Publications

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55. Zhaodi Liao#, Jixiang Zhang#, Shiyu Sun#, Yuzhuo Li, Yuting Xu, Chunyang Li, Jing Cao, Yanhong Nie, Zhuoyue Niu, Jingwen Liu, Falong Lu*, Zhen Liu*, and Qiang Sun*. (2024). Reprogramming mechanism dissection and trophoblast replacement application in monkey somatic cell nuclear transfer. Nature Communications 15(1): 5. DOI: 10.1038/s41467-023-43985-7 (Featured article)

News in Nature

54. Wei Zhu#, Guowei Bu#, Ruifeng Hu#, Jixiang Zhang#, Lianyong Qiao#, Kai Zhou, Tingting Wang, Qiao Li, Jingjing Zhang, Linhui Wu, Yali Xie, Taotao Hu, Shichun Yang, Jiaqi Guan, Xiaoyu Chu, Juanjuan Shi, Xia Zhang, Falong Lu*, Xin Liu*, and Yi-Liang Miao*. (2024). KLF4 facilitates chromatin accessibility remodeling in porcine early embryos. SCIENCE CHINA Life Sciences 67(1): 96-112. DOI: 10.1007/s11427-022-2349-9

53. Jingwen Liu# and Falong Lu* (2024). The piRNA size matters. National Science Review 11(2): nwad297. DOI: 10.1093/nsr/nwad297 (Research highlight)

52. Yusheng Liu#, Falong Lu*, and Jiaqiang Wang*. (2024). Sequencing of transcriptome-wide poly(A) tails by PAIso-seq. Deadenylation: Methods and Protocols. Methods in Molecular Biology vol 2723. Springer US: 215-232. DOI: 10.1007/978-1-0716-3481-3_13 (Book chapter)

51. Yusheng Liu#, Han Zhao#, Fanghong Shao#, Yiwei Zhang#, Hu Nie, Jingye Zhang, Cheng Li, Zhenzhen Hou, Zi-Jiang Chen, Jiaqiang Wang*, Bing Zhou*, Keliang Wu*, and Falong Lu*. (2023). Remodeling of maternal mRNA through poly(A) tail orchestrates human oocyte-to-embryo transition. Nature Structural & Molecular Biology 30(2): 200-215. DOI: 10.1038/s41594-022-00908-2

50. Yusheng Liu#*, Hu Nie#, Yiwei Zhang#, Falong Lu*, and Jiaqiang Wang*. (2023). Comprehensive analysis of mRNA poly(A) tails by PAIso-seq2. SCIENCE CHINA Life Sciences 66(1): 187-190. DOI: 10.1007/s11427-022-2186-8

49. Shuang Wu#, Yiwei Zhang#, Lan Yao#, Jiaqiang Wang*, Falong Lu*, and Yusheng Liu*. (2023). m6A-modified RNAs possess distinct poly(A) tails. Journal of Genetics and Genomics 50(3): 208-211. DOI: 10.1016/j.jgg.2022.10.001

47. Xiaoqian Liu#, Zunpeng Liu#, Zeming Wu#, Jie Ren#, Yanling Fan, Liang Sun, Gang Cao, Yuyu Niu, Baohu Zhang, Qianzhao Ji, Xiaoyu Jiang, Cui Wang, Qiaoran Wang, Zhejun Ji, Lanzhu Li, Concepcion Rodriguez Esteban, Kaowen Yan, Wei Li, Yusheng Cai, Si Wang, Aihua Zheng, Yong E. Zhang, Shengjun Tan, Yingao Cai, Moshi Song, Falong Lu, Fuchou Tang, Weizhi Ji, Qi Zhou, Juan Carlos Izpisua Belmonte, Weiqi Zhang*, Jing Qu*, and Guang-Hui Liu* (2023). Resurrection of endogenous retroviruses during aging reinforces senescence. Cell 186(2): 287-304.e26. DOI: 10.1016/j.cell.2022.12.017

46. Xiaoba Wu#*, Liqiong Xie#, Xizhe Sun, Ningning Wang, E Jean Finnegan, Chris Helliwell, Jialing Yao, Hongyu Zhang, Xianjun Wu, Phil Hands, Falong Lu, Lisong Ma, Bing Zhou, Abed Chaudhury, Xiaofeng Cao, Ming Luo* (2023). Mutation in Polycomb repressive complex 2 gene OsFIE2 promotes asexual embryo formation in rice. Nature Plants 9(11): 1848–1861 DOI: 10.1038/s41477-023-01536-4

45. Danni Hong#, Hongli Lin#, Lifang Liu, Muya Shu, Jianwu Dai, Falong Lu, Mengsha Tong, and Jialiang Huang. (2023). Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis. Briefings in Bioinformatics 24(1): bbac508. DOI: 10.1093/bib/bbac508

