Chromosome Research

, Volume 22, Issue 2, pp 225–240

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

Review

DOI: 10.1007/s10577-014-9425-9

Cite this article as:
Costa-Nunes, P., Vitins, A. & Pontes, O. Chromosome Res (2014) 22: 225. doi:10.1007/s10577-014-9425-9

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.

Keywords

RNA silencing Epigenetics DNA methylation Nuclear organization Cellular trafficking 

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

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Department of Biology, 167 Castetter Hall MSC03 2020University of New MexicoAlbuquerqueUSA
  2. 2.Laboratory for Health Protection ResearchNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
  3. 3.Shanghai Center for Plant Stress Biology, Chinese Academy of SciencesShanghaiPeople’s Republic of China

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