Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis

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Data availability
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Abstract

Small RNAs are central players in RNA silencing, yet their cytoplasmic compartmentalization and the effects it may have on their activities have not been studied at the genomic scale. Here we report that Arabidopsis microRNAs (miRNAs) and small interfering RNAs (siRNAs) are distinctly partitioned between the endoplasmic reticulum (ER) and cytosol. All miRNAs are associated with membrane-bound polysomes (MBPs) as opposed to polysomes in general. The MBP association is functionally linked to a deeply conserved and tightly regulated activity of miRNAs - production of phased siRNAs (phasiRNAs) from select target RNAs. The phasiRNA precursor RNAs, thought to be noncoding, are on MBPs and are occupied by ribosomes in a manner that supports miRNA-triggered phasiRNA production, suggesting that ribosomes on the rough ER impact siRNA biogenesis. This study reveals global patterns of cytoplasmic partitioning of small RNAs and expands the known functions of ribosomes and ER.

Data availability

The following data sets were generated

1. Li S
2. Le B
3. Ma X
4. Li S
5. You C
6. Yu Y
7. Zhang B
8. Liu L
9. Gao L
10. Shi T
11. Zhao Y
12. Mo B
13. Cao X
14. Chen X
(2016) Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis
Publicly available at the NCBI Gene Expression Omnibus (accession no. GSE82041).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82041

The following previously published data sets were used

(2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
Publicly available at the NCBI Gene Expression Omnibus (accession no. GSE6682).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6682

Article and author information

Author details

Shengben Li

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Brandon Le

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Xuan Ma

Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Shaofang Li

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Chenjiang You

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Yu Yu

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Bailong Zhang

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Lin Liu

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Lei Gao

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Ting Shi

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Yonghui Zhao

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

Competing interests
The authors declare that no competing interests exist.
Beixin Mo

Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Xiaofeng Cao

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Xuemei Chen

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States

For correspondence
xuemei.chen@ucr.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5209-1157

Funding

Howard Hughes Medical Institute

Xuemei Chen

Gordon and Betty Moore Foundation (GBMF3046)

Xuemei Chen

National Institutes of Health (GM061146)

Xuemei Chen

Guangdong Innovation Research Team Funds (2014ZT05S078)

Xuemei Chen

National Science Foundation of China (91440105)

Xuemei Chen

Shenzhen municipality (JCYJ20151116155209176)

Shengben Li

Shenzhen municipality (KQCX2015033110464302)

Shengben Li

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.