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Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells

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Abstract

The mammalian genome harbors thousands of long noncoding RNA (lncRNA) genes. Recent studies have indicated the involvement of several of these lncRNAs in the regulation of gene expression. lncRNAs play crucial roles in various biological processes ranging from epigenetic gene regulation, transcriptional control, to post-transcriptional regulation. lncRNAs are localized in various subcellular compartments, and major proportion of these are retained in the cell nucleus and could be broadly classified as nuclear-retained lncRNAs (nrRNAs). Based on the identified functions, members of the nrRNAs execute diverse roles, including providing architectural support to the hierarchical subnuclear organization and influencing the recruitment of chromatin modifier factors to specific chromatin sites. In this review, we will summarize the recently described roles of mammalian nrRNAs in controlling gene expression by influencing chromatin organization, transcription, pre-mRNA processing, nuclear organization, and their involvement in disease.

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Abbreviations

ANRIL:

Antisense nocoding RNA in the INK4 locus

AR:

Androgen receptor

A-to-I:

Adenine to inosine

CCAT2:

Colon cancer-associated transcript 2

CEBPA:

CCAAT/enhancer binding protein (C/EBP), Alpha

DBHS:

Drosophila behavior human splicing

DHFR:

Dihydrofolate reductase

ecCEBPA:

Extracoding CEBPA

eRNA:

Enhancer RNA

ERα:

Estrogen receptor α

H3K4me3:

Histone 3 lysine 4 trimethylation

H3K27me3:

Histone 3 lysine 27 trimethylation

HAT:

Histone acetyl transferase

hES:

Human embryonic stem cells

HMT:

Histone methyltransferase

hnRNP-K:

Heterogeneous nuclear ribonucleoprotein K

HOTAIR:

HOX transcript antisense RNA

HOTTIP:

HOXA transcript at the distal tip

Igf2r:

Insulin-like growth factor 2 receptor

IGS:

Intergenic spacer

lncRNA:

Long noncoding RNA

MALAT1:

Metastasis-associated lung adenocarcinoma transcript 1

mES:

Mouse embryonic stem cells

MIAT:

Myocardial infarction-associated transcript

ncRNA-a:

Noncoding RNA activator

nrRNA:

Nuclear-retained RNA

PRC2:

Polycomb repressive complex 2

PWS:

Prader–Willi syndrome

RepA:

Repeat A

Schlap1:

Second chromosome locus associated with prostate-1

TCF7L2:

transcription factor 7-like 2

treRNA:

Translational regulatory lncRNA

Uchl1:

Ubiquitin carboxyterminal hydrolase L1

VHL:

von Hippel–Lindau

XCI:

X-chromosome inactivation

Xi:

Inactive X-chromosome

Xic:

X-chromosome inactivation center

Xist:

X-inactive-specific transcript

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Acknowledgments

We would like to thank Drs. Stephanie Ceman (UIUC), Ashish Lal (NCI, NIH), and Supriya G. Prasanth (UIUC) for critical reading of the manuscript. We would like to thank Dr. Aparna Anantharaman, Dr. Vidisha Tripathi, and Sumanprava Giri for their assistance in RNA-FISH analyses. Research in the KVP laboratory is supported by grants from American Cancer Society (RSG-11-174-01-RMC) and NIH/NIGMS (GM088252).

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  1. Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Deepak K. Singh & Kannanganattu V. Prasanth

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  1. Deepak K. Singh
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Singh, D.K., Prasanth, K.V. Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells. Chromosome Res 21, 695–711 (2013). https://doi.org/10.1007/s10577-013-9391-7

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