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LncRNA Research

Irreplaceable benefits of Arraystar LncRNA Arrays

 

LncRNAs and mRNAs share certain common properties that allow them to be profiled together. However, lncRNAs also have characteristics significantly different from mRNAs, which pose special challenges for their expression profiling, particularly in the choice of profiling technologies. Arraystar lncRNA Arrays are specially designed to meet these challengers, offering irreplaceable benefits over the NGS platform. 

Benefit 1 – Profile LncRNAs often operating at lower abundance levels

Based on the analysis of GENCODE transcripts, the median expression level of lncRNAs is about 1/10 of the mRNAs (Fig. 1A) [1]. Many lncRNAs are present at only a few copies per cell. For example, ANRIL lncRNA is detected 1~2 copies in the quantitative single molecule RNA FISH, compared with numerous copies of FOXF1 mRNA (Fig.1B). lncRNAs may also appear low in abundance in the total RNA due to their highly specific and restricted expression in given cell types. For example, different hippocampal lncRNAs can express in different cell types and fine histological structures in the hippocampus (Fig. 1C). Even expressed at reasonably levels in the corresponding cells, these individual lncRNAs can be diluted in the total RNA extracted from the overall tissue mass.

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Figure 1. (A) A magnitude lower median abundance of lncRNAs compared with mRNAs. (B) A few detected ANRIL lncRNA copies compared with abundant pancellular presence of FOX1 mRNAs. (C) High specificities and the restricted expression of lncRNAs in the hippocampal cell types contribute to their diluted presence in the total RNA extracted from the tissue.

However, lncRNAs should not be dismissed for their lower abundance. Many of them do operate at low levels to exert gene regulatory functions. lncRNAs have been observed to regulate neighboring genes by mechanisms such as tethering the nascently transcribed lncRNAs to recruit chromatin modifier/remodelers to modify local chromatin active state, or spliceosomes to facilitate ongoing transcription, or acting as enhancer RNAs to activate gene transcription (Fig. 2). Unlike diffusible distal trans-acting factors, the local cis-acting lncRNAs do not need to be at high concentration in solution. For example, HOTTIP lncRNA is present at only 1~2 copies per cell on the chromatin, yet effectively controls the HOX gene cluster. Another class of lncRNAs, namely enhancer lncRNAs (eRNAs), are mostly at low levels, short in half lives, and difficult to detect by regular RNA-seq, yet they are functional components of active enhancers.

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Figure 2. A nascently transcribed lncRNA tethering chromatin modifiers and other factors in situ to cis-regulate local target gene expression. The copy number can be as low as the copy of genomic DNA locus in the cell.

The accuracy detection is essential for discovering how the functional LncRNAs operate at lower levels. In a typical 40 million sequencing depth designed for mRNA-seq, less than 10% of lncRNAs can be quantified reliably. To improve lncRNA coverage, a more reasonable lncRNA-seq would require > 100 M reads, which is a significant increase in cost[4]. For microarrays, the oligo probes on the solid phase are able affinity capture and enrich the rare target sequences, while at the same time measure the fluorescence intensity as the abundance levels. Therefore, microarray accuracy is less impacted by the transcripts at lower abundance levels, compared with RNA-seq, as shown in a very large clinical study published in PNAS[5].

Benefit 2 –Detect LncRNA transcript variants, complex and functionally significant

With less constraints of keeping open reading frames as in mRNAs, lncRNAs are often transcribed into multiple, alternatively spliced transcript isoforms having varying, sometimes opposing functions. For example, MEG3 gene can produce more than 10 MEG3-lncRNA transcript variants, having various p53 transactivation and tumor suppressing activities (Fig. 3) [6]. In another example, transcript isoforms BCL-XL, BCL-XS and ENST produced from the same BCL2L1 gene have the opposite oncogenic and tumor suppressing functions [7]. The transcript isoforms are difficult to be profiled by RNA-seq due to the insufficient read coverage divided among the transcripts and the complexity and unreliability of de novo transcripts assembly. In contrast, transcripts isoforms are easily, unambiguously and reliably detected by Arraystar lncRNA Array probes specially designed to target unique sequence sites and splice junctions (Fig. 4).

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Figure 3. Different MEG3-lncRNA transcript isoforms have varying p53 transactivation and tumor suppressing activities.

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Figure 4. BCL transcript isoforms are readily and reliably detected by microarray probes (color shaded) targeting unique sequence regions.

Benefit 3 – Offer specialized annotation and analysis dedicated for lncRNAs

lncRNAs do not have open reading frames as a reference. Even with recent active research, most lncRNAs are still much less characterized and annotated than protein coding genes. To effectively analyze the lncRNA profiling data and gain biological insights, Arraystar lncRNA Array standard package is integrated with rich, detailed, and systematic lncRNA annotation and analysis in sync with recent advances in the field. LncRNAs are classified at top level into enhancer lncRNAs (e-lncRNAs) from enhancer epigenetic marked regions and the promoter-lncRNAs (p-lncRNAs) from typical promoters [8]. Their genomic relationships with the closest neighboring protein coding genes, such as intergenic, divergent, antisense, and sense-intronic, provide important clues as to what the target genes are and how they may be regulated (Fig. 5). 

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Figure 5. Systematic lncRNA classification, annotation and analyses are integral part of the lncRNA array profiling.

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To learn more about the Arraystar LncRNA Arrays and its sample to data service, please contact 1-888-416-6343 or email to support@arraystar.com
 

References

[1] Cabili M.N. et al. (2015) "Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution." Genome Biol. 16:20 [PMID: 25630241].
[2] Wang K.C. et al. (2011) "A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression." Nature 472(7341):120-4 [PMID: 21423168]
[3] Engreitz J.M. et al. (2016) "Local regulation of gene expression by lncRNA promoters, transcription and splicing." Nature 539(7629):452-455 [PMID: 27783602]
[4] Labaj P.P. et al. (2011) "Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling." Bioinformatics 27(13):i383-91 [PMID: 21685096]
[5] Xu W. et al. (2011) "Human transcriptome array for high-throughput clinical studies." Proc. Natl. Acad. Sci. U.S.A.  [PMID: 21317363]
[6] Zhang X. et al. (2010) "Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions." Endocrinology 151(3):939-47 [PMID: 20032057]
[7] Boise L.H. et al. (1993) "bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death." Cell 74(4):597-608 [PMID: 8358789]
[8] Hon C.C. et al. (2017) "An atlas of human long non-coding RNAs with accurate 5' ends." Nature 543(7644):199-204 [PMID: 28241135]

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