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A small RNA pathway mediates allelic dosage in endosperm [sRNA-seq]

ABSTRACT: Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. We find an inverse relationship between the parent-of-origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates transcriptional balance between maternally and paternally inherited genomes in endosperm.

OTHER RELATED OMICS DATASETS IN: PRJNA374333PRJNA374335PRJNA374044

ORGANISM(S): Arabidopsis thaliana Arabidopsis lyrata

PROVIDER: GSE94787 | GEO | 2017/12/15

SECONDARY ACCESSION(S): PRJNA374333

REPOSITORIES: GEO

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A small RNA pathway mediates allelic dosage in endosperm [mRNA-seq]

Project description:Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. We find an inverse relationship between the parent-of-origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates transcriptional balance between maternally and paternally inherited genomes in endosperm.

2017-12-15 | GSE94786 | GEO

RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [PareSeq]

Project description:Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. thaliana endosperm from reciprocal heterozygotes produced by crossing wild-type plants to Pol IV mutants. We find that maternally and paternally acting Pol IV have divergent effects on endosperm. Losses of maternal and paternal Pol IV impact sRNAs and DNA methylation at distinct genomic sites. Strikingly, maternally and paternally-acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict

2022-03-04 | GSE197715 | GEO

RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [mRNA_seq libraries]

2022-03-04 | GSE197714 | GEO

RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [sRNA_seq libraries]

2022-03-04 | GSE197713 | GEO

RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [bisulfite_sequencing]

2022-03-04 | GSE197712 | GEO

Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent

Project description:Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes (‘paternal excess’) associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants.

2010-08-26 | GSE20006 | GEO

Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix

2010-08-26 | GSE20005 | GEO

Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix

2010-08-26 | E-GEOD-20005 | biostudies-arrayexpress

Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent

2010-08-26 | E-GEOD-20006 | biostudies-arrayexpress

Extensive imprinted gene expression in Arabidopsis endosperm

Project description:Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes, as well as by Polycomb group (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. Epigenetics Examination of genomic imprinting in Arabidopsis endosperm

2011-03-10 | E-GEOD-24644 | biostudies-arrayexpress

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