Publications  from Cheng Lab:

# co-first; * co-corresponding.

Cheng Lab members are underlined.

2025

Li Y#, Fischer P#, Wang M#, Zhou Q, Song A, Yuan R, Meng W, Chen FX, Lührmann R, Lau B*, Hurt E*, Cheng J*.(2025). Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates. Cell research, doi: 10.1038/s41422-025-01084-w. BioArt

Huang Z#,Diehl FF#, Wang M, Li Y, Song A, Chen FX, Rosa-Mercado NA, Beckmann R, Green R*, Cheng J*.(2025). RIOK3 mediates the degradation of 40S ribosomes. Molecular cell, S1097-2765(25)00048-6.doi: 10.1016/j.molcel.2025.01.013. BioArt

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*. (2025). Catalytic-independent functions of the Integrator-PP2A complex (INTAC) confer sensitivity to BET inhibition. Nature chemical biology , doi: 10.1038/s41589-024-01807-x.

2024

Saba JA#, Huang Z#, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J*, Green R*. (2024). LARP1 binds ribosomes and TOP mRNAs in repressed complexes. The EMBO journal,  43(24), 6555–6572. doi: 10.1038/s44318-024-00294-z. BioArt

Lian C#, Zhang C#, Tian P, Tan Q, Wei Y, Wang Z, Zhang Q, Zhang Q, Zhong M, Zhou LQ, Ke X, Zhang H, Zhu Y, Li Z, Cheng J , Wei GH*(2024). Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity. Signal Transduct Target Ther , 9(1), 258. doi: 10.1038/s41392-024-01961-7.

Miao B#, Ge L#, He C#, Wang X#, Wu J#, Li X , Chen K, Wan J, Xing S, Ren L, Shi Z, Liu S, Hu Y, Chen J, Yu Y, Feng L, Flores NM, Liang Z, Xu X, Wang R, Zhou J, Fan J, Xiang B, Li E, Mao Y, Cheng J , Zhao K, Mazur PK, Cai J, Lan F*.(2024). SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma. Cell Research doi: 10.1038/s41422-024-01013-3.

Li X#, Wang M# , Denk T# , Buschauer R, Li Y , Beckmann R* , Cheng J*.(2024). Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline . Nature Communications, 15(1), 5481. doi: 10.1038/s41467-024-49797-7. BioArt

Ye X#, Huang Z#, Li Y, Wang M, Meng W, Miao M , Cheng J*.(2024). Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation. Cell Research, 1-4. doi: 10.1038/s41422-024-00962-z. BioArt

2023

Saba J. A#, Huang Z#, Schole K. L, Ye X, Bhatt S. D, Li Y, Timp W, Cheng J*, Green, R*. (2023). LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins . bioRxiv. doi: 10.1101/2023.11.01.565189.

Lau B#, Huang Z#, Kellner N, Niu S, Berninghausen O, Beckmann R*, Cheng J*. (2023). Mechanism of 5S RNP recruitment and helicase‐surveilled rRNA maturation during pre‐60S biogenesis. EMBO reports, 24(7), e56910. doi: 10.15252/embr.202356910. BioArt

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*. (2023). R-loop-dependent promoter-proximal termination ensures genome stability. Nature, 621(7979), 610-619. doi: 10.1038/s41586-023-06515-5.

Zheng H#*, Jin Q#, Wang X#, Qi Y, Liu W, Ren Y, Zhao D, Chen FX, Cheng J , Chen X, Xu Y*. (2023). Structural basis of INTAC-regulated transcription. Protein & Cell, 14(9), 698-702. doi: 10.1093/procel/pwad010.

Hu S#, Peng L#, Song A#, Ji YX#, Cheng J , Wang M, & Chen FX*. (2023). INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II. Molecular cell , 83(10), 1588-1604. doi: 10.1016/j.molcel.2023.03.022.

Thoms M#, Lau B#, Cheng J , Fromm L, Denk T, Kellner N, ... & Beckmann R*, Hurt E*. (2023). Structural insights into coordinating 5S RNP rotation with ITS2 pre‐RNA processing during ribosome formation. EMBO reports , 24(12), e57984. doi: 10.15252/embr.202357984.

