Chunlong CHEN

Publications

Article dans une revue (42)

m6A modification in R-loop homeostasis: a potential target for cancer therapeutics Minh-Anh Vu,Manuela Spagnuolo,Chun-Long Chen NAR Cancer, 2025, 7 (3), pp.zcaf022. ⟨10.1093/narcan/zcaf022⟩ Article dans une revue hal-05406805v1
Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression Joseph M Josephides,Chun-Long Chen Nature Communications, 2025, 16, ⟨10.1038/s41467-025-56783-0⟩ Article dans une revue hal-05020639v1
Targeting Autophagy plus High-Dose CDK4/6 Inhibitors in Advanced HR+HER2-Breast Cancer: A Phase 1b/2 Trial Chang Gong,Qun Lin,Tao Qin,Yinduo Zeng,Fei Xuet al. Med, 2025, 6 (5), pp.100559. ⟨10.1016/J.MEDJ.2024.11.012⟩ Article dans une revue hal-05406829v1
Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication Xiaoxuan Zhu,Atabek Bektash,Yuki Hatoyama,Sachiko Muramatsu,Shin-Ya Isobeet al. Nature Communications, 2025, 16, pp.10069. ⟨10.1038/s41467-025-66278-7⟩ Article dans une revue hal-05406812v1
Editorial: Epigenetic regulation of genome integrity and its implications in human diseases Zhiming Li,Xiao Chen,Chun-Long Chen Frontiers in Cell and Developmental Biology, 2024, 12, ⟨10.3389/fcell.2024.1535839⟩ Article dans une revue hal-05020622v1
DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks Lia M Pinto,Alexandros Pailas,Max Bondarchenko,Abhishek Bharadwaj Sharma,Katrin Neumannet al. Nucleic Acids Research, 2024, 52, pp.1136 - 1155. ⟨10.1093/nar/gkad1141⟩ Article dans une revue hal-04716990v1
The human pre-replication complex is an open complex Jian Li,Jiangqing Dong,Weitao Wang,Daqi Yu,Xinyu Fanet al. Cell, 2023, 186 (1), pp.98-111.e21. ⟨10.1016/j.cell.2022.12.008⟩ Article dans une revue hal-03974204v1
OKseqHMM: a genome-wide replication fork directionality analysis toolkit Yaqun Liu,Xia Wu,Yves D’aubenton-Carafa,Claude Thermes,Chun-Long Chen Nucleic Acids Research, 2023, pp.gkac1239. ⟨10.1093/nar/gkac1239⟩ Article dans une revue hal-03974116v2
Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing Xia Wu,Yaqun Liu,Yves D’aubenton-Carafa,Claude Thermes,Olivier Hyrienet al. Nature Protocols, 2023, 18 (4), pp.1260-1295. ⟨10.1038/s41596-022-00793-5⟩ Article dans une revue (data paper) hal-04265334v1
Mistimed origin licensing and activation stabilize common fragile sites under tight DNA-replication checkpoint activation Olivier Brison,Stefano Gnan,Dana Azar,Stéphane Koundrioukoff,Rodrigo Melendez Garciaet al. Nature Structural and Molecular Biology, 2023, ⟨10.1038/s41594-023-00949-1⟩ Article dans une revue (data paper) hal-04070726v1
Editorial: Chromosomal fragile sites, genome instability and human diseases Qing Hu,Advaitha Madireddy,Stefano Gnan,Chun-Long Chen Frontiers in Genetics, 2023, 13, ⟨10.3389/FGENE.2022.1119532⟩ Article dans une revue hal-03974130v1
Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum Chenyu Ma,Chunyan Li,Huijing Ma,Daqi Yu,Yufei Zhanget al. Genome Biology, 2022, 23 (1), pp.251. ⟨10.1186/s13059-022-02821-9⟩ Article dans une revue hal-04304197v1
Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers Rachel Deweerd,Eszter Németh,Ádám Póti,Nataliya Petryk,Chun-Long Chenet al. Cell Reports, 2022, 38 (12), pp.110555. ⟨10.1016/j.celrep.2022.110555⟩ Article dans une revue hal-03817515v1
Cohesin-mediated loop anchors confine the locations of human replication origins Daniel J Emerson,Peiyao A Zhao,Ashley L Cook,R. Jordan Barnett,Kyle N Kleinet al. Nature, 2022, 606 (7915), pp.812 - 819. ⟨10.1038/s41586-022-04803-0⟩ Article dans une revue hal-03840949v1
Kronos scRT: a uniform framework for single-cell replication timing analysis Stefano Gnan,Joseph M Josephides,Xia Wu,Manuela Spagnuolo,Dalila Saulebekovaet al. Nature Communications, 2022, 13 (1), pp.2329. ⟨10.1038/s41467-022-30043-x⟩ Article dans une revue hal-03840947v2
GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium Stefano Gnan,Mélody Matelot,Marion Weiman,Olivier Arnaiz,Frédéric Guérinet al. Genome Research, 2022, pp.699-709. ⟨10.1101/2021.08.05.455221⟩ Article dans une revue hal-03400776v1
DNA molecular combing-based replication fork directionality profiling Marion Blin,Laurent Lacroix,Nataliya Petryk,Yan Jaszczyszyn,Chun-Long Chenet al. Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab219⟩ Article dans une revue hal-03195930v1
Topoisomerase I prevents transcription-replication conflicts at transcription termination sites Yaqun Liu,Yea-Lih Lin,Philippe Pasero,Chun-Long Chen Molecular & Cellular Oncology, 2021, 8 (1), pp.e1843951-3. ⟨10.1080/23723556.2020.1843951⟩ Article dans une revue hal-03083175v1
Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication Weitao Wang,Kyle N Klein,Karel Proesmans,Hongbo Yang,Claire Marchalet al. Molecular Cell, 2021, 81 (14), pp.2975 - 2988.e6. ⟨10.1016/j.molcel.2021.05.024⟩ Article dans une revue hal-03443178v2
DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans Shengjun Tan,Huijing Ma,Jinbo Wang,Man Wang,Mengxia Wanget al. Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-24585-9⟩ Article dans une revue hal-03436190v1
Editorial: DNA Replication Stress and Cell Fate Lin Deng,Chun-Long Chen,Yuanliang Zhai,Yunzhou Dong,Huiqiang Lou Frontiers in Cell and Developmental Biology, 2021, 9, ⟨10.3389/fcell.2021.778486⟩ Article dans une revue hal-03426812v1
Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer Ming-Jun Shi,Xiang-Yu Meng,Jacqueline Fontugne,Chun-Long Chen,François Radvanyiet al. Genome Medicine, 2020, 12 (1), ⟨10.1186/s13073-020-00781-y⟩ Article dans une revue hal-03015020v1
Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome Arijita Chakraborty,Piroon Jenjaroenpun,Jing Li,Sami El Hilali,Andrew Mcculleyet al. Cell Reports, 2020, 32 (12), pp.108179. ⟨10.1016/j.celrep.2020.108179⟩ Article dans une revue hal-03015043v1
The impact of transcription-mediated replication stress on genome instability and human disease Stefano Gnan,Yaqun Liu,Manuela Spagnuolo,Chun-Long Chen Genome Instability & Disease, 2020, 1 (5), pp.207-234. ⟨10.1007/s42764-020-00021-y⟩ Article dans une revue hal-03015011v1
DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands Zhiming Li,Xu Hua,Albert Serra-Cardona,Xiaowei Xu,Songlin Ganet al. Science Advances , 2020, 6 (35), pp.eabb5820. ⟨10.1126/sciadv.abb5820⟩ Article dans une revue hal-03015005v1
Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation. Aurore Sanchez,Céline Adam,Felix Rauh,Yann Duroc,Lepakshi Ranjhaet al. Proceedings of the National Academy of Sciences of the United States of America, 2020, ⟨10.1073/pnas.2013012117⟩ Article dans une revue hal-03020386v1
Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites Alexy Promonet,Ismaël Padioleau,Yaqun Liu,Lionel A. Sanz,Anna Biernackaet al. Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-020-17858-2⟩ Article dans une revue hal-02931000v1
APOBEC-mediated Mutagenesis as a Likely Cause of FGFR3 S249C Mutation Over-representation in Bladder Cancer Ming-Jun Shi,Xiang-Yu Meng,Philippe Lamy,A. Rouf Banday,Jie Yanget al. European Urology, 2019, 76 (1), pp.9-13. ⟨10.1016/j.eururo.2019.03.032⟩ Article dans une revue hal-02369388v1
Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide Olivier Brison,Sami El-Hilali,Dana Azar,Stéphane Koundrioukoff,Mélanie Schmidtet al. Nature Communications, 2019, 10, pp.5693. ⟨10.1038/s41467-019-13674-5⟩ Article dans une revue hal-02430920v1
Replication landscape of the human genome Nataliya Petryk,Malik Kahli,Yves d'Aubenton-Carafa,Yan Jaszczyszyn,Yimin Shenet al. Nature Communications, 2016, 7, ⟨10.1038/ncomms10208⟩ Article dans une revue hal-01412672v1
From the chromatin interaction network to the organization of the human genome into replication N/U-domains Rasha E Boulos,Hanna Julienne,Antoine Baker,Chun-Long Chen,Nataliya Petryket al. New Journal of Physics, 2014, 16 (11), pp.115014. ⟨10.1088/1367-2630/16/11/115014⟩ Article dans une revue cea-01120311v1
