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proteins. Cell 161:404–416. https://doi.org/10.1016/j.cell.2015.03.025
9. Engreitz JM, Ollikainen N, Guttman M (2016) Long non-coding RNAs: spatial amplifiers that
control nuclear structure and gene expression. Nat Rev Mol Cell Biol 17:756–770. https://doi.
org/10.1038/nrm.2016.126
10. Rinn JL, Kertesz M, Wang JK et al (2007) Functional demarcation of active and silent
chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323. https://
doi.org/10.1016/j.cell.2007.05.022
11. Tsai M, Manor O, Wan Y et al (2010) Long noncoding RNA as modular scaffold of histone
modification complexes. Science 329:689–693. https://doi.org/10.1126/science.1192002
12. Khalil AM, Guttman M, Huarte M et al (2009) Many human large intergenic noncoding RNAs
associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci
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0008-5472.CAN-10-4379
17. Pandey RR, Mondal T, Mohammad F et al (2008) Kcnq1ot1 antisense noncoding RNA
mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol
Cell 32:232–246. https://doi.org/10.1016/j.molcel.2008.08.022
18. Bao X, Wu H, Zhu X et al (2015) The p53-induced lincRNA-p21 derails somatic cell
reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res 25:80–92. https://doi.org/10.1038/cr.2014.165
19. Mohammad F, Pandey RR, Nagano T et al (2008) Kcnq1ot1/Lit1 noncoding RNA mediates
transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 28:3713–3728.
https://doi.org/10.1128/MCB.02263-07
20. Wang X, Arai S, Song X et al (2010) Induced ncRNAs allosterically modify RNA binding
proteins in cis to inhibit transcription. Nature 454:126–130. https://doi.org/10.1038/
nature06992.Induced
21. Bose DA, Donahue G, Reinberg D et al (2017) RNA binding to CBP stimulates histone
acetylation and transcription. Cell 168:135–149.e22. https://doi.org/10.1016/j.cell.2016.12.
020
22. Jacob R, Zander S, Gutschner T (2017) The dark side of the epitranscriptome: chemical
modifications in long non-coding rnas. Int J Mol Sci 18:E2387. https://doi.org/10.3390/
ijms18112387
23. Patil DP, Chen C-K, Pickering BF et al (2016) m6A RNA methylation promotes XISTmediated transcriptional repression. Nature 537:369–373. https://doi.org/10.1038/
nature19342
24. Engreitz JM, Pandya-jones A, Mcdonel P et al (2013) The Xist lncRNA exploits threedimensional genome architecture to spread across the X-chromosome. Science
341:1237973. https://doi.org/10.1126/science.1237973
Altered Long Non-coding RNA Expression in Cancer: Potential Biomarkers. . .
421
to silence transcription through HDAC3. Nature 521:232–236. https://doi.org/10.1038/
nature14443
8. Chu C, Zhang QC, Da Rocha ST et al (2015) Systematic discovery of Xist RNA binding
proteins. Cell 161:404–416. https://doi.org/10.1016/j.cell.2015.03.025
9. Engreitz JM, Ollikainen N, Guttman M (2016) Long non-coding RNAs: spatial amplifiers that
control nuclear structure and gene expression. Nat Rev Mol Cell Biol 17:756–770. https://doi.
org/10.1038/nrm.2016.126
10. Rinn JL, Kertesz M, Wang JK et al (2007) Functional demarcation of active and silent
chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323. https://
doi.org/10.1016/j.cell.2007.05.022
11. Tsai M, Manor O, Wan Y et al (2010) Long noncoding RNA as modular scaffold of histone
modification complexes. Science 329:689–693. https://doi.org/10.1126/science.1192002
12. Khalil AM, Guttman M, Huarte M et al (2009) Many human large intergenic noncoding RNAs
associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci
106:11667–11672. https://doi.org/10.1073/pnas.0904715106
13. Zhao J, Ohsumi TK, Kung JT et al (2010) Genome-wide identification of Polycombassociated RNAs by RIP-seq. Mol Cell 40:939–953. https://doi.org/10.1016/j.molcel.2010.
12.011
14. Portoso M, Ragazzini R, Brenčič Ž et al (2017) PRC2 is dispensable for HOTAIR-mediated
transcriptional repression. EMBO J 36:981–994. https://doi.org/10.15252/embj.201695335
15. Yap KL, Li S, Muñoz-Cabello AM et al (2010) Molecular interplay of the noncoding RNA
ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing
of INK4a. Mol Cell 38:662–674. https://doi.org/10.1016/j.molcel.2010.03.021
16. Aguilo F, Zhou MM, Walsh MJ (2011) Long noncoding RNA, polycomb, and the ghosts
haunting INK4b-ARF-INK4a expression. Cancer Res 71:5365–5369. https://doi.org/10.1158/
0008-5472.CAN-10-4379
17. Pandey RR, Mondal T, Mohammad F et al (2008) Kcnq1ot1 antisense noncoding RNA
mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol
Cell 32:232–246. https://doi.org/10.1016/j.molcel.2008.08.022
18. Bao X, Wu H, Zhu X et al (2015) The p53-induced lincRNA-p21 derails somatic cell
reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res 25:80–92. https://doi.org/10.1038/cr.2014.165
19. Mohammad F, Pandey RR, Nagano T et al (2008) Kcnq1ot1/Lit1 noncoding RNA mediates
transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 28:3713–3728.
https://doi.org/10.1128/MCB.02263-07
20. Wang X, Arai S, Song X et al (2010) Induced ncRNAs allosterically modify RNA binding
proteins in cis to inhibit transcription. Nature 454:126–130. https://doi.org/10.1038/
nature06992.Induced
21. Bose DA, Donahue G, Reinberg D et al (2017) RNA binding to CBP stimulates histone
acetylation and transcription. Cell 168:135–149.e22. https://doi.org/10.1016/j.cell.2016.12.
020
22. Jacob R, Zander S, Gutschner T (2017) The dark side of the epitranscriptome: chemical
modifications in long non-coding rnas. Int J Mol Sci 18:E2387. https://doi.org/10.3390/
ijms18112387
23. Patil DP, Chen C-K, Pickering BF et al (2016) m6A RNA methylation promotes XISTmediated transcriptional repression. Nature 537:369–373. https://doi.org/10.1038/
nature19342
24. Engreitz JM, Pandya-jones A, Mcdonel P et al (2013) The Xist lncRNA exploits threedimensional genome architecture to spread across the X-chromosome. Science
341:1237973. https://doi.org/10.1126/science.1237973
Altered Long Non-coding RNA Expression in Cancer: Potential Biomarkers. . .
421