TABLE 1.
Processes Controlled by lncRNAs
| Examples | References | |
|---|---|---|
| Nuclear processes | ||
| DNA methylation inhibition in cis | Extra-coding RNA, CpG island R-loop RNAs | Ginno et al. (2012); Di Ruscio et al. (2013) |
| DNA methylation recruitment in cis | Ribosomal DNA, promoter-associated non-coding RNA, piRNA-targeted RNA | Schmitz et al. (2010); Watanabe et al. (2011); Hamazaki et al. (2015) |
| Histone modification recruitment in cis | Xist, Airn, HOTTIP | Sleutels et al. (2002); Nagano et al. (2008); Zhao et al. (2008); Wang et al. (2011) |
| Histone modification recruitment in trans | HOTAIR | Rinn et al. (2007) |
| Histone modification state maintenance | Firre | Yang et al. (2015) |
| Nucleosome positioning | SCHLAP1, MHRT, enhancer RNAs | Mousavi et al. (2013); Prensner et al. (2013); Han et al. (2014) |
| Transcription interference | Airn | Latos et al. (2012) |
| Transcription factor sequestration | Gas5, PANDA | Kino et al. (2010); Hung et al. (2011) |
| Transcription factor recruitment | BCAR4 | Xing et al. (2014) |
| Organize chromatin domains and nuclear bodies | HOTTIP, Firre, MALAT1 | Tripathi et al. (2010); Wang et al. (2011); Yang et al. (2015) |
| Enhancer control | ncRNA-a3,4,5,7, enhancer RNAs LED LUNAR | Oram et al. (2010); Lam et al. (2013); Trimarchi et al. (2014); Leveille et al. (2015) |
| Histone variant recruitment | centromeric lncRNA | Quenet and Dalai (2014) |
| Splicing control | MALAT1, FGF2R antisense lncRNA | Tripathi et al. (2010); Gonzalez et al. (2015) |
| Cytoplasmic processes | ||
| Source of mi RNAs | H19 | Gao et al. (2012); Keniry et al. (2012) |
| miRNA sequestration | competing endogenous RNAs: HULC, linc-MD1, HncRNA-RoR, H19 circular RNAs | Franco-Zorrilla et al. (2007); Wang et al. (2010, 2013); Cesana et al. (2011); Hansen et al. (2013); Kallen et al. (2013) |
| Translation control RNA stability control | Uchl1 antisense lncRNA, HncRNA-p21 TINCR | Carrieri et al. (2012); Yoon et al. (2012) Kretz et al. (2013) |
| Source of siRNAs and piRNAs | piRNA-targeted RNA, centromeric transcripts | Hall et al. (2002); Volpe et al. (2002); Watanabe et al. (2011) |
BCAR4, breast cancer anti-estrogen resistance 4; FGF2R, fibroblast growth factor receptor 2; Firre, Firre Intergenic Repeating RNA Element; HOTTIP, HOXA distal transcript antisense RNA; MHRT, Myheart; myosin heavy chain-associated RNA transcript; PANDA, promoter of CDKN1A antisense DNA damage activated; RoR, regulator of reprogramming; TINCR, tissue differentiation-inducing non-protein coding RNA; Uchl1, ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase).