2025

Wang JN, Suo XG, Yu JT, Luo QC, Ji ML, Zhang MM, Zhu Q, Cheng XR, Hou C, Chen X, Wang F, Xu CH, Li C, Xie SS, Wei J, Zhang DF, Zhang XR, Wang ZJ, Dong YH, Zhu S, Peng LJ, Li XY, Chen HY, Xu T, Jin J, Chen FX, Meng XM. NAT10 exacerbates acute renal inflammation by enhancing N4-acetylcytidine modification of the CCL2/CXCL1 axis. Proc Natl Acad Sci U S A. 2025 Apr 29;122(17):e2418409122. doi: 10.1073/pnas.2418409122. Epub 2025 Apr 22. PubMed PMID: 40261924.

Tao B, Wang Z, Wang X, Song A, Liu J, Wang J, Zhang Q, Chen Z, Wang Z, Xu W, Sun M, Wang Y, Zhang P, Xu T, Wei GH, Chen FX, Wang M. An inherited predisposition allele promotes gastric cancer via enhancing deubiquitination-mediated activation of epithelial-to-mesenchymal transition signaling. J Clin Invest. 2025 Apr 15;135(8). doi: 10.1172/JCI179617. eCollection 2025 Apr 15. PubMed PMID: 39998882; PubMed Central PMCID: PMC11996917.

Dai P, Tan Y, Luo Y, Liu T, Huang Y, Shang Y, Huang ME, Liu X, Zhang S, Wang Y, Li QX, Li N, Li L, Qin Y, Liu J, Liu LD, Xie X, Cai Y, Chen FX, Zheng X, Yeap LS, Wang J, Hu J, Meng FL. Transcription-coupled AID deamination damage depends on ELOF1-associated RNA polymerase II. Mol Cell. 2025 Apr 3;85(7):1280-1295.e9. doi: 10.1016/j.molcel.2025.02.006. Epub 2025 Mar 5. PubMed PMID: 40049162.

Li Y, Fischer P, Wang M, Zhou Q, Song A, Yuan R, Meng W, Chen FX, Lührmann R, Lau B, Hurt E, Cheng J. Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates. Cell Res. 2025 Apr;35(4):296-308. doi: 10.1038/s41422-025-01084-w. Epub 2025 Feb 28. PubMed PMID: 40016598; PubMed Central PMCID: PMC11958768.

Wang H, Zhang S, Pan Q, Guo J, Li N, Chen L, Xu J, Zhou J, Gu Y, Wang X, Zhang G, Lian Y, Zhang W, Lin N, Jin Z, Zang Y, Lan W, Cheng X, Tan M, Chen FX, Jiang J, Liu Q, Zheng M, Qin J. Targeting the histone reader ZMYND8 inhibits antiandrogen-induced neuroendocrine tumor transdifferentiation of prostate cancer. Nat Cancer. 2025 Mar 18;. doi: 10.1038/s43018-025-00928-z. [Epub ahead of print] PubMed PMID: 40102673.

Liu W, Deng L, Wang M, Liu X, Ouyang X, Wang Y, Miao N, Luo X, Wu X, Lu X, Xv X, Zhang T, Li Y, Ji J, Qiao Z, Wang S, Guan L, Li D, Dang Y, Liu C, Li W, Zhang Y, Wang Z, Chen FX, Chen C, Lin C, Goh WSS, Zhou W, Luo Z, Gao P, Li P, Yu Y. Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation. Mol Cell. 2025 Mar 6;85(5):929-947.e10. doi: 10.1016/j.molcel.2025.01.023. Epub 2025 Feb 26. PubMed PMID: 40015272.

Cheng ZL, Zhang S, Wang Z, Song A, Gao C, Song JB, Wang P, Zhang L, Zhou Y, Shan W, Zhang C, Zhang J, Sun Y, Xu Y, Lan F, Zhong M, Lyu LD, Huang G, Chen FX, Li G, Wang Z, Chen F, Xue J, Shi J, Liu Y, Lin Z, Wu D, Na J, Chen LL, Guan KL, Xiong Y, Ye D. Pathogen-derived glyoxylate inhibits Tet2 DNA dioxygenase to facilitate bacterial persister formation. Cell Metab. 2025 Feb 26;. doi: 10.1016/j.cmet.2025.01.019. [Epub ahead of print] PubMed PMID: 40037360.

