Exploring the Dark Matter of the Human Genome Using Oligonucleotide-Based Molecules

References

• ENCODE Project Consortium . An integrated encyclopedia of DNA elements in the human genome. Nature489 (7414), 57–74 (2012).
   PubMed Web of Science ®Google Scholar
• Carthew RW , SontheimerEJ. Origins and mechanisms of miRNAs and siRNAs. Cell136 (4), 642–655 (2009).
   PubMed Web of Science ®Google Scholar
• Kung JT , ColognoriD, LeeJT. Long noncoding RNAs: past, present, and future. Genetics193 (3), 651–669 (2013).
   PubMed Web of Science ®Google Scholar
• Kapranov P , StLaurentG, RazTet al. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘darkmatter’ un-annotated RNA. BMC Biol.8, 149 (2011).
   Web of Science ®Google Scholar
• Avitabile C , CimminoA, RomanelliA. Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications. J. Med. Chem.57 (24), 10220–10240 (2014).
   PubMed Web of Science ®Google Scholar
• Sun L , GoffLA, TrapnellCet al. Long noncoding RNAs regulate adipogenesis. Proc. Natl Acad. Sci. USA110 (9), 3387–3392 (2013).
   PubMed Web of Science ®Google Scholar
• Zhang L , ZhouXF, PanGF, ZhaoJP. Enhanced expression of long non-coding RNA zxf1 promoted the invasion and metastasis in lung adenocarcinoma. Biomed. Pharmacother.68 (4), 401–407 (2014).
   PubMed Web of Science ®Google Scholar
• Yang F , HuoXS, YuanSXet al. Repression of the long noncoding RNA-let by histone deacetylase 3 contributes to hypoxia-mediated metastasis. Mol. Cell49 (6), 1083–1096 (2013).
   PubMed Web of Science ®Google Scholar
• Bramsen JB , KjemsJ. Development of therapeutic-grade small interfering RNAs by chemical engineering. Front. Genet.3, 154 (2012).
   PubMedGoogle Scholar
• Michalik KM , YouX, ManavskiYet al. Long noncoding RNA malat1 regulates endothelial cell function and vessel growth. Circ. Res.114 (9), 1389–1397 (2014).
   PubMed Web of Science ®Google Scholar
• Thomson DW , BrackenCP, GoodallGJ. Experimental strategies for microRNA target identification. Nucleic Acids Res.39 (16), 6845–6853 (2011).
   PubMed Web of Science ®Google Scholar
• Hendrickson DG , HoganDJ, HerschlagD, FerrellJE, BrownPO. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS ONE3 (5), e2126 (2008).
   PubMed Web of Science ®Google Scholar
• Ritchie W , FlamantS, RaskoJE. Predicting microRNA targets and functions: traps for the unwary. Nat. Methods6 (6), 397–398 (2009).
   PubMed Web of Science ®Google Scholar
• Hafner M , LandthalerM, BurgerLet al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by par-clip. Cell141 (1), 129–141 (2010).
   PubMed Web of Science ®Google Scholar
• Orom UA , LundAH. Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods43 (2), 162–165 (2007).
   PubMed Web of Science ®Google Scholar
• Hassan T , SmithSG, GaughanKet al. Isolation and identification of cell-specific microRNAs targeting a messenger RNA using a biotinylated anti-sense oligonucleotide capture affinity technique. Nucleic Acids Res.41 (6), e71 (2013).
   PubMed Web of Science ®Google Scholar
• Beletskii A , HongYK, PehrsonJ, EgholmM, StraussWM. PNA interference mapping demonstrates functional domains in the noncoding RNA XIST. Proc. Natl Acad. Sci. USA98 (16), 9215–9220 (2001).
   PubMed Web of Science ®Google Scholar
• Sarma K , LevasseurP, AristarkhovA, LeeJT. Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of XIST RNA localization to the X chromosome. Proc. Natl Acad. Sci. USA107 (51), 22196–22201 (2010).
   PubMedGoogle Scholar
• Chu C , SpitaleRC, ChangHY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat. Struct. Mol. Biol.22 (1), 29–35 (2015).
   PubMed Web of Science ®Google Scholar
• Chu C , QuK, ZhongFL, ArtandiSE, ChangHY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA–chromatin interactions. Mol. Cell44 (4), 667–678 (2011).
   PubMed Web of Science ®Google Scholar
• Chu C , ZhangQC, Da RochaSTet al. Systematic discovery of XIST RNA binding proteins. Cell161 (2), 404–416 (2015).
   PubMed Web of Science ®Google Scholar
• McHugh CA , ChenCK, ChowAet al. The XIST lncRNA interacts directly with sharp to silence transcription through HDAC3. Nature521 (7551), 232–236 (2015).
   PubMed Web of Science ®Google Scholar
• Kam Y , RubinsteinA, NaikSet al. Detection of a long non-coding RNA (ccat1) in living cells and human adenocarcinoma of colon tissues using FIT-PNA molecular beacons. Cancer Lett.352 (1), 90–96 (2014).
   PubMed Web of Science ®Google Scholar
• Choi CK , LiJ, WeiKet al. A gold@polydopamine core-shell nanoprobe for long-term intracellular detection of microRNAs in differentiating stem cells. J. Am. Chem. Soc.137 (23), 7337–7346 (2015).
   PubMed Web of Science ®Google Scholar
• Robertson KL , VoraGJ. Locked nucleic acid and flow cytometry-fluorescence in situ hybridization for the detection of bacterial small noncoding RNAs. Appl. Environ. Microbiol.78 (1), 14–20 (2012).
   PubMed Web of Science ®Google Scholar