Nian Liu's Lab at Tsinghua University

PUBLICATIONS

Li X#, Bie L#, Wang Y#, Hong Y#, Zhou Z, Fan Y, Yan X, Tao Y, Huang C, Zhang Y, Sun X, Li J, Zhang J, Chang Z, Xi Q, Meng A, Shen X, Xie W, Liu N*. LINE-1 transcription activates long-range gene expression. Nature Genetics 56, 1494–1502 (2024).
News & Views by: Liang, Y., Wang, T. LINE1 mediates long-range DNA interactions. Nature Genetics 56, 1328–1330 (2024).

LINE-1 transcription activates long-range gene expression.

Hong Y#, Bie L#, Zhang T#, Yan X, Jin G, Chen Z, Wang Y, Li X, Pei G, Zhang Y, Hong Y, Gong L, Li P, Xie W, Zhu Y, Shen X, Liu N*. SAFB restricts contact domain boundaries associated with L1 chimeric transcription. Molecular Cell (2024). [Featured Article]

SAFB restricts contact domain boundaries associated with L1 chimeric transcription.

Wang D, Yan K, Yu H, Li H, Zhou W, Hong Y, Guo S, Wang Y, Xu Chen, Pan C, Tang Y, Liu N, Wu W, Zhang L*, Xi Q*. Fimepinostat impairs NF­κB and PI3K/AKT signaling and enhances gemcitabine efficacy in H3K27M-mutated diffuse intrinsic pontine glioma. Cancer Research. (2024) 84(4), p. 598-615

Li Y, Yang J, Shen S, Wang W, Liu N, Guo H*, Wei W*. SARS-CoV-2-encoded inhibitors of human LINE-1 retrotransposition. Journal of Medical Virology (2022) DOI: 10.1002/jmv.28135.

Zuo F#, Jiang J#, Fu H#, Yan K, Liefke R, Zhang J, Hong Y, Chang Z, Liu N, Wang Z*, Xi Q*. A TRIM66/DAX1/Dux axis suppresses the totipotent 2-cell-like state in murine embryonic stem cells. Cell Stem Cell (2022) 29 (6), 948-961.

(#, co-first author; *, corresponding author)

2018 and Earlier (representative)

Liu, N.*, Lee, C.*, Swigut, T., Grow, E., Gu, B., Bassik, M., and Wysocka, J. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553, 228-232 (2018). [pdf]

HUSH and MORC2 bind young full-length L1s within transcriptionally active genes, and promote H3K9me3 deposition at target L1s to silence L1 transcription.

Liu, N., Dai, Q., Zheng, G., He, C., Parisien, M., Pan, T. N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions. Nature 518, 560-564 (2015). [pdf]
News & Views by: Theler, D., Allain, FT. RNA modification does a regulatory two-step. Nature 518, 492–493 (2015).

PAR-CLIP–MeRIP identifies m6A-switches transcriptome wide.

Liu, N.*, Pan, T.* N6-methyladenosine-coded RNA Epigenetics. Nat. Struct. Mol. Biol. 23, 98-102 (2016). [pdf]

m6A switch

Liu, N.*, Zhou, K.*, Parisien, M., Dai, Q., Diatchenko, L., and Pan, T. N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 45 (10), 6051-6063 (2017). [pdf]

Liu, N., Parisien, M., Dai, Q., Zheng, G., He, C., and Pan, T. Probing N6-methyl-adenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 19, 1848-1856 (2013). [pdf]

Using SCARLET to investigate m6A status

Liu, N., Pan, T. RNA epigenetics (Epitranscriptomics). Translating epigenetics to the clinic 19-30 (2017). ( Book chapter)

Liu, N.,Pan, T. Probing N6-methyl-adenosine (m6A) RNA modification in total RNA with SCARLET. Post-transcriptional gene regulation 1358, 285-292 (2016). [pdf]

Liu, N.,Pan, T. Probing RNA modification status at single nucleotide resolution in messenger and long non-coding RNA. Methods in enzymology 560, 149-159 (2015). ( Book chapter)

Liu, N., Pan, T. RNA epigenetics. Translational research 165, 28-35 (2015).[pdf] 

Zhou, K., Parisien, M., Dai, Q., Liu, N., Diatchenko, L., Sachleben, J., Pan, T. N6-methyladenosine modification in a long noncoding RNA hairpin predisposes its conformation to protein binding. Journal of molecular biology 428, 822-33 (2016). [pdf] 

Chen, K., Lu, Z., Wang, X., Fu, Y., Luo, G., Liu, N., Han, D., Dominissini, D., Dai, Q., Pan, T., He, C. High-resolution N6-methyladenosine (m6A) map using photo-crosslinking-assisted m6A sequencing. Angewandte chemie 127, 1607-1610 (2015). [pdf]