Huang Z, Diehl FF, Wang M, Li Y, Song A, Chen FX, Rosa-Mercado NA, Beckmann R, Green R, Cheng J. RIOK3 mediates the degradation of 40S ribosomes. Mol Cell. 2025 Feb 20;85(4):802-814.e12. doi: 10.1016/j.molcel.2025.01.013. Epub 2025 Feb 12. PubMed PMID: 39947183.

Du Y, Wang YR, Bao QY, Xu XX, Xu C, Wang S, Liu Q, Liu F, Zeng YL, Wang YJ, Liu W, Liu Y, Yu SX, Chen YC, Wang C, Zhang W, Gao H, Luo H, Liu B, Jing G, Guo M, Chen FX, Liu YJ. Personalized Vascularized Tumor Organoid-on-a-Chip for Tumor Metastasis and Therapeutic Targeting Assessment. Adv Mater. 2025 Feb;37(6):e2412815. doi: 10.1002/adma.202412815. Epub 2024 Dec 26. PubMed PMID: 39726096.

Yang Y, Liao J, Pan Z, Meng J, Zhang L, Shi W, Wang X, Zhang X, Zhou Z, Luo J, Chen X, Yang Z, Mei X, Ma J, Zhang Z, Jiang YZ, Shao ZM, Chen FX, Yu X, Guo X. Dual Inhibition of CDK4/6 and CDK7 Suppresses Triple-Negative Breast Cancer Progression via Epigenetic Modulation of SREBP1-Regulated Cholesterol Metabolism. Adv Sci (Weinh). 2025 Feb;12(5):e2413103. doi: 10.1002/advs.202413103. Epub 2024 Dec 10. PubMed PMID: 39656925; PubMed Central PMCID: PMC11791979.

Fan P, Shang XY, Song A, Chen S, Mao RY, Ma J, Chen J, Wang Z, Zheng H, Tao B, Hong L, Liu J, Xu W, Jiang W, Shen H, Zhang Q, Yang H, Meng XM, Lan F, Cheng J, Xu C, Zhang P, Jiang H, Chen FX. Catalytic-independent functions of the Integrator-PP2A complex (INTAC) confer sensitivity to BET inhibition. Nat Chem Biol. 2025 Jan 14;. doi: 10.1038/s41589-024-01807-x. [Epub ahead of print] PubMed PMID: 39809894.

2024

Wang Z, Song A, Tao B, Miao M, Luo YQ, Wang J, Yin Z, Xiao R, Zhou X, Shang XY, Hu S, Liang K, Danko CG, Chen FX. The phosphatase PP1 sustains global transcription by promoting RNA polymerase II pause release. Mol Cell. 2024 Dec 19;84(24):4824-4842.e7. doi: 10.1016/j.molcel.2024.10.046. Epub 2024 Nov 26. PubMed PMID: 39603240.

Lee JH, Sánchez-Rivera FJ, He L, Basnet H, Chen FX, Spina E, Li L, Torner C, Chan JE, Yarlagadda DVK, Park JS, Sussman C, Rudin CM, Lowe SW, Tammela T, Macias MJ, Koche RP, Massagué J. TGF-β and RAS jointly unmask primed enhancers to drive metastasis. Cell. 2024 Oct 31;187(22):6182-6199.e29. doi: 10.1016/j.cell.2024.08.014. Epub 2024 Sep 6. PubMed PMID: 39243762.

Shang XY, Xu C, Chen FX. From snapshots to a movie: Capturing eukaryotic transcription initiation at single-nucleotide resolution. Sci Bull (Beijing). 2024 Apr 15;69(7):853-855. doi: 10.1016/j.scib.2024.01.030. Epub 2024 Jan 23. PubMed PMID: 38320900.

Wang J, Xu C, Zhang Z, Chen FX. Mechanisms of SOSS-Integrator-PP2A complex in attenuating R-loops and promoting genome stability. Clin Transl Med. 2024 Jan;14(1):e1519. doi: 10.1002/ctm2.1519. PubMed PMID: 38226796; PubMed Central PMCID: PMC10790593.

2023

Ji YX, Hu S, Chen FX. Protocol for rapidly inducing genome-wide RNA Pol II hyperphosphorylation by ively disrupting INTAC phosphatase activity. STAR Protoc. 2023 Dec 15;4(4):102640. doi: 10.1016/j.xpro.2023.102640. Epub 2023 Oct 12. PubMed PMID: 37831607; PubMed Central PMCID: PMC10589876.

