Saidi Wang1, Amlan Talukder1, Mingyu Cha1, Xiaoman Li2, Haiyan Hu1

1. Computer Science, University of Central Florida, Orlando, FL-32816, US.

2. Burnett School of Biomedical Science, University of Central Florida, Orlando, FL-32816, US


  1. Corcoran, D.L., et al., Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One, 2009. 4(4): p. e5279.
  2. Landgraf, P., et al., A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 2007. 129(7): p. 1401-14.
  3. Marson, A., et al., Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell, 2008. 134(3): p. 521-33.
  4. Fujita, S. and H. Iba, Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates. Bioinformatics, 2008. 24(3): p. 303-8.
  5. Ozsolak, F., et al., Chromatin structure analyses identify miRNA promoters. Genes Dev, 2008. 22(22): p. 3172-83.
  6. Saini, H.K., S. Griffiths-Jones, and A.J. Enright, Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A, 2007. 104(45): p. 17719-24.
  7. Chien, C.H., et al., Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res, 2011. 39(21): p. 9345-56.
  8. Marsico, A., et al., PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol, 2013. 14(8): p. R84.
  9. Georgakilas, G., et al., microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun, 2014. 5: p. 5700.
  10. Hua, X., et al., Identifying cell-specific microRNA transcriptional start sites. Bioinformatics, 2016. 32(16): p. 2403-10.
  11. Liu, Q., et al., Identification of active miRNA promoters from nuclear run-on RNA sequencing. Nucleic Acids Res, 2017. 45(13): p. e121.
  12. Yu, N.Y., et al., Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res. 43(14): p. 6787-98.
  13. Bouvy-Liivrand, M., et al., Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. Nucleic Acids Res, 2017. 45(17): p. 9837-9849.
  14. Georgakilas, G., et al., DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res, 2015. 44(D1): p. D190-5.
  15. Lu, J., et al., MicroRNA expression profiles classify human cancers. Nature, 2005. 435(7043): p. 834-8.
  16. Ramaswamy, S., et al., Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A, 2001. 98(26): p. 15149-54.
  17. Huang, J.C., Q.D. Morris, and B.J. Frey, Bayesian inference of MicroRNA targets from sequence and expression data. J Comput Biol, 2007. 14(5): p. 550-63.
  18. Muniategui, A., et al., Quantification of miRNA-mRNA interactions. PLoS One, 2012. 7(2): p. e30766.
  19. Wang, Z., W. Xu, and Y. Liu, Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions. Bioinformatics, 2015. 31(21): p. 3529-36.
  20. He, S., et al., MicroRNA-encoding long non-coding RNAs. BMC Genomics, 2008. 9: p. 236.
  21. Sun, Q., et al., MIR100 host gene-encoded lncRNAs regulate cell cycle by modulating the interaction between HuR and its target mRNAs. Nucleic Acids Res, 2018. 46(19): p. 10405-10416.
  22. Bao, Z., et al., LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res, 2019. 47(D1): p. D1034-D1037.
  23. Warnatz, H.J., et al., Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res, 2010. 38(18): p. 6112-23.
  24. Baekgyu Kim, Kyowon Jeong, and V. Narry Kim. Genome-widemapping of DROSHA cleavage sites on primary MicroRNAs andnoncanonical substrates.Molecular Cell, 66(2):258–269.e5, apr 2017.