Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

High-resolution analysis of parent-of-origin-allelic expression in Arabidopsis seeds

ABSTRACT: We report the identification of parent-of-origin specific gene expression in Arabidopsis seeds. F1 hybrid seeds were generated by reciprocally crossing Arabidopsis accessions Col-0 and Bur-0. Seeds were harvested at 4 DAP and total RNA was isolated and analyzed by deep sequencing. Overall identification of parent-of-origin-allelic expression by analysis of SNP distribution

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Marc Rehmsmeier

PROVIDER: E-GEOD-27292 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm.

Wolff Philip P Weinhofer Isabelle I Seguin Jonathan J Roszak Pawel P Beisel Christian C Donoghue Mark T A MT Spillane Charles C Nordborg Magnus M Rehmsmeier Marc M Köhler Claudia C

PLoS genetics 20110616 6

Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal c ...[more]

PMID: 21698132

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Project description:In animals, maternal gene products deposited into eggs regulate embryonic development before activation of the zygotic genome. In plants, an analogous period of prolonged maternal control over embryogenesis is thought to occur based on gene-expression studies. However, other gene-expression studies and genetic analyses show that some transcripts must derive from the early zygotic genome, implying that the prevailing model does not fully explain the nature of zygotic genome activation in plants. To determine the maternal, paternal and zygotic contributions to the early embryonic transcriptome, we sequenced the transcripts of hybrid embryos from crosses between two polymorphic inbred lines of Arabidopsis thaliana and used single-nucleotide polymorphisms (SNPs) diagnostic of each parental line to quantify parental contributions. Although some transcripts appeared to be either inherited from primarily one parent or transcribed from imprinted embryonic loci, the vast majority of transcripts were produced in near-equal amounts from both maternal and paternal alleles, even during the initial stages of embryogenesis. Results of reporter experiments and analyses of transcripts from genes that are not expressed in sperm and egg indicate early and widespread zygotic transcription. Thus, in contrast to early animal embryogenesis, early plant embryogenesis is mostly under zygotic control. Col-0 and Cvi-0 seed stocks were obtained from the Arabidopsis Biological Resource Center. Plants were grown at 22M-BM-0 C in a Conviron growth chamber with a 16-h light/8-h dark cycle. Flowers were emasculated one day before crossing, and pools of twenty 1-cell/2-cell, 8-cell and ~32-cell embryos were hand-dissected approximately 40, 64 and 78 hours after pollination, respectively. Embryo dissections, RNA isolation, linear amplification of poly(A) RNA and strand-specific RNA-Seq was as described (Nodine and Bartel, 2010, Genes & Development), except that embryos were extensively washed prior to RNA isolation. After removing adaptor sequences, reads were mapped to both the A. thaliana genome and transcript models (Col-0 genome reference, TAIR10) with the Bowtie short-read aligner. Reads were also mapped to a M-bM-^@M-^XpseudoM-bM-^@M-^Y Cvi-0 genome and Cvi-0 transcript models, in which SNPs in the Col-0 genome and transcript models were replaced with Cvi-0 variants (ftp://ftp.arabidopsis.org/home/tair/Sequences/Ecker_Cvi_snps.txt) generated by the 1,001 Genomes Project. Reads that both perfectly and uniquely matched either the genomes or transcript models were retained, and those overlapping transcribed regions of annotated genes were evaluated for overlap with SNPs. To normalize for differences in library sizes, the numbers of reads representing each transcript were divided by the total number of reads matching the genome and transcript models. SNP-overlapping reads were assigned to one of the parental genomes and tallied for each transcript, combining tallies for multiple SNPs within the same transcript.

Dataset Information

High-resolution analysis of parent-of-origin-allelic expression in Arabidopsis seeds

Publications

High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm.

Similar Datasets

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