Table 1 Examples of lncRNAs discovered with various approaches described in the text
From: Strategies to identify long noncoding RNAs involved in gene regulation
lncRNA name | Types of RNA | lncRNA identification methods* | Reference |
|---|---|---|---|
ANRIL | RNA-ChIP (UV cross-linking) and CLIP | RT-PCR | [12] |
RepA | RIP (no cross-linking) | Northern blotting | [13] |
TRE-1, -2 and -3 | RNA-ChIP (cross-linked with formaldehyde) | RT-PCR | [14] |
Xist | RIP (no cross-linking) | RT-PCR | [13] |
LincRNA-EPS | Polyadenylated RNA | Microarrays of 10,802 lncRNAs and RNA-seq | [15] |
lincRNA-SFMBT2, lincRNA-RoR, and lincRNA-VLDLR | Total RNA | Microarrays of 900 lincRNAs | [16] |
lncRNA_ES1, ES2 and ES3 | Total RNA | Microarrays of 6,671 lncRNAs | [17] |
ncRNA-a1-7 | Polyadenylated RNA | Microarrays of 3,019 lncRNAs | [18] |
HOTAIR | Polyadenylated RNA | Tiling arrays of 39 HOX genes | [19] |
RIP (no cross-linking) | Validation with RT-PCR | ||
HOTAIRM1 | Polyadenylated RNA | Tiling arrays of HOXA genes | [20] |
lincRNA-p21 | Polyadenylated RNA | Tiling arrays of 400 lincRNAs | [21] |
Mistral | RNA-ChIP (no cross-linking) | Tiling arrays of chromosomes 6, 8 and 16 | [22] |
300 lincRNAs | RIP (no cross-linking) | Tiling arrays of 900 lincRNAs | [23] |
1,600 lincRNAs | Polyadenylated RNA | Tiling arrays of 350 K4-K36 domains | [24] |
ANCR | Polyadenylated RNA | RNA-seq | [25] |
BANCR | Polyadenylated RNA | RNA-seq | [26] |
5 lncRNAs | CLIP | RNA-seq | [27] |
216 lincRNAs | RIP (no cross-linking) | RNA-seq | [28] |
RIP (UV cross-linking) | Validation with RT-PCR | ||
>8,000 lncRNAs | Polyadenylated RNA | Analysis of existing RNA-seq data | [29] |