Li C, Liao J, Wang X, Chen FX, Guo X, Chen X. Combined Aurora Kinase A and CHK1 Inhibition Enhances Radiosensitivity of Triple-Negative Breast Cancer Through Induction of Apoptosis and Mitotic Catastrophe Associated With Excessive DNA Damage. Int J Radiat Oncol Biol Phys. 2023 Dec 1;117(5):1241-1254. doi: 10.1016/j.ijrobp.2023.06.022. Epub 2023 Jun 30. PubMed PMID: 37393021.

Zheng H, Jin Q, Wang X, Qi Y, Liu W, Ren Y, Zhao D, Xavier Chen F, Cheng J, Chen X, Xu Y. Structural basis of INTAC-regulated transcription. Protein Cell. 2023 Sep 14;14(9):698-702. doi: 10.1093/procel/pwad010. PubMed PMID: 36869814; PubMed Central PMCID: PMC10501182.

Xu C, Li C, Chen J, Xiong Y, Qiao Z, Fan P, Li C, Ma S, Liu J, Song A, Tao B, Xu T, Xu W, Chi Y, Xue J, Wang P, Ye D, Gu H, Zhang P, Wang Q, Xiao R, Cheng J, Zheng H, Yu X, Zhang Z, Wu J, Liang K, Liu YJ, Lu H, Chen FX. R-loop-dependent promoter-proximal termination ensures genome stability. Nature. 2023 Sep;621(7979):610-619. doi: 10.1038/s41586-023-06515-5. Epub 2023 Aug 9. PubMed PMID: 37557913; PubMed Central PMCID: PMC10511320.

Zeng C, Chen J, Cooke EW, Subuddhi A, Roodman ET, Chen FX, Cao K. Demethylase-independent roles of LSD1 in regulating enhancers and cell fate transition. Nat Commun. 2023 Aug 22;14(1):4944. doi: 10.1038/s41467-023-40606-1. PubMed PMID: 37607921; PubMed Central PMCID: PMC10444793.

Hu S, Peng L, Song A, Ji YX, Cheng J, Wang M, Chen FX. INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II. Mol Cell. 2023 May 18;83(10):1588-1604.e5. doi: 10.1016/j.molcel.2023.03.022. Epub 2023 Apr 19. PubMed PMID: 37080207.

Hu S, Song A, Peng L, Tang N, Qiao Z, Wang Z, Lan F, Chen FX. H3K4me2/3 modulate the stability of RNA polymerase II pausing. Cell Res. 2023 May;33(5):403-406. doi: 10.1038/s41422-023-00794-3. Epub 2023 Mar 15. PubMed PMID: 36922644; PubMed Central PMCID: PMC10156655.

2022

Song A, Chen FX. The pleiotropic roles of SPT5 in transcription. Transcription. 2022 Feb-Jun;13(1-3):53-69. doi: 10.1080/21541264.2022.2103366. Epub 2022 Jul 25. Review. PubMed PMID: 35876486; PubMed Central PMCID: PMC9467590.

Wang X, Qi Y, Wang Z, Wang L, Song A, Tao B, Li J, Zhao D, Zhang H, Jin Q, Jiang YZ, Chen FX, Xu Y, Chen X. RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex. Cell Rep. 2022 Apr 26;39(4):110732. doi: 10.1016/j.celrep.2022.110732. PubMed PMID: 35476980.

Wang Z, Song A, Xu H, Hu S, Tao B, Peng L, Wang J, Li J, Yu J, Wang L, Li Z, Chen X, Wang M, Chi Y, Wu J, Xu Y, Zheng H, Chen FX. Coordinated regulation of RNA polymerase II pausing and elongation progression by PAF1. Sci Adv. 2022 Apr;8(13):eabm5504. doi: 10.1126/sciadv.abm5504. Epub 2022 Apr 1. PubMed PMID: 35363521; PubMed Central PMCID: PMC11093130.

2021

Hu S, Peng L, Xu C, Wang Z, Song A, Chen FX. SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape. Mol Cell. 2021 Nov 4;81(21):4425-4439.e6. doi: 10.1016/j.molcel.2021.08.029. Epub 2021 Sep 16. PubMed PMID: 34534457.

2021

Zheng H, Qi Y, Hu S, Cao X, Xu C, Yin Z, Chen X, Li Y, Liu W, Li J, Wang J, Wei G, Liang K, Chen FX, Xu Y. Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase. Science. 2020 Nov 27;370(6520). doi: 10.1126/science.abb5872. PubMed PMID: 33243860.

