Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing
Summary
Conventional RNA interference (RNAi) pathways suppress eukaryotic gene expression at the post-transcriptional or transcriptional level. At the core of RNAi are small RNAs (sRNAs) and effector Argonaute proteins. Arabidopsis AGO1 is known to bind microRNAs (miRNAs) and post-transcriptionally repress target genes via mRNA cleavage and/or translational inhibition in the cytoplasm. Here, we report that AGO1 binds to the chromatin of transcriptionally active genes and promotes their transcription. We show that sRNAs and SWI/SNF are required for AGO1 binding to chromatin and its function in promoting gene transcription. Moreover, we show that various stimuli including plant hormones and stresses specifically trigger AGO1 binding to the stimulus-responsive genes. Finally, we show that AGO1 facilitates the induction of genes in the jasmonate (JA) signaling pathways and the activation of JA responses. Our findings reveal an unsuspected role for AGO1 in facilitating gene transcription in response to plant hormones and stresses.
Overall design
We conducted AGO1 ChIP-seq with Arabidopsis wild-type (WT, Col-0) and ago1-36 seedlings under normal growth condition or treatment with MeJA, BTH, IAA, Flg22 or cold; RNA-seq with WT and ago1-36 seedlings under normal or MeJA treatment condition; Pol II, Pol II Ser2 and Pol II Ser5 ChIP-seq with WT and ago1-36; GRO-seq with WT and ago1-36; and small RNA-seq of nuclear AGO1-associated small RNAs purified from WT and coi1 under normal or MeJA treatment condition. 5 treatment conditions: Methyl jasmonate (MeJA), indole-3-acetic acid (IAA), Benzothiadiazole (BTH), flagellin22 (Flg22), 4 Centigrade (Cold).
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