Ikeuchi K#, Ivic N, Buschauer R, Cheng J , Fröhlich T, Matsuo Y, ... & Becker T*, Beckmann R*. (2023). Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nature Communications , 14(1), 2730. doi: 10.1038/s41467-023-38161-w.

Zhou F#*, Aroua N#, Liu Y, Rohde C, Cheng J , Wirth A. K, ... & Trumpp A*, Müller-Tidow C*. (2023). A dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia. Cancer discovery , 13(2), 332-347. doi: 10.1158/2159-8290.CD-22-0210.

2022

Cheng J #, Lau B, Thoms M, Ameismeier M, Berninghausen O, Hurt E*, Beckmann R*. (2022). The nucleoplasmic phase of pre-40S formation prior to nuclear export. Nucleic acids research , 50(20), 11924-11937. doi: 10.1093/nar/gkac961.

Cheng J #, La Venuta G#, Lau B#, Berninghausen O, Beckmann R*, Hurt E*. (2022). In vitro structural maturation of an early stage pre-40S particle coupled with U3 snoRNA release and central pseudoknot formation. Nucleic acids research , 50(20), 11916-11923. doi: 10.1093/nar/gkac910.

Lau B, Beine-Golovchuk O, Kornprobst M, Cheng J , Kressler D, Jády B, ... & Beckmann R*, Hurt E*. (2022). Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release. Cell Reports , 41(8). doi: 10.1016/j.celrep.2022.111684.

Qiao S#, Lee CW, Sherpa D, Chrustowicz J, Cheng J , Duennebacke M, ... & Schulman BA*. (2022). Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation. Nature Communications , 13(1), 3041. doi: 10.1038/s41467-022-30803-9.

2021

Cheng J #*, Berninghausen O., Beckmann R*. (2021). A distinct assembly pathway of the human 39S late pre-mitoribosome. Nature communications , 12(1), 4544. doi: 10.1038/s41467-021-24818-x.

Weng T. H#, Steinchen W, Beatrix B, Berninghausen O, Becker T, Bange G, Cheng J *, Beckmann R*. (2021). Architecture of the active post‐translational Sec translocon. The EMBO Journal , 40(3), e105643. doi: 10.15252/embj.2020105643.

Su T#, Kudva R, Becker T, Buschauer R, Komar T, Berninghausen O, von Heijne G, Cheng J *, Beckmann R* (2021). Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide. Nucleic Acids Research , 49(16), 9539-9547. doi: 10.1093/nar/gkab665.

Lau B#, Cheng J #, Flemming D, La Venuta G, Berninghausen O, Beckmann R*, Hurt E*. (2021). Structure of the maturing 90S pre-ribosome in association with the RNA exosome. Molecular cell , 81(2), 293-303. doi: 10.1371/journal.pbio.3000780.

Kratzat H#, Mackens‐Kiani T#, Ameismeier M, Potocnjak M, Cheng J , Dacheux E, ... & Becker T*, Beckmann R*. (2021). A structural inventory of native ribosomal ABCE1‐43S pre‐initiation complexes. The EMBO journal , 40(1), e105179. doi: 10.15252/embj.2020105179.

Huang B#, Guo Q#, Niedermeier ML#, Cheng J , Engler T, Maurer M, ... & Fernandez-Busnadiego R*. (2021). Pathological polyQ expansion does not alter the conformation of the Huntingtin-HAP40 complex. Structure , 29(8), 804-809. doi: 10.1016/j.str.2021.04.003.

Before 2021

Cheng J #, Lau B#, La Venuta G, Ameismeier M, Berninghausen O, Hurt E*, Beckmann R*. (2020). 90 S pre-ribosome transformation into the primordial 40 S subunit. Science , 369(6510), 1470-1476. doi: 10.1126/science.abb4119.

Wells JN, Buschauer R, Mackens-Kiani T, Best K, Kratzat H, Berninghausen O, Becker T, Gilbert W, Cheng J *, Beckmann R*. (2020). Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. PLoS biology  18(7), e3000780. doi: 10.1371/journal.pbio.3000780.

