Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

ABSTRACT: Imprinted gene expression occurs during seed development in plants and is closely tied to differential DNA methylation of maternal and paternal alleles, particularly at proximal transposable elements (TEs). Since the epigenetic modification of TEs can vary within species, we investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three strains of Arabidopsis that display diverse seed size phenotypes. Unexpectedly we found that one strain, Cvi, is globally CG hypomethylated. We discovered three examples of strain-specific imprinting caused by epigenetic variation at a TE. Our data allowed us to predict and experimentally validate an instances of allele-specific imprinting in additional strains based only on methylation patterns. We conclude that numerous differences in imprinting can evolve in highly similar, recently diverged genotypes due to epiallelic variation present within the species. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Examination of parent-of-origin specific and total gene expression in embryo, endosperm, and whole seeds. Samples with the same heading are biological replicates (e.g. CVN1, CVN2, and CVN3). High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col, Ler and Cvi reciprocal F1 hybrid embryo and endosperm tissue isolated at 6 days after pollination to identify imprinted genes.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Mary Gehring

PROVIDER: E-GEOD-52806 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Contribution of NAC transcription factors to plant adaptation to land.

Xu Bo B Ohtani Misato M Yamaguchi Masatoshi M Toyooka Kiminori K Wakazaki Mayumi M Sato Mayuko M Kubo Minoru M Nakano Yoshimi Y Sano Ryosuke R Hiwatashi Yuji Y Murata Takashi T Kurata Tetsuya T Yoneda Arata A Kato Ko K Hasebe Mitsuyasu M Demura Taku T

Science (New York, N.Y.) 20140320 6178

The development of cells specialized for water conduction or support is a striking innovation of plants that has enabled them to colonize land. The NAC transcription factors regulate the differentiation of these cells in vascular plants. However, the path by which plants with these cells have evolved from their nonvascular ancestors is unclear. We investigated genes of the moss Physcomitrella patens that encode NAC proteins. Loss-of-function mutants formed abnormal water-conducting and supportin ...[more]

PMID: 24652936

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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.

Project description:We carried out a five-generation selection experiment in which two Arabidopsis accessions (Ler and Cvi) and 17 Recombinant Inbred Lines (RILs) derived from them were subjected in 24 replicated populations to four levels of micro-landscape fragmentation and two levels of disturbance, factorially crossed with each other to yield 8 experimental selection regimes. We used 19 lines (including the two parental Ler and Cvi) in generation 1 of our experiment, nine of which contained the erecta mutation and ten of which did not. Lines expressing the erecta mutation are short and compact and are likely to disperse seeds over shorter distances. Both the non-erecta and the erecta lines spanned the full available range of seed sizes from the original 162 RILs in the collection. We set up 24 experimental landscapes consisting of 2, 4, 8, or 16 patches where the total area was constrained to be equal. Plants that germinated outside the designated suitable patches were removed. In half of the landscapes which we termed static the top 2-3 mm of seeds and soil were removed from the surface of the suitable patches after 8 weeks of growth and reproduction. In the other half of the landscapes which we termed dynamic a number of Petri dishes, equivalent in size and number to the existing suitable patches, were distributed around the landscape at random, to catch dispersing seeds. The seeds collected by these two methods were cold-treated for one week while all patches were replenished with fresh substrate. Seeds were then returned to the surface of the new patches at the beginning of the next generation. Thus, in dynamic landscapes, seeds must disperse to have any chance of entering the next generation, while in static landscapes, only seeds that do not disperse have any chance of further propagation. After five generations of such selection, a single pod from approximately 70 individuals from each landscape was removed. Single individuals derived from such pods were reared under standardized conditions to measure several phenotypic characters, such as seed mass, height, presence of the erecta mutation, flowering time etc. Clear phenotypic differences are apparent between the different landscapes. However, we have no information as to the underlying genes, which might have been selected or the epigenetic modifications that might have occurred. Material for DNA extraction from each population (? 50 plants/population) was collected for subsequent genetic analyses. The allele frequencies of Ler and Cvi alleles was determined at the genome-wide level using ATH1 Affymetrix GeneChips® (each in quadruplicate = 8 parental microarrays). 26638 single feature polymorphisms (SFPs) between these two accessions could be detected. The relative contribution of Ler and Cvi alleles in a population at each locus, for which a single feature polymorphism can be detected, was assessed. We then analyzed the DNA isolated from the experimental populations (24 landscapes of generation 5 = 24 microarrays & original populations in triplicate = 3 microarrays) and determine the relative contributions of Ler and Cvi alleles for the 26638 identified SFPs (i.e. allele frequency shifts).

Dataset Information

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

Publications

Contribution of NAC transcription factors to plant adaptation to land.

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