Before 2020

Sze CC, Ozark PA, Cao K, Ugarenko M, Das S, Wang L, Marshall SA, Rendleman EJ, Ryan CA, Zha D, Douillet D, Chen FX, Shilatifard A. Coordinated regulation of cellular identity-associated H3K4me3 breadth by the COMPASS family. Sci Adv. 2020 Jun;6(26):eaaz4764. doi: 10.1126/sciadv.aaz4764. eCollection 2020 Jun. PubMed PMID: 32637595; PubMed Central PMCID: PMC7314515.

Huang YH, Hu J, Chen F, Lecomte N, Basnet H, David CJ, Witkin MD, Allen PJ, Leach SD, Hollmann TJ, Iacobuzio-Donahue CA, Massagué J. ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer. Cancer Discov. 2020 Jan;10(1):142-157. doi: 10.1158/2159-8290.CD-19-0529. Epub 2019 Oct 3. PubMed PMID: 31582374; PubMed Central PMCID: PMC6954299.

Xu C, Wang X, Zhou Y, Chen FX, Wang H, Li K, Fan H, Tang X, Jiang G, Zhang J. Synergy between arsenic trioxide and JQ1 on autophagy in pancreatic cancer. Oncogene. 2019 Nov;38(47):7249-7265. doi: 10.1038/s41388-019-0930-3. Epub 2019 Aug 16. PubMed PMID: 31420604.

Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol. 2018 Jul;19(7):464-478. doi: 10.1038/s41580-018-0010-5. Review. PubMed PMID: 29740129.

Chen FX, Marshall SA, Deng Y, Tianjiao S. Measuring Nascent Transcripts by Nascent-seq. Methods Mol Biol. 2018;1712:19-26. doi: 10.1007/978-1-4939-7514-3_2. PubMed PMID: 29224065.

Sze CC, Cao K, Collings CK, Marshall SA, Rendleman EJ, Ozark PA, Chen FX, Morgan MA, Wang L, Shilatifard A. Histone H3K4 methylation-dependent and -independent functions of Set1A/COMPASS in embryonic stem cell self-renewal and differentiation. Genes Dev. 2017 Sep 1;31(17):1732-1737. doi: 10.1101/gad.303768.117. Epub 2017 Sep 22. PubMed PMID: 28939616; PubMed Central PMCID: PMC5666672.

Chen FX, Xie P, Collings CK, Cao K, Aoi Y, Marshall SA, Rendleman EJ, Ugarenko M, Ozark PA, Zhang A, Shiekhattar R, Smith ER, Zhang MQ, Shilatifard A. PAF1 regulation of promoter-proximal pause release via enhancer activation. Science. 2017 Sep 22;357(6357):1294-1298. doi: 10.1126/science.aan3269. Epub 2017 Aug 31. PubMed PMID: 28860207; PubMed Central PMCID: PMC6055228.

Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, Shiekhattar R, Shilatifard A. PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II. Cell. 2015 Aug 27;162(5):1003-15. doi: 10.1016/j.cell.2015.07.042. Epub 2015 Aug 13. PubMed PMID: 26279188; PubMed Central PMCID: PMC4679144.

Chen F, Gao X, Shilatifard A. Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide. Genes Dev. 2015 Jan 1;29(1):39-47. doi: 10.1101/gad.246173.114. PubMed PMID: 25561494; PubMed Central PMCID: PMC4281563.

Fang R, Chen F, Dong Z, Hu D, Barbera AJ, Clark EA, Fang J, Yang Y, Mei P, Rutenberg M, Li Z, Zhang Y, Xu Y, Yang H, Wang P, Simon MD, Zhou Q, Li J, Marynick MP, Li X, Lu H, Kaiser UB, Kingston RE, Xu Y, Shi YG. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell. 2013 Feb 7;49(3):558-70. doi: 10.1016/j.molcel.2012.11.019. Epub 2012 Dec 20. PubMed PMID: 23260659; PubMed Central PMCID: PMC3625064.

Chen F, Yang H, Dong Z, Fang J, Wang P, Zhu T, Gong W, Fang R, Shi YG, Li Z, Xu Y. Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Cell Res. 2013 Feb;23(2):306-9. doi: 10.1038/cr.2013.17. Epub 2013 Jan 29. PubMed PMID: 23357850; PubMed Central PMCID: PMC3567815.