1. Chromosomes and Gene Expression
  2. Plant Biology
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Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis

  1. Shengben Li
  2. Brandon Le
  3. Xuan Ma
  4. Shaofang Li
  5. Chenjiang You
  6. Yu Yu
  7. Bailong Zhang
  8. Lin Liu
  9. Lei Gao
  10. Ting Shi
  11. Yonghui Zhao
  12. Beixin Mo
  13. Xiaofeng Cao
  14. Xuemei Chen  Is a corresponding author
  1. University of California, Riverside, United States
  2. Shenzhen University, China
  3. Institute of Genetics and Developmental Biology, China
Research Article
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Cite this article as: eLife 2016;5:e22750 doi: 10.7554/eLife.22750

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.

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Article and author information

Author details

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
    ORCID icon "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.

Reviewing Editor

  1. Yijun Qi, Tsinghua University, China

Publication history

  1. Received: October 27, 2016
  2. Accepted: December 11, 2016
  3. Accepted Manuscript published: December 12, 2016 (version 1)
  4. Version of Record published: January 3, 2017 (version 2)
  5. Version of Record updated: August 10, 2017 (version 3)

Copyright

© 2016, Li et al.

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.

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Further reading

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    Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Prior studies showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of TF spacing alterations resulting from naturally occurring insertions and deletions (InDels) has not been systematically analyzed. To address this question, we first characterized the genome-wide spacing relationships of 73 TFs in human K562 cells as determined by ChIP-seq. We found a dominant pattern of a relaxed range of spacing between collaborative factors, including 45 TFs exclusively exhibiting relaxed spacing with their binding partners. Next, we exploited millions of InDels provided by genetically diverse mouse strains and human individuals to investigate the effects of altered spacing on TF binding and local histone acetylation. These analyses suggested that spacing alterations resulting from naturally occurring InDels are generally tolerated in comparison to genetic variants directly affecting TF binding sites. To experimentally validate this prediction, we introduced synthetic spacing alterations between PU.1 and C/EBPβ binding sites at six endogenous genomic loci in a macrophage cell line. Remarkably, collaborative binding of PU.1 and C/EBPβ at these locations tolerated changes in spacing ranging from 5-bp increase to >30-bp decrease. Collectively, these findings have implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation.

    1. Chromosomes and Gene Expression
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    Research Article Updated

    Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal the order of chromatin states in establishing developmental gene poising in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of polycomb repressive complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.