Advanced search
Publication Cover
RNA Biology Volume 15, 2018 - Issue 12
Submit an article Journal homepage
3,035
Views
19
CrossRef citations to date
0
Altmetric
Research Paper

Deep learning identifies genome-wide DNA binding sites of long noncoding RNAs

Fan WangDepartment of Oncology, The First Affiliated Hospital of Xian Jiaotong University, Xi’an, P.R. China;Department of Biology and Biochemistry, University of Houston, Houston, TX, USAView further author information
,
Pranik ChainaniComputer Science and Engineering Technology, University of Houston-Downtown, Houston, TX, USAView further author information
,
Tommy WhiteComputer Science and Engineering Technology, University of Houston-Downtown, Houston, TX, USAView further author information
,
Jin YangDepartment of Oncology, The First Affiliated Hospital of Xian Jiaotong University, Xi’an, P.R. ChinaView further author information
,
Yu LiuDepartment of Biology and Biochemistry, University of Houston, Houston, TX, USAORCID Iconhttp://orcid.org/0000-0002-1282-4897View further author information
ORCID Icon &
Benjamin SoibamComputer Science and Engineering Technology, University of Houston-Downtown, Houston, TX, USACorrespondence[email protected]
View further author information
Pages 1468-1476 | Received 06 Jul 2018, Accepted 09 Nov 2018, Published online: 28 Nov 2018

References

  • Li Y, Syed J, Sugiyama H. RNA-DNA triplex formation by long noncoding RNAs. Cell Chem Biol. 2016;23:1325–1333.
  • Grote P, Herrmann BG. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol. 2013;10:1579–1585.
  • Xue Z, Hennelly S, Doyle B, et al. A G-Rich Motif in the lncRNA braveheart interacts with a zinc-finger transcription factor to specify the cardiovascular lineage. Mol Cell. 2016;64:37–50.
  • Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol. 2016;17:756–770.
  • Kalwa, M., Hänzelmann S, Otto S, et al. The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation. Nucleic Acids Res. 2016;44:10631–10643. DOI:10.1093/nar/gkw802.
  • Mondal T, Subhash S, Vaid R, et al. MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 2015;6.
  • Long J, Badal SS, Ye Z, et al. Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy. J Clin Invest. 2016;126:4205–4218.
  • Chu C, Qu K, Zhong FL, et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011;44:667–678.
  • Carlson HL, Quinn JJ, Yang YW, et al. LncRNA-HIT functions as an epigenetic regulator of chondrogenesis through its recruitment of p100/CBP complexes. PLoS Genet. 2015;11:e1005680.
  • Terashima M, Tange S, Ishimura A, et al. MEG3 long noncoding RNA contributes to the epigenetic regulation of epithelial-mesenchymal transition in lung cancer cell lines. J Biol Chem. 2017;292:82–99.
  • Krizhevsky A, Sutskever I, Hinton GE. ImageNet classification with deep convolutional neural networks. Adv Neural Inf Process Syst. 2012;6:1–9.
  • Salakhutdinov R. Learning deep generative models. Annu Rev Stat Appl. 2015;2:361–385.
  • Alipanahi B, Delong A, Weirauch MT, et al. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol. 2015;33:831–838.
  • Zhou J, Troyanskaya OG. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015;12:931–934.
  • Pan X, Shen H-B. Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks. Bioinformatics. 2018;34:3427–3436.
  • Zeng H, Edwards MD, Liu G, et al. Convolutional neural network architectures for predicting DNA-protein binding. Bioinformatics. 2016;32:i121–i127.
  • Soibam B. Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation. RNA. 2017;23:1729–1742.
  • Buske FA, Bauer DC, Mattick JS, et al. Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res. 2012;22:1372–1381.
  • Modali SD, Parekh VI, Kebebew E, et al. Epigenetic regulation of the lncRNA MEG3 and its target c-MET in pancreatic neuroendocrine tumors. Mol Endocrinol. 2015;29:224–237.
  • Zhang L, Yang Z, Trottier J, et al. Long noncoding RNA MEG3 induces cholestatic liver injury by interaction with PTBP1 to facilitate shp mRNA decay. Hepatology. 2017;65:604–615.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.