to loss of function of OsRDR1. All small RNA data have been submitted to GenBank under the accession numbers of SRP042238.
Locus-specific alteration of DNA methylation in Osrdr1
As the Arabidopsis RDR1 has been shown to play a role in the non-canonical, NERD-dependent RdDM pathway [20, 21], we were interested to know if OsRDR1 might have a similar function in rice. We therefore examined cytosine methylation and gene expression levels of 10 selected genomic loci in Osrdr1 and its sibling WT using bisulphite sequencing and qRT-PCR analysis. These loci overlapped with two transposable elements (TEs) and three protein-coding genes, which were chosen as representatives because they all showed alteration in smRNA clusters in Osrdr1 relative to WT (Additional file 5). The bisulphite-sequenced regions for the two TEs (retrotransposon Tos17 and DNA transposon Pong) included: (1) portions of the 5’- and 3’-LTRs together with their immediate flanking regions of two Tos17 copies (located on chromosomes 10 and 7, respectively) (Additional file 5a, b); (2) the 5’ termini along with their immediate flanking regions of two Pong copies (located on chromosomes 2 and 9, respectively) (Additional file 5c, d), and; (3) a body-region of the transposase-encoding ORF of Pong (Additional file 5e) that is shared by all conserved copies of the element. The bisulphite-sequenced regions of the three protein-coding genes are all within their 5’-upstream regions (Additional file 5f, g, h).
The two TEs showed significant up-regulation in Osrdr1 relative to WT (Figure 5b), consistent with a decrease in methylation at the 5’ regions of one copy of each TEs in Osrdr1 (Figure 5a). Notably, all the three genes analyzed did not show the expected relationship between DNA methylation state of their 5’-regulatory regions and expression levels. Specifically, one gene (Os06g0316000) that showed increase in CG methylation in Osrdr1 was up-regulated in expression (Figure 5b); the remaining two genes showed down-regulation in Osrdr1 relative to WT despite the lack of methylation changes in the bisulphite-sequenced regions (Figure 5b).
We next investigated possible relationships between smRNA accumulation and DNA methylation. We found that almost all of the altered CHH methylation was associated with changes in smRNA clusters. For example, the increased CHH methylation of the Pong copy located on chromosome 2 was associated with a moderate increase in smRNA accumulation, whereas the slight decrease in CHH methylation in the flanking region and the increase in CHH methylation in the gene body region of the Pong copy located on chromosome 9 were associated with moderate decrease and increase in smRNA accumulations, respectively (Additional file 5c). These positive correlations of smRNA accumulation and CHH methylation suggests that OsRDR1 plays a role in the de novo CHH methylation in a subset of genomic loci in rice, probably by affecting the production/accumulation of smRNAs required for RdDM, as shown in Arabidopsis[20, 21]. The locus-specificity of methylation changes or the two analyzed TEs indicated that their methylation patterns were determined by either or both the flanking sequences and the local chromatin environment, an issue which warrants further investigations.
Phenotypes in Osrdr1under normal and abiotic stress conditions
RNA silencing pathways have been well characterized in the dicot model plant Arabidopsis but remain poorly studied in other plants like monocots to which many major crops belong. Utilizing a retransposon Tos17 insertion mutant of OsRDR1 in rice, we performed genome-wide analysis to unveil the function of OsRDR1, a component recently shown in Arabidopsis to be involved in non-canonical, 21 nt siRNA-directed RdDM pathway [20, 21], on expression of endogenous genes. By deep sequencing of smRNAs and microarray analysis of gene expression in the Osrdr1 mutant and its sibling WT, we showed that the expression of > 1,000 genes were significantly changed in Osrdr1 relative to WT, suggesting that OsRDR1 plays a role in genome-wide gene regulation in rice. In addition, the Osrdr1 mutant showed regional alterations in smRNA accumulation and/or titration across the rice genome, and at least some of which are associated with locus-specific alteration of DNA methylation.
Among the differentially accumulated smRNAs, many were miRNAs both previously known and newly identified in this study. Expression changes in many of these miRNAs are associated with changes in their target gene expression, which could partly be responsible for the gene expression changes observed in the Osrdr1 mutant relative to WT. The mechanism by which mutation of OsRDR1 caused changes in miRNA expression in rice was not clear. It was found in Arabidopsis that none of the RDRs has a direct role in miRNA biogenesis [2, 38]. However, RDRs could impact miRNA accumulation indirectly by either affecting miRNA precursor gene expression through the TGS or PTGS pathways [1, 2, 38] or generating dsRNAs that compete for DCL1 function that is required for miRNA biogenesis [1, 2].