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm Benjamin Audit,Antoine Baker,Chun-Long Chen,Aurélien Rappailles,Guillaume Guilbaudet al. Nature Protocols, 2013, 8 (1), pp.98-110. ⟨10.1038/nprot.2012.145⟩ Article dans une revue hal-01557077v1
From Simple Bacterial and Archaeal Replicons to Replication N/U-Domains Olivier Hyrien,Aurélien Rappailles,Guillaume Guilbaud,Antoine Baker,Chun-Long Chenet al. Journal of Molecular Biology, 2013, 425 (23), pp.4673-4689. ⟨10.1016/j.jmb.2013.09.021⟩ Article dans une revue istex hal-01557075v1
Linking the DNA strand asymmetry to the spatio-temporal replication program II. Accounting for neighbor-dependent substitution rates A. Baker,C. L. Chen,H. Julienne,B. Audit,Y. d'Aubenton-Carafaet al. European Physical Journal E: Soft matter and biological physics, 2012, 35 (11), pp.12. ⟨10.1140/epje/i2012-12123-9⟩ Article dans une revue hal-01557084v1
Linking the DNA strand asymmetry to the spatio-temporal replication program I. About the role of the replication fork polarity in genome evolution A. Baker,H. Julienne,C. L. Chen,B. Audit,Y. d'Aubenton-Carafaet al. European Physical Journal E: Soft matter and biological physics, 2012, 35 (9), pp.25. ⟨10.1140/epje/i2012-12092-y⟩ Article dans une revue hal-01557082v1
Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. Antoine Baker,Benjamin Audit,Chun-Long Chen,Benoit Moindrot,Antoine Leleuet al. PLoS Computational Biology, 2012, 8 (4), pp.e1002443. ⟨10.1371/journal.pcbi.1002443⟩ Article dans une revue inserm-00706043v1
Replication-Associated Mutational Asymmetry in the Human Genome C. L. Chen,L. Duquenne,B. Audit,G. Guilbaud,A. Rappailleset al. Molecular Biology and Evolution, 2011, 28 (8), pp.2327-2337. ⟨10.1093/molbev/msr056⟩ Article dans une revue hal-01557088v1
Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. Guillaume Guilbaud,Aurélien Rappailles,Antoine Baker,Chun-Long Chen,Alain Arneodoet al. PLoS Computational Biology, 2011, 7 (12), pp.e1002322. ⟨10.1371/journal.pcbi.1002322⟩ Article dans une revue inserm-00691534v1
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Chun-Long Chen,Aurélien Rappailles,Lauranne Duquenne,Maxime Huvet,Guillaume Guilbaudet al. Genome Research, 2010, 20 (4), pp.447-57. ⟨10.1101/gr.098947.109⟩ Article dans une revue ensl-00517756v1
Genome-Wide Evolutionary Analysis of the Non-Coding RNA Genes and Non-Coding DNA of Paramecium tetraurelia. Chen C.L.,H. Zhou,Liao J.Y.,Qu L.H.,Laurence Amar RNA, 2009, 15(4), pp.503-14 Article dans une revue hal-00413942v1
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Sabeeha S Merchant,Simon E Prochnik,Olivier Vallon,Elizabeth H Harris,Steven J Karpowiczet al. Science, 2007, 318 (5848), pp.245-50. ⟨10.1126/science.1143609⟩ Article dans une revue hal-00198837v1
The Chlamydomonas genome reveals the evolution of key animal and plant functions S.S. Merchant,S.E. Prochnik,O. Vallon,E.H. Harris,S.J. Karpowiczet al. Science, 2007, 318, pp.245-250 Article dans une revue hal-00188075v1

Pré-publication, Document de travail (3)

The balance between ATR and DDK activities controls TopBP1-mediated locking of dormant origins at the pre-IC stage Stéphane Koundrioukoff,Su-Jung Kim,Nathan Alary,Antoine Toffano,Rodrigo Melendez-Garciaet al. 2024 Pré-publication, Document de travail hal-04754215v1
MnM: a machine learning approach to detect replication states and genomic subpopulations for single-cell DNA replication timing disentanglement Joseph M Josephides,Chun-Long Chen 2023 Pré-publication, Document de travail hal-04794817v1
Unscheduled origin building in S-phase upon tight CDK1 inhibition suppresses CFS instability Olivier Brison,Stefano Gnan,Dana Azar,Mélanie Schmidt,Stéphane Koundrioukoffet al. 2021 Pré-publication, Document de travail hal-03443067v1