Unknown,Transcriptomics,Genomics,Proteomics

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Global identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA.


ABSTRACT: Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis. Two replicate input fraction samples were used as controls for two replicate IP fraction samples. Total RNA from input fractions and small RNA that co-immunoprecipitated with HA-AGO1 complexes were size fractionated by polyacrylamide gel electrophoresis to recover 18-24 nucleotide small RNA. 3' and then 5' adaptors were serially ligated on to each small RNA followed by PAGE purification. RT-PCR was used to convert RNA to DNA amplicons. Amplicons were sequenced using the Illumina GAIIx platform. Resulting reads were parsed and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: James Carrington 

PROVIDER: E-GEOD-22252 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis.

Cuperus Josh T JT   Carbonell Alberto A   Fahlgren Noah N   Garcia-Ruiz Hernan H   Burke Russell T RT   Takeda Atsushi A   Sullivan Christopher M CM   Gilbert Sunny D SD   Montgomery Taiowa A TA   Carrington James C JC  

Nature structural & molecular biology 20100618 8


RNA interference pathways can involve amplification of secondary siRNAs by RNA-dependent RNA polymerases. In plants, RDR6-dependent secondary siRNAs arise from transcripts targeted by some microRNAs (miRNAs). Here, Arabidopsis thaliana secondary siRNAs from mRNA as well as trans-acting siRNAs are shown to be triggered through initial targeting by a 22-nucleotide (nt) miRNA that associates with AGO1. In contrast to canonical 21-nt miRNAs, 22-nt miRNAs primarily arise from foldback precursors cont  ...[more]

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