Our results suggested that OsRDR1 might play a role in maintaining the intrinsic locus-specific DNA methylation patterns, as its mutation caused alteration of methylation at some of the loci we analyzed. In particular, the changes in CHH methylation, which are indicative of de novo methylation by the RdDM pathway, showed correlation with changes in smRNA accumulation. In the respect of reduced CHH methylation and concomitant reduced smRNA accumulation, OsRDR1 may functionally resemble the Arabidopsis RDR1 and plays a role in the 21 nt siRNA-dependent non-canonical RdDM pathway [20, 21]. However, some of the analyzed loci showed increased CHH methylation that is associated with increased smRNA accumulation in Osrdr1. We should caution that because we analyzed only 10 loci, the results observed may not be extrapolated to global scale. In Arabidopsis, it was documented that mutation of RDR1 resulted in near complete loss of methylated cytosine of all three sequence contexts (CG, CHG and CHH) within the 4,949 CHH hypomethylation DMRs (differentially methylated regions) between drm1/2 and WT . Therefore, genome-wide methylation analysis (methylome) of the Osrdr1 mutant will be required to confirm whether OsRDR1 plays a similar role globally in rice.
Previous studies in Arabidopsis and Nicotiana have defined an established role of RDR1 in plant virus responses [24, 26, 27]. We showed here that Osrdr1 exhibited no phenotypic differences from its sibling WT plants under normal growing condition, but displayed ephemeral phenotypic fluctuations contingent with presence of several abiotic stress conditions. This observation, together with the enriched GO categories including those involved in metabolic process of the differentially expressed genes between Osrdr1 and WT (Figure 2b), suggest that the effects of altered gene expression due to OsRDR1 mutation has been largely canalized under normal condition but can be released by certain abiotic stress conditions , an issue that merits further investigations. Regardless, our results suggest that, apart from its established role in the production and amplification of exogenous, virus-derived siRNAs (vsiRNAs) in infected plants [26, 27], the rice RDR1 homolog (OsRDR1) might also play a role in certain abiotic stress responses, which however may not involve stable epigenetic changes in this respect. In this regard, it should be emphasized again that the genome-wide analyses of both smRNA profiles and gene expression in Osrdr1 were conducted on plants grown under normal conditions. Therefore, further studies are needed to conduct the analyses in plants of the mutant and WT under both short- and long-term stress conditions. It would also be interesting to analyze the progeny of stress-treated Osrdr1 plants to investigate if OsRDR1 is involved in transgenerational inheritance of stress-induced epigenetic changes, if they occurred.
How RDR1 affects global gene expression and smRNA profiles have not been previously investigated in any plant species. By analyzing a null mutant of the rice RDR1 gene (OsRDR1), we showed that expression of more than 1,000 endogenous genes of diverse gene ontology (GO) categories were significantly altered in the mutant, indicating a functional role of OsRDR1 in regulating endogenous gene expression in rice. By smRNA deep-sequencing, we found that extensive alteration in smRNA clusters occurred across each of the 12 rice chromosomes in the mutant, indicating a role of OsRDR1 in smRNA biogenesis and/or titration in rice. We also found that at least some of the gene expression changes are correlated with differences in miRNAs. We further showed that changes in smRNAs can be concomitant with locus-specific alteration of cytosine methylation primarily of the CHH contexts, thus linking OsRDR1 to DNA methylation in rice. Finally, we showed that whereas no apparent phenotypic abnormality was associated with loss of function of OsRDR1, ephemeral phenotypic fluctuations could be generated by various short-term abiotic stress conditions as a result of OsRDR1 mutation, suggesting a role of OsRDR1 in plant abiotic stress response.
Based on information about the rice retrotransposon Tos17 insertion lines (http://tos.nias.affrc.go.jp/), we obtained a line (#RDR704) of rice cultivar Hitomebore with Tos17 being inserted into the second exon of OsRDR1 in a heterozygous state (accession # H0643). According to BlastN search at the NCBI website (http://blast.ncbi.nlm.nih.gov/Blast.cgi), we found that rice contains a single copy of the insert gene (OsRDR1). The three OsRDR1 genotypes, WT (RDR1/RDR1), heterozygous (RDR1/rdr1) and homozygous mutant (rdr1/rdr1) were identified by two pairs of specific primers (Figure 1a). Specifically, WT was identified by a pair of primers anchored within the OsRDR1 gene but flanking the Tos17 insertion site; homozygous mutant was identified by a pair primers with on anchored to the OsRDR1 gene and the other one targeting to the terminal of Tos17; and the heterozygote was identified by combinations of both types of primers. The heterozygotes of OsRDR1(+/−) were selfed for five successive generations, and in each of the first four generation (S1-S4) only heterozygous individuals were selected based on PCR identification. At the last generation (S5), the newly segregated homozygous mutant, i.e., OsRDR1−/− (designated as Osrdr1), and its sibling wild type (WT), i.e., OsRDR1+/+, were selected and propagated for an additional generation to have sufficient seeds for this study. In this way, the mutant and WT should be genetically identical except for the locus in concern, i.e., OsRDR1. Seeds of the two genotypes were thoroughly washed with distilled water and then germinated in the dark in Petri dishes containing distilled water at 28°C. After a 2-day incubation, germinated seeds were transferred to a greenhouse at 26°C under 16 h/8 h light/dark regime for the four kinds of abiotic stress treatments: 0.15 mMol/L NaCl (salt), 0.25 mMol/L CuSO4 (heavy metal Cu2+), 0.25 mMol/L HgCl2 (heavy metal Hg2+), 1 mMol/L Sodium nitroferricyanide(III) dehydrate (SNP, for NO stress) in Hoagland nutrient solution for 7- day. Mock controls (CK) were grown in parallel. Then, all seedling plants were transplanted to normal paddy field. Plants were surveyed at appropriate growth and developmental stages, seedling, heading and maturity.