44. Jingwen Liu# and Falong Lu* (2023). Visualization of in vivo cell-cell contact in the present and in the past. SCIENCE CHINA Life Sciences 66(4): 889-891. DOI: 10.1007/s11427-022-2262-y

43. Muya Shu#, Danni Hong#, Hongli Lin, Jixiang Zhang, Zhengnan Luo, Yi Du, Zheng Sun, Man Yin, Yanyun Yin, Lifang Liu, Shilai Bao, Zhiyong Liu, Falong Lu*, Jialiang Huang*, and Jianwu Dai*. (2022). Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse. Developmental Cell 57(24): 2761-2775.e6. DOI: 10.1016/j.devcel.2022.11.011

42. Zhengnan Luo#, Yi Du#, Shuting Li, He Zhang, Muya Shu, Di Zhang, Shunji He, Guangqin Wang, Falong Lu*, and Zhiyong Liu*. (2022). Three distinct Atoh1 enhancers cooperate for sound receptor hair cell development. Proc Natl Acad Sci USA 119(32): e2119850119. DOI: 10.1073/pnas.2119850119

41. Yusheng Liu#*, Yiwei Zhang, Jiaqiang Wang*, and Falong Lu*. (2022). Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq. Nature Protocols 17(9): 1980-2007. DOI: 10.1038/s41596-022-00704-8

40. Honglian Zhang#, Ying Liu#, Yali Xie#, Yunji Zhu#, Jingwen Liu, and Falong Lu*. (2022). H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination. SCIENCE CHINA Life Sciences 65(9): 1685-1700. DOI: 10.1007/s11427-022-2155-0

39. Yujun Quan#, Meijiao Wang#, Chengpeng Xu, Xiaoxiao Wang, Yu Wu, Dandan Qin, Yuxuan Lin, Xukun Lu, Falong Lu*, and Lei Li*. (2022). Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Research 50(8): 4414-4435. DOI: 10.1093/nar/gkac236

38. Yan Yao#, Mengyao Xu, Lianyong Qiao, Hu Nie, Falong Lu, and Xun Huang*. (2022). BAP60 plays an opposite role to the MRT-NURF complex in regulating lipid droplet size. Journal of Genetics and Genomics 49(4): 377-379. DOI: 10.1016/j.jgg.2022.02.003

37. Muya Shu#, Xiaoyu Xue#, Hu Nie, Xianming Wu, Minghan Sun, Lianyong Qiao, Xing Li, Bai Xu, Zhifeng Xiao, Yannan Zhao, Yongheng Fan, Bing Chen, Jixiang Zhang, Ya Shi, Yaming Yang, Falong Lu*, and Jianwu Dai*. (2022). Single-cell RNA sequencing reveals Nestin+ active neural stem cells outside the central canal after spinal cord injury. SCIENCE CHINA Life Sciences 65(2): 295–308. DOI: 10.1007/s11427-020-1930-0

36. Zhengnan Luo#, Jixiang Zhang#, Lianyong Qiao, Falong Lu*, and Zhiyong Liu*. (2021). Mapping genome-wide binding sites of Prox1 in mouse cochlea using the CUT&RUN approach. Neuroscience Bulletin 37(12): 1703–1707. DOI: 10.1007/s12264-021-00757-x

35. Wenhui Mu#, Si Li#, Jingkai Xu#, Xize Guo, Haoda Wu, Zhenhua Chen, Lianyong Qiao, Gisela Helfer, Falong Lu, Chong Liu, and Qing-Feng Wu*. (2021). Hypothalamic Rax(+) tanycytes contribute to tissue repair and tumorigenesis upon oncogene activation in mice. Nature Communications 12(1): 2288. DOI: 10.1038/s41467-021-22640-z

34. Yusheng Liu#, Hu Nie, and Falong Lu*. (2020). Dynamic RNA 3' uridylation and guanylation during mitosis. iScience 23(8): 101402. DOI: 10.1016/j.isci.2020.101402

33. Le-Yun Wang#, Zhi-Kun Li#, Li-Bin Wang#, Chao Liu#, Xue-Han Sun#, Gui-Hai Feng#, Jia-Qiang Wang, Yu-Fei Li, Lian-Yong Qiao, Hu Nie, Li-Yuan Jiang, Hao Sun, Ya-Li Xie, Si-Nan Ma, Hai-Feng Wan, Fa-Long Lu*, Wei Li*, and Qi Zhou*. (2020). Overcoming intrinsic H3K27me3 imprinting barriers improves post-implantation development after somatic cell nuclear transfer. Cell Stem Cell 27(2): 315-325.e5. DOI: 10.1016/j.stem.2020.05.014

