The maize pericarp color1 gene is regulated by RdDM and non-RdDM types of chromatin silencing
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE68510 | GEO | 2017/10/23
SECONDARY ACCESSION(S): PRJNA282953
REPOSITORIES: GEO
Similar Datasets
Project description:P1 encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize silks and red phlobaphene pigments in pericarps and other floral tissues, which contributed to making P1 an important visual marker since the dawn of modern genetics. We conducted RNA-Seq using pericarps at two different stages, 14 and 25 days after pollination (DAP). High-throughput sequencing using the Illumina platform resulted in the generation of ~20 million high quality reads, from which ~90% aligned to the recently completed maize genome sequence corresponding to ~5 million reads for each one of the four samples.
2012-09-14 | GSE38413 | GEO
Project description:Allelic variation at the Zea mays (maize) pericarp color1 (p1) gene has been attributed to epigenetic gene regulation. A p1 distal enhancer, 5.2 kb upstream of the transcriptional start site, has demonstrated variation in DNA methylation in different p1 alleles/epialleles. In addition, DNA methylation of sequences within the 3' end of intron 2 also plays a role in tissue-specific expression of p1 alleles. We show here a direct evidence for small RNAs' involvement in regulating p1 that has not been demonstrated previously. The role of mediator of paramutation1 (mop1) was tested in the maintenance of somatic silencing at distinct p1 alleles: the non-paramutagenic P1-wr allele and paramutagenic P1-rr' epiallele. The mop1-1 mutation gradually relieves the silenced phenotype after multiple generations of exposure; P1-wr;mop1-1 plants display a loss of 24-nt small RNAs and DNA methylation in the 3' end of the intron 2, a region close to a Stowaway transposon. In addition, a MULE sequence within the proximal promoter of P1-wr shows depletion of 24nt siRNAs in mop1-1 plants. Release of silencing was not correlated with small RNAs at the distal enhancer region of the P1-wr allele. We found that the somatic silencing of the paramutagenic P1-rr' is correlated with significantly reduced H3K9me2 in the distal enhancer of P1-rr'; mop1-1 plants, while symmetric DNA methylation is not significantly different. This study highlights that the epigenetic regulation of p1 alleles is controlled both via RdDM as well as non-RdDM mechanisms.
| S-EPMC5675401 | biostudies-literature
Project description:P1 encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize silks and red phlobaphene pigments in pericarps and other floral tissues, which contributed to making P1 an important visual marker since the dawn of modern genetics. We conducted RNA-Seq using pericarps at two different stages, 14 and 25 days after pollination (DAP). High-throughput sequencing using the Illumina platform resulted in the generation of ~20 million high quality reads, from which ~90% aligned to the recently completed maize genome sequence corresponding to ~5 million reads for each one of the four samples. Examination of two different RNA samples from two different stages of maize pericarp tissues.
2012-09-14 | E-GEOD-38413 | biostudies-arrayexpress
Project description:MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.
2020-03-22 | GSE132167 | GEO
Project description:Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wildtype maize and in the isogenic mop1-1 loss-of-function mutant using Illumina’s sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24 nt (nucleotide) endogenous heterochromatic short-interfering siRNAs were dramatically reduced resulting in an enrichment of miRNAs and trans-acting siRNAs (ta-siRNAs). In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ~22 nt class of small RNAs. These data suggest that maize, unlike Arabidopsis, has a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24 nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced.
