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SRX3318188: GSM2829910: col_293457; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 36.1M spots, 7.3G bases, 4.7Gb downloads

Submitted by: NCBI (GEO)
Study: microRNA-triggered transposon small RNAs mediate genome dosage response (RNA-Seq)
show Abstracthide Abstract
Chromosome dosage plays a significant role in reproductive isolation and speciation in both plants and animals, but underlying mechanisms are largely obscure. Transposable elements can promote hybridity through maternal small RNA, and have been postulated to regulate dosage response via neighboring imprinted genes. Here, we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of LTR-retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21 to 22-nucleotide small RNA in a dose dependent fashion via RNA polymerase IV. We show that these epigenetically activated small-interfering RNAs (easiRNAs) mediate hybridization barriers between diploid seed parents and tetraploid pollen parents (“the triploid block”), and that natural variation for miR845 may account for “endosperm balance” allowing formation of triploid seeds. Targeting the PBS with small RNA is a common mechanism for transposon control in mammals and plants, and provides a uniquely sensitive means to monitor chromosome dosage and imprinting in the developing seed. Overall design: RNA-seq of Arabidopsis pollen
Sample: col_293457
SAMN07830380 • SRS2623759 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10% Sucrose, pH 7.5) for 3 min (31), followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Pollen was suspended in 50ul of PEB, immediately frozen in liquid nitrogen and stored at -80ºC until further use. Libraries for RNA sequencing from Col-0 and Ler-0 pollen were prepared using rRNA-depleted total RNA samples and the ScriptSeq-v2 RNA-Seq Library Prep kit (Epicenter/Illumina), following manufacturer instructions.
Experiment attributes:
GEO Accession: GSM2829910
Runs: 1 run, 36.1M spots, 7.3G bases, 4.7Gb
Run# of Spots# of BasesSizePublished


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