32. Chunyan Fan#, Honglian Zhang#, Liangzheng Fu, Yuejiao Li, Yi Du, Zilong Qiu, and Falong Lu*. (2020). Rett mutations attenuate phase separation of MeCP2. Cell Discovery 6: 38. DOI: 10.1038/s41421-020-0172-0

31. Chenrui An#, Guihai Feng#, Jixiang Zhang, Shiwei Cao, Ying Wang, Nannan Wang, Falong Lu, Qi Zhou, and Haoyi Wang*. (2020). overcoming autocrine fgf signaling-induced heterogeneity in naïve human ESCs enables modeling of random X chromosome inactivation. Cell Stem Cell 27(3): 482-497.e4. DOI: 10.1016/j.stem.2020.06.002

30. Yusheng Liu#, Hu Nie#, Hongxiang Liu, and Falong Lu*. (2019). Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails. Nature Communications 10(1): 5292. DOI: 10.1038/s41467-019-13228-9

29. Luis Tuesta#, Mohamed Djekidel, Renchao Chen, Falong Lu, Wengang Wang, Bernardo Sabatini, and Yi Zhang*. (2019). In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function. Nature Communications 10(1): 2508. DOI: 10.1038/s41467-019-10267-0

28. Qi Qiu#, Hailiang Mei#, Xian Deng#, Kaixuan He#, Baixing Wu#, Qingqing Yao, Jixiang Zhang, Falong Lu, Jinbiao Ma*, and Xiaofeng Cao*. (2019). DNA methylation repels targeting of Arabidopsis REF6. Nature Communications 10(1): 2063. DOI: 10.1038/s41467-019-10026-1

27. Shogo Matoba#, Huihan Wang, Lan Jiang, Falong Lu, Kumiko Iwabuchi, Xiaoji Wu, Kimiko Inoue, Lin Yang, William Press, Jeannie Lee, Atsuo Ogura, Li Shen*, and Yi Zhang*. (2018). Loss of H3K27me3 imprinting in somatic cell nuclear transfer embryos disrupts post-implantation development. Cell Stem Cell 23(3): 343-354.e5. DOI: 10.1016/j.stem.2018.06.008

26. Mohamed Nadhir Djekidel#, Azusa Inoue#, Shogo Matoba, Tsukasa Suzuki, Chunxia Zhang, Falong Lu, Lan Jiang, and Yi Zhang*. (2018). reprogramming of chromatin accessibility in somatic cell nuclear transfer is DNA replication independent. Cell Reports 23(7): 1939-1947. DOI: 10.1016/j.celrep.2018.04.036

25. Falong Lu#*. (2018). The start of a human life program. Journal of Genetics and Genomics 45(4): 183-184. DOI: 10.1016/j.jgg.2018.04.001

24. Azusa Inoue#, Lan Jiang, Falong Lu, and Yi Zhang*. (2017). Genomic imprinting of Xist by maternal H3K27me3. Genes & Development 31(19): 1927-1932. DOI: 10.1101/gad.304113.117

23. Azusa Inoue#, Lan Jiang#, Falong Lu#, Tsukasa Suzuki, and Yi Zhang*. (2017). Maternal H3K27me3 controls DNA methylation-independent imprinting. Nature 547(7664): 419-424. DOI: 10.1038/nature23262

22. Falong Lu#, Yuting Liu#, Azusa Inoue#, Tsukasa Suzuki, Keji Zhao, and Yi Zhang*. (2016). Establishing chromatin regulatory landscape during mouse preimplantation development. Cell 165(6): 1375-1388. DOI: 10.1016/j.cell.2016.05.050

21. Xia Cui#, Falong Lu#, Qi Qiu#, Bing Zhou#, Lianfeng Gu, Shuaibin Zhang, Yanyuan Kang, Xiekui Cui, Xuan Ma, Qingqing Yao, Jinbiao Ma, Xiaoyu Zhang, and Xiaofeng Cao*. (2016). REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nature Genetics 48(6): 694-699. DOI: 10.1038/ng.3556

20. Minchul Kim#, Falong Lu, and Yi Zhang*. (2016). Loss of HDAC-mediated repression and gain of NF-kappaB activation underlie cytokine induction in ARID1A- and PIK3CA-mutation-driven ovarian cancer. Cell Reports 17(1): 275-288. DOI: 10.1016/j.celrep.2016.09.003

19. Fangfang Jiang#, Falong Lu, Peixue Li, Wei Liu*, Lu Zhao, Qifu Wang, Xiaofeng Cao, Lei Zhang, and Yong Q. Zhang*. (2016). Drosophila homolog of FMRP maintains genome integrity by interacting with Piwi. Journal of Genetics and Genomics 43(1): 11-24. DOI: 10.1016/j.jgg.2015.11.001