2008-10-01 | GSE12173 | GEO
Project description:Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wildtype maize and in the isogenic mop1-1 loss-of-function mutant using Illumina’s sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24 nt (nucleotide) endogenous heterochromatic short-interfering siRNAs were dramatically reduced resulting in an enrichment of miRNAs and trans-acting siRNAs (ta-siRNAs). In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ~22 nt class of small RNAs. These data suggest that maize, unlike Arabidopsis, has a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24 nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced. This library was derived from maize variety K55 wild-type and mop1 mutant. Immature ears were harvested from plants grown outdoors in Tuscon, AZ. The material was harvested from plants 68 days after germination, with the floral tissue including young tassels 2-3 cm long. Total RNA was isolated using a standard TRIZOL-based method and the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined. Raw data are unavailable from Illumina
2008-09-30 | E-GEOD-12173 | biostudies-arrayexpress
Project description:To understand the molecular mechanisms underlying paramutation, we examined the role of Unstable factor for orange1 (Ufo1) in maintaining paramutation at the maize pericarp color1 (p1) and booster1 (b1) loci. Genetic tests revealed that the Ufo1-1 mutation disrupted silencing associated with paramutation at both p1 and b1. The level of up regulation achieved at b1 was lower than that at p1, suggesting differences in the role Ufo1-1 plays at these loci. We characterized the interaction of Ufo1-1 with two silenced p1 epialleles, P1-rr' and P1-pr(TP), that were derived from a common P1-rr ancestor. Both alleles are phenotypically indistinguishable, but differ in their paramutagenic activity; P1-rr' is paramutagenic to P1-rr, while P1-pr(TP) is non-paramutagenic. Analysis of cytosine methylation revealed striking differences within an enhancer fragment that is required for paramutation; P1-rr' exhibited increased methylation at symmetric (CG and CHG) and asymmetric (CHH) sites, while P1-pr(TP) was methylated only at symmetric sites. Both silenced alleles had higher levels of dimethylation of lysine 9 on histone 3 (H3K9me2), an epigenetic mark of silent chromatin, in the enhancer region. Both epialleles were reactivated in the Ufo1-1 background; however, reactivation of P1-rr' was associated with dramatic loss of symmetric and asymmetric cytosine methylation in the enhancer, while methylation of up-regulated P1-pr(TP) was not affected. Interestingly, Ufo1-1-mediated reactivation of both alleles was accompanied with loss of H3K9me2 mark from the enhancer region. Therefore, while earlier studies have shown correlation between H3K9me2 and DNA methylation, our study shows that these two epigenetic marks are uncoupled in the Ufo1-1-reactivated p1 alleles. Furthermore, while CHH methylation at the enhancer region appears to be the major distinguishing mark between paramutagenic and non-paramutagenic p1 alleles, H3K9me2 mark appears to be important for maintaining epigenetic silencing.
| S-EPMC3464198 | biostudies-literature
Project description:Although paramutation has been well-studied at a few hallmark loci involved in anthocyanin biosynthesis in maize, the cellular and molecular mechanisms underlying the phenomenon remain largely unknown. Previously described actors of paramutation encode components of the RNA-directed DNA-methylation (RdDM) pathway that participate in the biogenesis of 24-nucleotide small interfering RNAs (24-nt siRNAs) and long non-coding RNAs. In this study, we uncover an ARGONAUTE (AGO) protein as an effector of the RdDM pathway that is in charge of guiding 24-nt siRNAs to their DNA target to create de novo DNA methylation. We combined immunoprecipitation, small RNA sequencing and reverse genetics to, first, validate AGO104 as a member of the RdDM effector complex and, then, investigate its role in paramutation. We found that AGO104 binds 24-nt siRNAs involved in RdDM, including those required for paramutation at the b1 locus. We also show that the ago104-5 mutation causes a partial reversion of the paramutation phenotype at the b1 locus, revealed by intermediate pigmentation levels in stem tissues. Therefore, our results place AGO104 as a new member of the RdDM effector complex that plays a role in paramutation at the b1 locus in maize.
| S-EPMC9426929 | biostudies-literature
Project description:Transposable elements (TEs) are among the most dynamic parts of genomes. Since TEs are potentially deleterious, eukaryotes silence them through epigenetic mechanisms such as repressive histone modifications and DNA methylation. We previously reported that Arabidopsis TEs, called VANDALs, counteract epigenetic silencing through a group of sequence-specific anti-silencing proteins, VANCs. VANC proteins bind to noncoding regions of specific VANDAL copies and induce loss of silent chromatin marks. The VANC-target regions form tandem repeats, which diverge rapidly. Sequence-specific anti-silencing allows these TEs to proliferate with minimum host damage. Here, we show that RNA-directed DNA methylation (RdDM) efficiently targets noncoding regions of VANDAL TEs to silence them de novo. Thus, escape from RdDM could be a primary event leading to the rapid evolution and diversification of sequence-specific anti-silencing systems. We propose that this selfish behavior of TEs paradoxically could make them diverse and less harmful to the host.
| S-EPMC10398659 | biostudies-literature
Project description:Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression, and inhibited recombination. Here, we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p1 gene is null and the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. By screening for kernels with red pericarp, we identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp. To our knowledge, this is the first report of multiple recurrent inversions that change the position of a gene promoter relative to an enhancer to induce ectopic expression in a eukaryote.
| S-EPMC8225341 | biostudies-literature