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Regulatory RNAs pp 319–340Cite as

Identification of lncRNAs Using Computational and Experimental Approaches

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Abstract

Over the last decade, we have been illuminated by the startling discovery that many long noncoding RNAs (lncRNAs) are implicated in diverse and substantial biological processes. The identification of most lncRNAs to date has been unintentional and was mainly from subtractive hybridization or mutagenesis screening, initially aimed to identify protein-coding genes of interest. However, the characterization of lncRNAs and their acceptance as important regulators of many developmental and biological pathways have led to strategies specific to their isolation. Experimental methodologies to identify lncRNAs include RNA sequencing, lncRNA-specific microarray, and RNA-immunoprecipitation by taking advantage of their association with known RNA-binding proteins. The past decade has also generated a significant number of EST (expressed sequence tag)-based transcriptome databases which enabled computational methodologies to target their isolation. This chapter discusses several current and powerful computational and experimental approaches to identify lncRNAs.

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Abbreviations

ChIP:

Chromatin immunoprecipitation

COOLAIR:

Cold-induced long antisense intragenic RNA

DHFR:

Dihydrofolate reductase

DRS:

Direct RNA sequencing

FLC:

Flowering locus C

Gas5:

Growth arrest–specific 5

H3K4me3:

Trimethylation of lysine 4 of histone H3

H3K36me3:

Trimethylation of lysine 36 of histone H3

lincRNAs:

Large intervening noncoding RNAs

lncRNA:

Long noncoding RNA

PRC2:

Polycomb repressive complex 2

RNA-IP:

RNA-immunoprecipitation

SRA:

Steroid receptor RNA activator

TUs:

Transcript units

Xist:

X-inactive specific transcript

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Acknowledgments

This work was partly supported by an Australian Research Council Future Fellowship (FT0991956). We thank Dr. Ming-Bo Wang for his assistance in the revision of this manuscript.

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  1. Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, ACT, Australia

    Phil Chi Khang Au & Qian-Hao Zhu

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  1. Phil Chi Khang Au
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Correspondence to Phil Chi Khang Au .

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  1. , New York State Department of Health, Wadsworth Center, New Scotland Avenue 120, New York, 12208, New York, USA

    Bibekanand Mallick

  2. A.J.C. Bose Centenary Building, P-1/12, CIT Scheme - VII M, Bose Institute, Kolkata, 700054, India

    Zhumur Ghosh

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Au, P.C.K., Zhu, QH. (2012). Identification of lncRNAs Using Computational and Experimental Approaches. In: Mallick, B., Ghosh, Z. (eds) Regulatory RNAs. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22517-8_13

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