Transcriptomics

Dataset Information

103

Characterization of AGO1-/AGO4-associated smRNAs


ABSTRACT: To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by Illumina’s technology. We identified some additional miRNAs, collateral miRNAs encoded in known miRNA precursors, phased smRNA clusters and nat-siRNAs. Organ specific sequencing provided digital expression profiles of all obtained smRNAs, especially miRNAs. We used extracts from Arabidopsis flowers, leaves and roots as well as ten-day old seedlings to purify smRNAs associated with AGO1 and AGO4 protein complexes using a two-step immunoprecipitation method.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Nam-Hai Chua  Thomas Tuschl   Tolulope Ojo   Xiu-Jie Wang   Markus Hafner   Jun Liu   Jongchan Woo   Takatoshi Kiba   Huan Wang   Xiuren Zhang    

PROVIDER: E-GEOD-28591 | ArrayExpress | 2013-04-03

SECONDARY ACCESSION(S): SRP006477GSE28591PRJNA139119

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions.

Wang Huan H   Zhang Xiuren X   Liu Jun J   Kiba Takatoshi T   Kiba Takatoshi T   Woo Jongchan J   Ojo Tolulope T   Hafner Markus M   Tuschl Thomas T   Chua Nam-Hai NH   Wang Xiu-Jie XJ  

The Plant journal : for cell and molecular biology 20110510 2


As important components of small RNA (smRNA) pathways, Argonaute (AGO) proteins mediate the interaction of incorporated smRNAs with their targets. Arabidopsis contains 10 AGO proteins with specialized or redundant functions. Among them, AGO1 mainly acts in microRNA (miRNA) and small-interfering RNA (siRNA) pathways for post-transcriptional gene silencing (PTGS), whereas AGO4 regulates transcriptional gene silencing (TGS) via endogenous 24-nucleotide (nt) smRNAs. To fully characterize smRNAs asso  ...[more]

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