18. Falong Lu# and Yi Zhang*. (2015). Cell totipotency: molecular features, induction, and maintenance. National Science Review 2(2): 217-225. DOI: 10.1093/nsr/nwv009

17. Young Gie Chung#, Shogo Matoba#, Yuting Liu, Jin Hee Eum, Falong Lu, Wei Jiang, Jeoung Eun Lee, Vicken Sepilian, Kwang Yul Cha, Dong Ryul Lee*, and Yi Zhang*. (2015). Histone demethylase expression enhances human somatic cell nuclear transfer efficiency and promotes derivation of pluripotent stem cells. Cell Stem Cell 17(6): 758-766. DOI: 10.1016/j.stem.2015.10.001

15. Falong Lu#, Yuting Liu#, Lan Jiang#, Shinpei Yamaguchi, and Yi Zhang*. (2014). Role of Tet proteins in enhancer activity and telomere elongation. Genes & Development 28(19): 2103-2119. DOI: 10.1101/gad.248005.114

14. Shogo Matoba#, Yuting Liu#, Falong Lu, Kumiko A. Iwabuchi, Li Shen, Azusa Inoue, and Yi Zhang*. (2014). Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation. Cell 159(4): 884-895. DOI: 10.1016/j.cell.2014.09.055

13. Li Shen#, Azusa Inoue#, Jin He, Yuting Liu, Falong Lu, and Yi Zhang*. (2014). Tet3 and DNA replication mediate demethylation of both the maternal and paternal genomes in mouse zygotes. Cell Stem Cell 15(4): 459-470. DOI: 10.1016/j.stem.2014.09.002

12. Runlai Hang#, Chunyan Liu, Ayaz Ahmad, Yong Zhang, Falong Lu, and Xiaofeng Cao*. (2014). Arabidopsis protein arginine methyltransferase 3 is required for ribosome biogenesis by affecting precursor ribosomal RNA processing. Proc Natl Acad Sci USA 111(45): 16190-16195. DOI: 10.1073/pnas.1412697111

11. Xia Cui#*, Falong Lu#, Yue Li, Yongming Xue, Yanyuan Kang, Shuaibin Zhang, Qi Qiu, Xiekui Cui, Suzhi Zheng, Bin Liu, Xiaodong Xu, and Xiaofeng Cao. (2013). Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis. Plant Physiology 162(2): 897-906. DOI: 10.1104/pp.112.213009

10. Lifang Niu#, Falong Lu#, Taolan Zhao#, Chunyan Liu, and Xiaofeng Cao*. (2012). The enzymatic activity of Arabidopsis protein arginine methyltransferase 10 is essential for flowering time regulation. Protein & Cell 3(6): 450-459. DOI: 10.1007/s13238-012-2935-3

9. Falong Lu#, Xia Cui#, Shuaibin Zhang, Thomas Jenuwein, and Xiaofeng Cao*. (2011). Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nature Genetics 43(7): 715-719. DOI: 10.1038/ng.854

8. Yuan Cheng#, Monica Frazier, Falong Lu, Xiaofeng Cao, and Matthew R. Redinbo*. (2011). Crystal structure of the plant epigenetic protein arginine methyltransferase 10. Journal of Molecular Biology 414(1): 106-122. DOI: 10.1016/j.jmb.2011.09.040

7. Falong Lu#, Xia Cui#, Shuaibin Zhang, Chunyan Liu, and Xiaofeng Cao*. (2010). JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Research 20(3): 387-390. DOI: 10.1038/cr.2010.27

6. Chunyan Liu#, Falong Lu, Xia Cui, and Xiaofeng Cao*. (2010). Histone methylation in higher plants. Annual Review of Plant Biology 61: 395-420. DOI: 10.1146/annurev.arplant.043008.091939

5. Soichi Inagaki#, Asuka Miura-Kamio, Yasukazu Nakamura, Falong Lu, Xia Cui, Xiaofeng Cao*, Hiroshi Kimura, Hidetoshi Saze, and Tetsuji Kakutani*. (2010). Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO Journal 29(20): 3496-3506. DOI: 10.1038/emboj.2010.227

4. Xian Deng#, Lianfeng Gu#, Chunyan Liu#, Tiancong Lu#, Falong Lu, Zhike Lu, Peng Cui, Yanxi Pei, Baichen Wang, Songnian Hu, and Xiaofeng Cao*. (2010). Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing. Proc Natl Acad Sci USA 107(44): 19114-19119. DOI: 10.1073/pnas.1009669107