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The maize methylome modulates mRNA splicing and reveals widespread paramutation guided by small RNA.

ABSTRACT: Methylation of chromosomal DNA in animals and plants is a fundamental mechanism of epigenetic regulation, and the maize genome, with its diverse complement of transposons and repeats, is a paradigm for transgenerational mechanisms such as paramutation and imprinting. We have determined the genome-wide cytosine methylation map of two maize inbred lines, B73 and Mo17, at high coverage and at single nucleotide resolution. Transposon methylation is highest in CG (65%) and CHG (50%) contexts (where H = A, C or T), while methylation in CHH (5%) contexts is guided by 24nt small interfering RNA (siRNA), and not by 21-22nt siRNA. We have found that CG (8%) methylation seems to deter insertion of Mutator transposons into exons, while CHH and CHG methylation at splice donor and acceptor sites strongly inhibits RNA splicing. Methylation differences between parents are inherited in recombinant inbred lines, but methylation switches, guided by siRNA, are widespread and persist for up to 8 generations. These differences influence splicing, and recurrent switching suggest that paramutation is much more common than previously supposed, and may contribute to heterosis. Our results provide a comprehensive high resolution resource for maize genome methylation, as well as a map of recurrent transgenerational epigenetic shifts (paramutation) in the two most commonly used inbred maize lines.

ORGANISM(S): Zea mays

PROVIDER: GSE39232 | GEO | 2013/06/03

SECONDARY ACCESSION(S): PRJNA170520

REPOSITORIES: GEO

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The maize methylome modulates mRNA splicing and reveals widespread paramutation guided by small RNA.

Project description:Methylation of chromosomal DNA in animals and plants is a fundamental mechanism of epigenetic regulation, and the maize genome, with its diverse complement of transposons and repeats, is a paradigm for transgenerational mechanisms such as paramutation and imprinting. We have determined the genome-wide cytosine methylation map of two maize inbred lines, B73 and Mo17, at high coverage and at single nucleotide resolution. Transposon methylation is highest in CG (65%) and CHG (50%) contexts (where H = A, C or T), while methylation in CHH (5%) contexts is guided by 24nt small interfering RNA (siRNA), and not by 21-22nt siRNA. We have found that CG (8%) methylation seems to deter insertion of Mutator transposons into exons, while CHH and CHG methylation at splice donor and acceptor sites strongly inhibits RNA splicing. Methylation differences between parents are inherited in recombinant inbred lines, but methylation switches, guided by siRNA, are widespread and persist for up to 8 generations. These differences influence splicing, and recurrent switching suggest that paramutation is much more common than previously supposed, and may contribute to heterosis. Our results provide a comprehensive high resolution resource for maize genome methylation, as well as a map of recurrent transgenerational epigenetic shifts (paramutation) in the two most commonly used inbred maize lines. Genome-wide cytosine methylation map in 2 maize strains by bisulfite sequencing, and RNA and small RNA profiles in the same tissue using Illumina platform.

2013-06-03 | E-GEOD-39232 | biostudies-arrayexpress

Genome-wide analysis of DNA methylation in maize inbred lines

Project description:Analysis of whole genome bisulfite data for 3 maize inbred lines (B73, PH207, and W22) with data aligned to the corresponding genome for determination of methylation level (CG, CHG, and CHH) across 100bp windows of the maize genome.

2020-03-01 | GSE128859 | GEO

Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens RNA-Seq]

Project description:Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. We discovered that specific elimination of CG methylation is fully complemented by non-CG methylation but not vice versa. Between the symmetrically-methylated sites, CHG methylation silenced transposons stronger than CG methylation did. Finally, non-CG methylation revealed as crucial for the silencing of CG depleted transposons. Our results suggest that non-CG methylation evolved to silence transposons due to functional limitations and/or rapid mutability of methylated-CGs.

2020-12-30 | GSE142053 | GEO

Non-CG methylation is more potent than CG methylation in moss genome regulation [Athaliana RNA-Seq]

2020-12-30 | GSE142052 | GEO

Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens BS-Seq]

2020-12-30 | GSE142051 | GEO

The ortholog of DDM1 is mainly required for CHG and CG methylation of heterochromatin and is involved in DRM2-mediated CHH methylation that targets mostly genic regions of the rice genome

Project description:OsDDM1 and OsDRM2 display functional specificities that define distinct DNA methylation pathways in the bulk of DNA methylation of the rice genome Cr_DJ.CG.bw: Cr_DJ CG methylation Cr_DJ.CHG.bw: Cr_DJ CHG methylation Cr_DJ.CHH.bw: Cr_DJ CHH methylation ddm1ab.CG.bw: ddm1a/1b CG methylation ddm1ab.CHG.bw: ddm1a/1b CHG methylation ddm1ab.CHH.bw: ddm1a/1b CHH methylation S706.CG.bw: osdrm2 CG methylation S706.CHG.bw: osdrm2 CHG methylation S706.CHH.bw: osdrm2 CHH methylation H3k9me2_macs_peaks.xls: CrDJ H3K9me2 modification peaks H3k9me2_macs_treat_afterfiting.wig: CrDJ H3K9me2 modification wig CrDJ_K27_macs_peaks.xls: CrDJ H3K27me3 modification peaks CrDJ_K27_macs_treat_afterfiting.wig: CrDJ H3K27me3 modification wig DJvsddm1a1b_DESeq2_treated_results.xls: CrDJ and osddm1a1b different expression genes DJvsS706_DEseq2_treated.results.xls: CrDJ and osdrm2 different expression genes smRNA24nt.gff: CrDJ 24nt smRNA smRNA24nt.706.gff: osdrm2 24nt smRNA

2016-06-13 | E-GEOD-81436 | biostudies-arrayexpress

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice [ncRNA-Seq]

Project description:RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long non-coding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.

2021-07-07 | GSE158709 | GEO

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice [Bisulfite-Seq]

2021-07-07 | GSE158710 | GEO

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

2021-07-06 | GSE158711 | GEO

Widespread natural variation of DNA methylation within angiosperms

Project description:DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species. Bisulfite-seq of leaf tissue from plants representing diverse angiosperms. RNA-seq and small RNA-seq was performed on leaf tissue of a subset of the species.

2016-09-02 | E-GEOD-79526 | biostudies-arrayexpress

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