Genomic DNA was isolated from seedlings of Osrdr1 and WT at the same developmental stage using a modified CTAB method. Total RNA was isolated from the same seedlings with the Trizol Reagent (Invitrogen) according to the manufacturer’s instructions. The RNA was then treated with RNase-free DNase I (Invitrogen) to eliminate possible genomic DNA contamination before being reverse transcribed with the SuperScript RNase H- Reverse Transcriptase (Invitrogen).
SmRNA library construction and sequencing
Total RNA was prepared for smRNA sequencing based on the Illumina Sample Preparation Protocol. The samples were quantified and equalized so that equivalent amounts of RNA from Osrdr1 and WT were analyzed. In brief, total RNA was purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel and smRNA regions corresponding to the 15–30 nucleotide bands in the marker lane were excised and recovered. The 15–30 nt smRNAs were 5’ and 3’ RNA adapter-ligated by T4 RNA ligase and at each step length validated and purified by urea PAGE gel electrophoretic separation. The adapter-ligated smRNA was subsequently transcribed into cDNA by Super- Script II reverse transcriptase (Invitrogen) and PCR amplified, using primers that anneal to the ends of the adapters. The amplified cDNA, too, was purified and recovered. The final quality of the library was ensured by validation of the size, purity and concentration using an Agilent Technologies 2100 Bioanalyzer. The two constructed cDNA libraries subsequently underwent Solexa/Illumina’s proprietary flowcell cluster generation and bridge amplification.
Analysis of smRNA clusters
SmRNA reads of 18-26 nt in size were counted within every sliding 100 bp window along the rice genome. The reads were normalized to RPM (reads per million), and comparison was then made between Osrdr1 and WT plants using the median RPM values, which are denoted as X for Osrdr1 and Y for WT plants. The fold value was calculated by the formula log2X-log2Y = log2(X/Y).
Affymetrix GeneChip® Rice Genome Array
The microarray transcriptional profiling was performed by the Affymetrix, Inc. in the Gene Company Ltd. (Shanghai, China), using procedures described in the GeneChip® Expression Analysis Technical Manual.
Real-time quantitative (q) reverse transcriptase (RT)-PCR analysis
The qRT-PCR experiments were performed using SYBR Premix Ex Taq (TOYOBO) according to the manufacturer’s instruction on a Roche LightCycler480 apparatus (Roche Inc.). The primers for amplifying the 18 studied genes were designed using the Primer 5 software and listed in Additional file 6. Primers for qRT-PCR analysis of transposase genes were described in a previous report . Expression of a rice β-actin gene, eEF gene and UBQ5 gene were used as internal control with the primer pairs of5’-atgccattctccgtctt and 5’-gctcctgctcgtagtc; 5’-tttcactcttggtgtgaagcagat and 5’-gacttccttcacgatttcatcgtaa; 5’-accacttcgaccgccactact and 5’-acgcctaagcctgctggtt, respectively. Conditions of RT-qPCR were as reported .
Hemi-nested RT-PCR for detecting miRNA expression
Four miRNA-specific oligonucleotide primers were designed according to a previous report [41, 42] to reverse transcribe the specific miRNAs, and four pairs of specific primers corresponding to the RT primers were designed to amplify the cDNA (Additional file 6). RT-PCR was performed as previously described [41, 42].
DNA (~1 μg) from each plant was treated with bisulphite using the EZ DNA Methylation-Gold Kit and amplified using specific primers (Additional file 6). Bisulphite PCR product was cloned into vector NTI and positive clones were sent for sequencing. The results were analyzed using analysis software on the website http://katahdin.mssm.edu/kismeth based on a previous report .
This study was supported by the National Natural Science Foundation of China (30990243, 31200198), by the State Key Basic Research and Development Plan of China (2013CBA01404), the Jilin Provincial Research Foundation for Basic Research, China (201201097, 201205048), and a Special Foundation for Young Scientists of Jilin Agricultural University (201201).
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