2025
Chua GNL, Beckwitt EC, Miller-Browne V, Yurieva O, Zhang D, Katch BJ, Watters JW, Abrantes K, Funabiki R, Zhao X#, O’Donnell ME#, Liu S#. A non-catalytic role for RFC in PCNA-mediated processive DNA synthesis. bioRxiv 10.1101/2025.08.08.669392. (In press at Cell)
Wang Y, Chen X, Kuemmecke M, Watters JW, Cohen JE, Xu Y#, Liu S#. Kinetic control of mammalian transcription elongation. Nature Structural & Molecular Biology (2025) doi: 10.1038/s41594-025-01707-1, Epub ahead of print
Nitsch S, Coraor AE, Schauer T, Wu Y, Sun J, Moritz N, Funke J, Nagpal H, Chua GNL, Battistini F, Lauberth SM, Richard E, Orozco M, Liu S, Desviat LR, Fierz B, Dietz H, Roeder RG, de Pablo JJ, Schneider R. H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations. Molecular Cell (2025) doi: 10.1016/j.molcel.2025.11.030, Epub ahead of print
Chang JTH*, Miller-Browne V*, Chua GNL, Zheng J, Beckwitt EC, Li S, Katch BJ, O’Donnell M, Liu S#, Zhao X#. Molecular determinants of Smc5/6 association with DNA junctions. (In press at Nature Communications)
2024
Chua GNL, Watters JW, Olinares PDB, Begum M, Vostal LE, Luo JA, Chait BT, Liu S#. Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes. Nature Structural & Molecular Biology (2024) 31: 1789-1797
NSMB Research Briefing: Chua GNL, Liu S. Dynamics of an epigenetic regulator on chromatin observed at the single-molecule level
Rockefeller News: “New insight into the protein mutations that cause Rett syndrome”
Rett Syndrome News: “MeCP2 protein more dynamic than known, new study into Rett finds”
Ng H*, Begum M*, Chua GNL*#, Liu S#. In situ nucleosome assembly for single-molecule correlative force and fluorescence microscopy. Journal of Visualized Experiments (2024) e66579
Chua GNL, Liu S#. When force met fluorescence: single-molecule manipulation and visualization of protein-DNA interactions. Annual Reviews Biophysics (2024) 53: 169-191
Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM#, Liu S#. Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. Nature (2024) 627, 424–430
Rockefeller News: "New Mtb study offers a novel paradigm for understanding bacterial transcription"
2023
Abini-Agbomson S, Gretarsson K, Shih RM, … Liu S, Lu C, Armache K-J#. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Molecular Cell (2023) 83 (16), 2872-2883. e7
Liu K, Grasso EM, Pu S, Zou M, Liu S, Eliezer D, Keeney S#. Structure and DNA-bridging activity of the essential Rec114-Mei4 trimer interface. Genes & Development (2023) 37 (11-12), 518-534
Wang L, Watters JW, Ju X, Lu G, Liu S#. Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination. Molecular Cell (2023) 83 (7), 1153-1164. e4
2022
Chang JT*, Li S*, Beckwitt EC, Than T, Haluska C, Chandanani J, O’Donnell ME, Zhao X#, Liu S#. Smc5/6’s multifaceted DNA binding capacities stabilize branched DNA structures. Nature Communications (2022) 13:7179
Li S, Wasserman MR, Yurieva O, Bai L, O’Donnell ME#, Liu S#. Origin recognition complex harbors an intrinsic nucleosome remodeling activity. Proceedings of the National Academy of Sciences of the United States of America (2022) 119:e2211568119
Li S, Wasserman MR, Yurieva O, Bai L, O'Donnell ME#, Liu S#. Nucleosome-directed replication origin licensing independent of a consensus DNA sequence. Nature Communications (2022) 13:4947
Editors’ Highlights: "Structural biology, biochemistry and biophysics"
Cao X, Liu K, Yan S, Li S, Li Y, Jin T#, Liu S#. Mechanical regulation of the helicase activity of Zika virus NS3. Biophysical Journal (2022) Dec 20;121(24):4900-4908
Nguyen T, Li S, Chang JT, Watters JW, Ng H, Osunsade A, David Y, Liu S. Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA. Nature Communications (2022) 13:3988
Editors’ Highlights: "Genetics, Genomics and Epigenetics"
Leicher R*, Osunsade A*, Chua GNL*, Faulkner SC*, Latham AP, Watters JW, Nguyen T, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y#, Liu S#. Single-stranded nucleic acid binding and coacervation by linker histone H1. Nature Structural & Molecular Biology (2022) 29(5):463-471 (Featured as journal cover)
Leicher R, Liu S. Probing the interaction between chromatin and chromatin-associated complexes with optical tweezers. Methods in Molecular Biology (2022) 2478:313-327
Mickolajczyk KJ, Olinares PDB, Chait BT, Liu S, Kapoor TM. The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates. eLife (2022) 11:e73534
2021
Bustamante CJ#, Chemla YR#, Liu S#, Wang MD#. Optical tweezers in single-molecule biophysics. Nature Reviews Methods Primers (2021) 1:25
PrimeView: "Optical tweezers in single-molecule biophysics"
Lin X, Leicher R, Liu S, Zhang B. Cooperative DNA looping by PRC2 complexes. Nucleic Acids Research (2021) 49:6238-6248
Mickolajczyk KJ*, Shelton PM*, Grasso M*, Cao X*, Warrington SE, Aher A, Liu S#, Kapoor TM#. Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase. Biophys J (2021) 120:1020-1030
Biophysical Society Newsroom: "A tool encoded in coronaviruses provides a potential target for COVID-19 and future coronavirus outbreaks"
Academic Times: "Coronavirus replication protein could be future treatment target"
2020
Leicher R, Ge EJ, Lin X, Reynolds MJ, Xie W, Walz T, Zhang B#, Muir TW, Liu S#. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Proceedings of the National Academy of Sciences of the United States of America (2020) 117:30465-30475
Mei L, Espinosa de Los Reyes S, Reynolds MJ, Leicher R, Liu S, Alushin GM. Molecular mechanism for direct actin force-sensing by α-catenin. eLife (2020) 9:e62514
Wang L*, Johnson ZL*, Wasserman MR*, Levring J*, Chen J#, Liu S#. Characterization of the kinetic cycle of an ABC transporter by single-molecule and cryo-EM analyses. eLife (2020) 9:e56451
2019
Li S, Zheng EB, Zhao L, Liu S. Nonreciprocal and conditional cooperativity directs the pioneer activity of pluripotency transcription factors. Cell Reports (2019) 28:2689-2703
Wasserman MR*, Schauer GD*, O'Donnell ME#, Liu S#. Replication fork activation is enabled by a single-stranded DNA gate in CMG helicase. Cell (2019) 178:600-611
Ju X, Li D, Liu S. Full-length RNA profiling reveals pervasive bidirectional transcription terminator in bacteria. Nature Microbiology (2019) 4:1907-1918
Wasserman MR, Liu S. A tour de force on the double helix: Exploiting DNA mechanics to study DNA-based molecular machines. Biochemistry (2019) 58:4667-4676
Zheng Q, Omans ND, Leicher R, Osunsade A, Agustinus AS, Finkin-Groner E, D’Ambrosio H, Liu B, Chandariapaty S, Liu S, David Y. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nature Communications (2019) 10:1289
Wang L, Mo CY, Wasserman MR, Rostol JT, Marraffini LA, Liu S. Dynamics of Cas10 govern discrimination between self and non-self in type III CRISPR-Cas immunity. Molecular Cell (2019) 73:278-290