RNA-protein interaction during cell fate transition

Patents

1. Bao Xichen, Zhao Wenxue, Xiong Zhi, Yin Chao, Zhang Yuqi, Pan Weiqi; Lin Yingying, Wang Xiwei, He Jun; 用于抑制SARS-Cov-2的组合物及载体系统. Chinese patent, ZL 2021 1 0448000.8

2. Pei Duanqing, Migule Esteban, Bao Xichen, Liao Baojian, Zhang Biliang, 一种将微小核糖核酸簇用于改变细胞命运的方法. Chinese patent, ZL 2011 1 0067834.0

3. Zhang Biliang, Migule Esteban, Bao Xichen, Guo Hengpeng, Yin Menghui, Wang Xiwei, 一种捕获核酸结合蛋白的方法和试剂盒, Chinese patent, 201710080808.9

1. Li P, Lan Y, Yan X, Cao Z, Ji J, Deng M, He D, Huang R, Qu Y, Wu Y, Zhang X , Cui J, Luo G, Bao X*, Shi S*. Apoptotic metabolites synthesize and inherit unique de novo L2a/L2b RNAs to prevent virus infection[J]. Bioactive Materials, 2026, 58: 236-251.*Co-corresponding author

2. Deng M^#, He D^#, Wang X^#, Yuan Y, Wang L, Hou Y, Zhu Q, Zhou C, Mai Z, Zhang Y, Nie Z, Song Y, Wu Q, Pan L, Dong B, Xiong Z, Li D, Liu D, Xu J, Qin D, Zheng H, Zhao Y, Tang P, Wang J, Print C, Jauch R, Zhang W*, Wu G* , and Bao X*.Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts[J]. Nature Communications, 2025 Dec 8;17(1) :486.*Co-corresponding author

3. Yuan Y^#, He D^#, Deng M^#, Ye Y, Chen P, Wu H, Zhang J , Bao X*, Wang X*, Zhang W*. Systematic identification of Oct4 transcriptional targets in embryonic stem cells using the auxin-inducible degron system and nascent RNA sequencing[J]. Cell Regeneration, 2025, 14(1): 49.*Co-corresponding author

4. Mai Z^#, Li D^#, Tang P, Zhou C, Zhao Y, Chen J, Bao X*. NaRaDa: A comprehensive nascent RNA database, The Innovation Life, 2025, 3:100143.

5. Bao X,* Li X,* William K. K Wu*, Zhang Y*, Zhou L,*Editorial: Protein-RNA interplay-regulated signaling in stem cells and cancer, Front Cell Dev Biol.2023 Oct 16:11:1304817. doi: 10.3389/fcell.2023.1304817. eCollection 2023.

6. Zhao R^#; Fang X^#; Mai Z^#; Chen X; Mo J; Lin Y; Xiao R; Bao X*; Weng X*; Zhou X*. Transcriptome-wide identification of single-stranded RNA binding proteins, CHEMICAL SCIENCE, 2023, 14(15): 4038-4047. *Co-corresponding author

7. Zheng M, Lin Y, Wang W, Zhao Y, Bao X*. Application of nucleoside or nucleotide analogues in RNA dynamics and RNA-binding protein analysis. Wiley Interdiscip Rev RNA. 2022 Feb 25:e1722. doi: 10.1002/wrna.1722. Epub ahead of print. PMID: 35218164.

8. Guo X^#, Tariq M^#, Lai Y^#, Kanwal S^#, Lv Y^#, Wang X^#, Li N, Jiang M, Meng J, Hu J, Yuan J, Luo Z, Ward C, Volpe G, Wang D, Yin M, Qin B, Zhang B*, Bao X*, Esteban MA*. Capture of the newly transcribed RNA interactome using click chemistry. Nat Protoc. 2021 Oct 25. *Co-corresponding author

9. Lv Y^#, Bu C^#, Meng J, Ward C, Volpe G, Hu J, Jiang M, Guo L, Chen J, Esteban MA*, Bao X*, Cheng Z*. Global Profiling of the Lysine Crotonylome in Different Pluripotent States. Genomics Proteomics Bioinformatics. 2021 Feb;19(1):80-93. *Co-corresponding author

10. Kanwal S, Guo X, Ward C, Volpe G, Qin B, Miguel A. Esteban *, Bao X*. Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency, Genomics Proteomics Bioinformatics，2020 18，16-25.