Osterman IA#, Wieland M#, Maviza TP#, Lashkevich KA, Lukianov DA, Komarova S, Zakalyukina YV, Buschauer R, Shiriaev DI, Leyn S, Zlamal JE, Biryukov MV, Skvortsov DA, Tashlitsky VN, Polshakov VI, Cheng J , … & Wilson DN*, Sergiev PV*. (2020). Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel. Nature chemical biology , 16(10), 1071-1077. doi: 10.1038/s41589-020-0578-x.

Thoms M#, Buschauer R#, Ameismeier M#, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-kiani T, Cheng J , ... & Beckmann R*. (2020). Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science , 369(6508), 1249-1255. doi: 10.1126/science.abc8665.

Buschauer R#, Matsuo Y#, Sugiyama T, Chen YH, Alhusaini N, Sweet T, Ikeuchi K, Cheng J ,... & Coller J*, Inada T*, Beckmann R*. (2020). The Ccr4-Not complex monitors the translating ribosome for codon optimality. Science , 368(6488), eaay6912. doi: 10.1126/science.aay6912.

Kater L#, Mitterer V, Thoms M, Cheng J , Berninghausen O, Beckmann R*, & Hurt E*. (2020). Construction of the central protuberance and L1 stalk during 60S subunit biogenesis. Molecular cell , 79(4), 615-628. doi: 10.1016/j.molcel.2020.06.032.

Matsuo Y#, Tesina P#, Nakajima S, Mizuno M, Endo A, Buschauer R, Cheng J , ... & Beckmann R*, Inada T*. (2020). RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Nature structural & molecular biology , 27(4), 323-332. doi: 10.1038/s41594-020-0393-9.

Tesina P#, Lessen LN#, Buschauer R, Cheng J , Wu CCC, Berninghausen O, Buskirk AR, Becker T*, Beckmann R*, Green R*. (2020). Molecular mechanism of translational stalling by inhibitory codon combinations and poly (A) tracts. The EMBO journal , 39(3), e103365. doi: 10.15252/embj.2019103365.

Shanmuganathan V#, Schiller N#, Magoulopoulou A, Cheng J , Braunger K, Cymer F., ... & von Heijne G *, Beckmann R*. (2019). Structural and mutational analysis of the ribosome-arresting human XBP1u. elife , 8, e46267. doi: 10.7554/eLife.46267.

Su T#, Izawa T, Thoms M, Yamashita Y, Cheng J , Berninghausen O, ... & Neupert W*, Beckmann R*. (2019). Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis. Nature , 570(7762), 538-542. doi: 10.1038/s41586-019-1307-z.

Tesina P#, Heckel E, Cheng J , Fromont-Racine M, Buschauer R, Kater L, Beatrix B, Berninghausen O, Jacquier A*, Becker T*, Beckmann R*. (2019). Structure of the 80S ribosome–Xrn1 nuclease complex. Nature Structural & Molecular Biology , 26(4), 275-280. doi: 10.1038/s41594-019-0202-5.

Ikeuchi K#, Tesina P#, Matsuo Y, Sugiyama T, Cheng J , Saeki Y, ... & Beckmann R*, Inada T*. (2019). Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways. The EMBO journal , 38(5), e100276. doi: 10.15252/embj.2018100276.

Cheng J #, Baßler J#, Fischer P#, Lau B, Kellner N, Kunze R, Griesel S, Kallas M, Berninghausen O, Strauss D, Beckmann R*, Hurt E*. (2019). Thermophile 90S pre-ribosome structures reveal the reverse order of co-transcriptional 18S rRNA subdomain integration. Molecular cell , 75(6), 1256-1269. doi: 10.1016/j.molcel.2019.06.032.

Ameismeier M#, Cheng J #, Berninghausen O, Beckmann R*. (2018). Visualizing late states of human 40S ribosomal subunit maturation. Nature , 558(7709), 249-253. doi: 10.1038/s41586-018-0193-0.

