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Maintenance of epigenetic information: a noncoding RNA perspective

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Abstract

Along the lines of established players like chromatin modifiers and transcription factors, noncoding RNA (ncRNA) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription. With increasing evidence of ncRNAs in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature. In addition, we attempt to understand and speculate how these RNA dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.

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Abbreviations

DMR:

Differentially methylated region

Dnmt1:

DNA (cytosine-5)-methyltransferase 1

Dnmt3a:

DNA (cytosine-5)-methyltransferase 3 alpha

Dnmt3b:

DNA (cytosine-5)-methyltransferase 3 beta

Eed:

Embryonic ectoderm development

ES cells:

Embryonic stem cells

EZH2:

Enhancer of zeste homolog 2

H3K4me1:

Histone H3 monomethylated at lysine 4

H3K4me3:

Histone H3 trimethylated at lysine 4

H3K27Ac:

Histone H3 acetylated at lysine 27

H3K27me3:

Histone H3 trimethylated at lysine 27

Kb:

Kilobase

lncRNA:

Long noncoding RNA

MEFs:

Mouse embryonic fibroblasts

ncRNA:

Noncoding RNA

PcG:

Polycomb group of proteins

PIGs:

Placentally imprinted genes

piRNA:

Piwi-interacting RNA

pit-RNA:

piRNA-targeted long noncoding RNA

PRC1:

Polycomb Repressive Complex 1

PRC2:

Polycomb Repressive Complex 2

Suz12:

Suppressor Of Zeste 12 Homolog

TrxG:

Trithorax Group proteins

UIGs:

Ubiquitously imprinted genes

Xa:

Active X chromosome

XCI:

X chromosome inactivation

Xi:

Inactive X chromosome

Xist:

X-inactive specific transcript

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Acknowledgments

This work was supported by the grants from the Swedish Cancer Research foundation (Cancerfonden: Kontrakt no.100422), Swedish Research Council (VR-M:K2011-66X-20781-04-3; VR-NT: 621-2011-4996), and Barncancerfonden (PROJ11/067) to CK. CK is a Senior Research Fellow supported by VR-M.

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Authors and Affiliations

  1. Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Medicinaregatan 9A, 40530, Gothenburg, Sweden

    Tanmoy Mondal & Chandrasekhar Kanduri

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  1. Tanmoy Mondal
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  2. Chandrasekhar Kanduri
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Correspondence to Chandrasekhar Kanduri.

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Responsible Editors: Brian P. Chadwick, Kristin C. Scott, and Beth A. Sullivan

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Mondal, T., Kanduri, C. Maintenance of epigenetic information: a noncoding RNA perspective. Chromosome Res 21, 615–625 (2013). https://doi.org/10.1007/s10577-013-9385-5

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