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Connecting the dots of RNA-directed DNA methylation in Arabidopsis thaliana

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Abstract

Noncoding RNAs are the rising stars of genome regulation and are crucial to an organism’s metabolism, development, and defense. One of their most notable functions is its ability to direct epigenetic modifications through small RNA molecules to specific genomic regions, ensuring transcriptional regulation, proper genome organization, and maintenance of genome integrity. Here, we review the current knowledge of the spatial organization of the Arabidopsis thaliana RNA-directed DNA methylation pathway within the cell nucleus, which, while known to be essential for the proper establishment of epigenetic modifications, remains poorly understood. We will also discuss possible future cytological approaches that have the potential of unveiling functional insights into how small RNA-directed epigenetics is regulated through the spatiotemporal regulation of its major components within the cell.

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Abbreviations

smRNA:

Small RNA

miRNA:

Micro RNA

siRNA:

Short interfering RNA

RdDM:

RNA-directed DNA methylation

piRNA:

PIWI-interacting RNA

ssRNA:

Single-stranded RNA

dsRNA:

Double-stranded RNA

RdRP:

RNA-dependent RNA polymerase

AGO:

Argonaute

RISC:

RNA-induced silencing complex

Pol II:

RNA polymerase II

hc-siRNA:

Heterochromatic short interfering RNA

Pol IV:

RNA polymerase IV

Pol V:

RNA polymerase V

RDR2:

RNA-dependent RNA polymerase 2

nat-siRNA:

Natural antisense short interfering RNA

NERD:

Needed for RDR2 independent DNA methylation

siRNA:

short interfering RNA

H3K4met:

Trimethylated lysine 4 of histone H3

H3K9met:

Dimethylated lysine 9 of histone H3

MET1:

Methyltransferase 1

CMT3:

Chromomethylase 3

DRM2:

Domains rearranged methyltransferase 2

DRM3:

Domains rearranged methyltransferase 3

RDM4:

Reduced DNA methylation 4

DMS4:

Defective in meristem silencing 4

CLSY1:

Classy 1

SHH1:

Sawadee homeodomain homolog 1

DCL3:

Dicer-like 3

HEN1:

HUA enhancer 1

AGO4:

Argonaute 4

AGO6:

Argonaute 6

AGO9:

Argonaute 9

SPTL5:

Suppressor of TY insertion 5-like

IDN2:

Involved in de novo 2

RDM2:

Reduced DNA methylation 2

DRD1:

Defective in RNA-dependent DNA methylation 1

SWI3B:

Switch subunit 3

DMS3:

Defective in meristem silencing 3

DMS11:

Defective in meristem silencing 11

RDM1:

Reduced DNA methylation 1

DDR:

DRD1-DMS3-RDM1 complex

JMJ14:

Jumonji 14

NORs:

Nucleolus organizer regions

rRNA:

ribosomal RNA

CB:

Cajal body

PML:

Promyelocytic leukemia protein

PRC1:

Polycomb repressive complex 1

PRC2:

Polycomb repressive complex 2

SPC:

Short interfering RNA processing center

NRPE1:

DNA-directed RNA polymerase V subunit 1

RDR6:

RNA-dependent RNA polymerase 6

SGS3:

Suppressor of gene silencing 3

P-Bodies:

Processing bodies

STED:

Stimulated emissions depletion

SIM:

Super-resolution structured illumination

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Acknowledgments

We apologize to all colleagues whose papers were not cited due to space limitations. This work was supported by the University of New Mexico startup funds.

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  1. Olga Pontes

    Present address: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai, 201602, People’s Republic of China

Authors and Affiliations

  1. Department of Biology, 167 Castetter Hall MSC03 2020, University of New Mexico, Albuquerque, NM, 87131-0001, USA

    Pedro Costa-Nunes & Olga Pontes

  2. Laboratory for Health Protection Research, National Institute for Public Health and the Environment, Bilthoven, The Netherlands

    Alexa Vitins

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  1. Pedro Costa-Nunes
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Correspondence to Olga Pontes.

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Costa-Nunes, P., Vitins, A. & Pontes, O. Connecting the dots of RNA-directed DNA methylation in Arabidopsis thaliana . Chromosome Res 22, 225–240 (2014). https://doi.org/10.1007/s10577-014-9425-9

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