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Deep-sequencing of total RNA from manually dissected wild-type and kyp-2m/KYPp Arabidopsis embryos

ABSTRACT: This dataset provide deep-profiling of the embryonic transcriptome of total RNA at an early developmental stage (2-to-4 cells stage) and at the globular stage in Arabidopsis. Embryos were derived from either a cross between a Landsberg erecta (Ler) maternal parent and a Columbia (Col0) paternal parent or a cross between a kyp-2 Ler maternal parent and a Columbia paternal parent. Embryos were manually dissected ensuring no contamination with maternal seed coat or endosperm.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE24198 | GEO | 2011/06/01

SECONDARY ACCESSION(S): PRJNA130171

REPOSITORIES: GEO

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Deep-sequencing of total RNA from manually dissected wild-type and kyp-2m/KYPp Arabidopsis embryos

Project description:This dataset provide deep-profiling of the embryonic transcriptome of total RNA at an early developmental stage (2-to-4 cells stage) and at the globular stage in Arabidopsis. Embryos were derived from either a cross between a Landsberg erecta (Ler) maternal parent and a Columbia (Col0) paternal parent or a cross between a kyp-2 Ler maternal parent and a Columbia paternal parent. Embryos were manually dissected ensuring no contamination with maternal seed coat or endosperm. 6 samples: crosses between Ler and Col, or kyp-2 (Ler) and Col; Ler seed coat at 2-4cells embryo stage # SC_2.

2011-06-01 | E-GEOD-24198 | biostudies-arrayexpress

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Genome-widebinding maps of arabidopsis KYP

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of KYP in 10 days old KYPpro::KYP:3xFLAG arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide binding levels of KYP:3xFLAG. ChIP was performed using anti-FLAG antibody (sigma M2), and ChIP DNA were analyzed by Illumina NovoSeq.

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Maternal to zygotic transition：A two-step process with two phases of ZGA occurs in zygote right after fertilization in Arabidopsis

Project description:The goal of the present study is to analyze the characteristics of maternal to zygotic transition (MZT) in Arabidopsis. The maternal-to-zygotic transition (MZT) is an essential developmental turning point during the alternation of generations in both plants and animals. In animals, early embryogenesis is maternally controlled and zygotic genome activation (ZGA) starts much later. However, in plants, the timing of MZT and parental contributions to the zygotic transcriptome remain unclear. To address above mentioned questions, we selected Arabidopsis as model plant for the analysis. Regarding to the characteristics of MZT, egg cells, embryos including spherical zygote, elongated zygote, 1-cell embryo and 32-cell embryo were isolated and collected for RNA sequencing. Hybrid zygotes at two representative stages from the reciprocal crosses between polymorphic Arabidopsis Columbia (Col) and Landsberg erecta (Ler) accessions were also sequenced for investigating the parental contributions. We demonstrate that plant MZT occurs during the zygote stage and is a two-step process, first involving rapid maternal transcript degradation and, second, large-scale de novo transcription. Parental contributions to the zygotic transcriptome are stage dependent over the course of zygote development; the spherical zygote is characterized by a maternally dominated transcriptome, whereas the elongated zygote genome shows equal parental contributions.

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Project description:Wild type and mutanat Arabiposis plants grown in short days (9L:15D) for 30 days at 21Â°C, then shifted to long days (16L:8D).,Genotypes:,Columbia wild type (Col-0),Landsberg erecta (Ler),leafy-12 (lfy-12, in Col-0),constans-2 (co-2, in Ler),flowering locus T-2 (ft-2, in Ler),Time points:,0, 3, 5, and 7 days after shift to long days

2007-07-10 | E-GEOD-576 | biostudies-arrayexpress

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2009-04-11 | E-GEOD-15515 | biostudies-arrayexpress

Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense.

Project description:Transcriptional gene silencing (TGS) can serve as an innate immunity against invading DNA viruses throughout Eukaryotes. Geminivirus code for TrAP protein to suppress the TGS pathway. Here we identified an Arabidopsis H3K9me2 histone methyltransferase, Su(var)3-9 homolog 4 (SUVH4/KYP), as a bona fide cellular target of TrAP. TrAP interacts with the catalytic domain of KYP and inhibits its activity in vitro. TrAP elicits developmental anomalies phenocopying several TGS mutants, reduces the repressive H3K9me2 mark and CHH DNA methylation, and reactivates numerous endogenous KYP-repressed loci in vivo. Moreover, KYP binds to the viral chromatin, and controls its methylation to combat virus infection. Notably, kyp mutants support systemic infection of TrAP-deficient Geminivirus. We conclude that TrAP attenuates the TGS of the viral chromatin by inhibiting KYP activity to evade host surveillance. These findings provide new insight on the molecular arms race between host antiviral defense and virus counter defense at an epigenetic level.

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Deep-sequencing of total RNA from manually dissected wild-type Arabidopsis embryos at the 2-to-4 cell stage

Project description:This dataset provide deep-profiling of the embryonic transcriptome of total RNA at the 2-to-4 cell stage in Arabidopsis. Embryos were derived from a cross between Col0 (mother) and Ler (father). Embryos were manually dissected ensuring no contamination with maternal seed coat or endosperm. For details on the method, see PMID: 21620136. 1 sample: cross between Col0 and Ler

2012-01-26 | E-GEOD-33866 | biostudies-arrayexpress

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