Molecular mechanisms that control gene function and cell behavior are central to our understanding of and exerting influence on how biological systems integrate system- wide information for growth, development and adaptation. In contrast to DNA and protein, the epigenetics of RNA is a much less explored area. We propose that post- transcriptional RNA modifications could be functionally analogous to post-translational protein modifications. The extent of RNA modifications could depend on the physiological state of the cell. The simultaneous presence of distinctly modified RNA species, all derived from the same gene, would greatly increase the number of functional RNAs that can perform subtle or even significantly different tasks. RNA modification may represent a fundamental source of epigenetic diversity in biological regulation.
We aim to discover whether post-transcriptional modifications in biological RNAs are reversible in the cell, to identify the biological RNA targets and the enzymes that catalyze the reversal reactions. We will develop new, high throughput methods to address these questions in /E. coli/ and in human cells.

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Epigenetics controls gene expression through chemical modifications of DNA, RNA and proteins.
We aim to discover the importance of epigenetics of RNA, in order to fully understand how human cells respond and adapt to varying physiological conditions.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZGM1-CBB-7 (EU))
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Bender, Michael T
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University of Chicago
Schools of Medicine
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Liu, Nian; Pan, Tao (2016) N6-methyladenosine–encoded epitranscriptomics. Nat Struct Mol Biol 23:98-102
Liu, Nian; Pan, Tao (2016) Probing N⁶-methyladenosine (m⁶A) RNA Modification in Total RNA with SCARLET. Methods Mol Biol 1358:285-92
Liu, Nian; Dai, Qing; Zheng, Guanqun et al. (2015) N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518:560-4
Liu, Nian; Pan, Tao (2015) Probing RNA Modification Status at Single-Nucleotide Resolution in Total RNA. Methods Enzymol 560:149-59
Liu, Nian; Pan, Tao (2015) RNA epigenetics. Transl Res 165:28-35
Fu, Ye; Dominissini, Dan; Rechavi, Gideon et al. (2014) Gene expression regulation mediated through reversible m⁶A RNA methylation. Nat Rev Genet 15:293-306
Wang, Xiao; Lu, Zhike; Gomez, Adrian et al. (2014) N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505:117-20
Liu, Jianzhao; Yue, Yanan; Han, Dali et al. (2014) A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol 10:93-5
Liu, Nian; Parisien, Marc; Dai, Qing et al. (2013) Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 19:1848-56
Vilfan, Igor D; Tsai, Yu-Chih; Clark, Tyson A et al. (2013) Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology 11:8

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