11. Hou L*, Wei Y, Lin Y, Wang X, Lai Y, Yin M, Chen Y, Guo X, Wu S, Zhu Y, Yuan J, Tariq M, Li N, Sun H, Wang H, Zhang X, Chen J, Bao X*, Jauch R*. Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2. Nucleic Acids Res. 2020 Feb 4:gkaa067. *Co-corresponding author

12. Bao X*^#, Guo X^#, Yin M#, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, Shao C, Lim DH, Liu X, LiN, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B*, Esteban MA*. Capturing the interactome of newly transcribed RNA. Nat Methods. 2018 Mar;15(3):213-220. *Co-corresponding author

13. Bao X*^#, Wu H^#, Zhu X^#, Guo X, Hutchins AP, Luo Z, Song H, Chen Y, Lai K, Yin M, Xu L, Zhou L, Chen J, Wang D, Qin B, Frampton J, Tse HF, Pei D, Wang H, Zhang B, Esteban MA*. The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res. 2015 Jan; 25(1): 80-92. *Co-corresponding author

14. Bao X, Zhu X, Liao B, Benda C, Zhuang Q, Pei D, Qin B, Esteban MA. MicroRNAs in somatic cell reprogramming. Curr Opin Cell Biol. 2013 Apr; 25(2): 208-14.

15. Liao B^#, Bao X^#, Liu L, Feng S, Zovoilis A, Liu W, Xue Y, Cai J, Guo X, Qin B, Zhang R, Wu J, Lai L, Teng M, Niu L, Zhang B, Esteban MA, Pei D. MicroRNA cluster 302-367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition. J Biol Chem. 2011 May 13; 286(19): 17359-64.

16. Liu J^#, Gao M^#, He J^#, Wu K, Lin S, Jin L, Chen Y, Liu H, Shi J, Wang X, Chang L, Lin Y, Zhao YL, Zhang X, Zhang M, Luo GZ, Wu G, Pei D, Wang J, Bao X, Chen J. The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature. 2021 Mar;591(7849):322-326.

17. Liu X, Wang X, Li J, Hu S, Deng Y, Yin H, Bao X, Zhang Q, Wang G, Wang B, Shi Q, Shan G. Identification of mecciRNAs and their roles in the mitochondrial entry of proteins. Sci China Life Sci. 2020 Jan 21:10.1007/s11427-020-1631-9.

18. Zhao Y, Zhou J, He L, Li Y, Yuan J, Sun K, Chen X, Bao X, Esteban MA, Sun H, Wang H. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nat Commun. 2019 Dec 19;10(1):5787.

19. Wu Y, Li Y, Zhang H, Huang Y, Zhao P, Tang Y, Qiu X, Ying Y, Li W, Ni S, Zhang M, Liu L, Xu Y, Zhuang Q, Luo Z, Benda C, Song H, Liu B, Lai L, Liu X, Tse HF, Bao X, Chan WY, Esteban MA, Qin B, Pei D. Autophagy and mTORC1 regulate the stochastic phase of somatic cell reprogramming. Nat Cell Biol. 2015 Jun;17(6):715-25.

20. Liu L, Xu Y, He M, Zhang M, Cui F, Lu L, Yao M, Tian W, Benda C, Zhuang Q, Huang Z, Li W, Li X, Zhao P, Fan W, Luo Z, Li Y, Wu Y, Hutchins AP, Wang D, Tse HF, Schambach A, Frampton J, Qin B, Bao X, Yao H, Zhang B, Sun H, Pei D, Wang H, Wang J, Esteban MA. Transcriptional pause release is a rate-limiting step for somatic cell reprogramming. Cell Stem Cell. 2014 Nov 6;15(5):574-88.