Guo Q#, Bin Huang#, Cheng J , Seefelder M, Engler T, Pfeifer G, Oeckl P, Otto M, Moser F, Maurer M, Pautsch A, Baumeister W*, Fernández-Busnadiego R*, Kochanek S*. (2018). The cryo-electron microscopy structure of huntingtin. Nature ,555(7694):117-120. doi: 10.1038/nature25502.

Cheng J #, Kellner N, Berninghausen O, Hurt E*, Beckmann R*. (2017). 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Nature structural & molecular biology , 24(11), 954-964. doi: 10.1038/nsmb.3476. doi: 10.1038/nsmb.3476.

Sturm M, Cheng J , Baßler J, Beckmann R*, Hurt E*. (2017). Interdependent action of KH domain proteins Krr1 and Dim2 drive the 40S platform assembly. Nature communications , 8(1), 2213. doi: 10.1038/s41467-017-02199-4.

Kater L, Thoms M, Barrio-Garcia C, Cheng J , Ismail S, Ahmed YL, ... & Beckmann, R. (2017). Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Cell , 171(7), 1599-1610. doi: 10.1016/j.cell.2017.11.039.

Su T, Cheng J , Sohmen D, Hedman R, Berninghausen O, von Heijne G, Wilson DN*, Beckmann R*. (2017). The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. elife , 6, e25642. doi: 10.7554/eLife.25642.

Kornprobst M#, Turk M#, Kellner N, Cheng J , Flemming D, Koš-Braun I, ... & Beckmann R*, Hurt E*. (2016). Architecture of the 90S pre-ribosome: a structural view on the birth of the eukaryotic ribosome. Cell , 166(2), 380-393. doi: 10.1016/j.cell.2016.06.014.

Fang J#, Cheng J #, Wang J#, Zhang Q#, Liu M, Gong R, ... & Xu Y*. (2016). Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition. Nature communications , 7(1), 11197. doi: 10.1038/ncomms11197.

Lu J#, Hu L#, Cheng J #, Fang D, Wang C, Yu K, ... & Xu Y*, Luo C*. (2016). A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2). Physical Chemistry Chemical Physics , 18(6), 4728-4738. doi: 10.1039/c5cp07266b.

Hu L#, Lu J#, Cheng J #, Rao Q, Li Z, Hou H, ... & Luo C*, Xu Y*. (2015). Structural insight into substrate preference for TET-mediated oxidation. Nature , 527(7576), 118-122. doi: 10.1038/nature15713.

Cheng J #, Li Z#, Gong R, Fang J, Yang Y, Sun C, ... & Xu Y*. (2015). Molecular mechanism for the substrate recognition of USP7. Protein & cell , 6(11), 849-852. doi: 10.1007/s13238-015-0192-y.

Cheng J #, Yang H#, Fang J, Ma L, Gong R, Wang P, ... & Xu Y*. (2015). Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation. Nature communications , 6(1), 7023. doi: 10.1038/ncomms8023.

Hu L#, Li Z#, Cheng J #, Rao Q, Gong W, Liu M, ... & Xu Y. (2013). Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell , 155(7), 1545-1555. doi: 10.1016/j.cell.2013.11.020.

Liu J#, Dyer DH, Cheng J , Wang J, Wang S, Yang Z, ... & Hu W*. (2013). Aldose reductase from Schistosoma japonicum: crystallization and structure-based inhibitor screening for discovering antischistosomal lead compounds. Parasites & vectors , 6, 1-10. doi: 10.1186/1756-3305-6-162.

Cheng J #, Yang Y, Fang J, Xiao J, Zhu T, Chen F, ... & Xu Y*. (2013). Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein. Journal of Biological Chemistry , 288(2), 1329-1339. doi: 10.1074/jbc.M112.41539

Gong R#, Li L#, Liu Y#, Wang P, Yang H, Wang L, Cheng J , Guan K, Xu Y*. (2011). Crystal structure of the Gtr1p–Gtr2p complex reveals new insights into the amino acid-induced TORC1 activation. Genes & development  25(16), 1668-1673. doi: 10.1101/gad.16968011.

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