Chunlong CHEN

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Publications

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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-05020639 v1
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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-05020622 v1
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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 Neumann et al.
Nucleic Acids Research, 2024, 52, pp.1136 - 1155. ⟨10.1093/nar/gkad1141⟩
Article dans une revue hal-04716990 v1
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The human pre-replication complex is an open complex

Jian Li , Jiangqing Dong , Weitao Wang , Daqi Yu , Xinyu Fan et al.
Cell, 2023, 186 (1), pp.98-111.e21. ⟨10.1016/j.cell.2022.12.008⟩
Article dans une revue hal-03974204 v1
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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-03974116 v2
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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 Hyrien et al.
Nature Protocols, 2023, 18 (4), pp.1260-1295. ⟨10.1038/s41596-022-00793-5⟩
Article dans une revue (data paper) hal-04265334 v1
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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 Garcia et al.
Nature Structural and Molecular Biology, 2023, ⟨10.1038/s41594-023-00949-1⟩
Article dans une revue (data paper) hal-04070726 v1
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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-03974130 v1
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Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers

Rachel Deweerd , Eszter Németh , Ádám Póti , Nataliya Petryk , Chun-Long Chen et al.
Cell Reports, 2022, 38 (12), pp.110555. ⟨10.1016/j.celrep.2022.110555⟩
Article dans une revue hal-03817515 v1
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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 Zhang et al.
Genome Biology, 2022, 23 (1), pp.251. ⟨10.1186/s13059-022-02821-9⟩
Article dans une revue hal-04304197 v1
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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 Klein et al.
Nature, 2022, 606 (7915), pp.812 - 819. ⟨10.1038/s41586-022-04803-0⟩
Article dans une revue hal-03840949 v1
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GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium

Stefano Gnan , Mélody Matelot , Marion Weiman , Olivier Arnaiz , Frédéric Guérin et al.
Genome Research, 2022, pp.699-709. ⟨10.1101/2021.08.05.455221⟩
Article dans une revue hal-03400776 v1
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Kronos scRT: a uniform framework for single-cell replication timing analysis

Stefano Gnan , Joseph M Josephides , Xia Wu , Manuela Spagnuolo , Dalila Saulebekova et al.
Nature Communications, 2022, 13 (1), pp.2329. ⟨10.1038/s41467-022-30043-x⟩
Article dans une revue hal-03840947 v2
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DNA molecular combing-based replication fork directionality profiling

Marion Blin , Laurent Lacroix , Nataliya Petryk , Yan Jaszczyszyn , Chun-Long Chen et al.
Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab219⟩
Article dans une revue hal-03195930 v1
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DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

Shengjun Tan , Huijing Ma , Jinbo Wang , Man Wang , Mengxia Wang et al.
Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-24585-9⟩
Article dans une revue hal-03436190 v1
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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 Marchal et al.
Molecular Cell, 2021, 81 (14), pp.2975 - 2988.e6. ⟨10.1016/j.molcel.2021.05.024⟩
Article dans une revue hal-03443178 v2
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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-03083175 v1
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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-03426812 v1
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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 Radvanyi et al.
Genome Medicine, 2020, 12 (1), ⟨10.1186/s13073-020-00781-y⟩
Article dans une revue hal-03015020 v1
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Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome

Arijita Chakraborty , Piroon Jenjaroenpun , Jing Li , Sami El Hilali , Andrew Mcculley et al.
Cell Reports, 2020, 32 (12), pp.108179. ⟨10.1016/j.celrep.2020.108179⟩
Article dans une revue hal-03015043 v1
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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-03015011 v1
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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 Gan et al.
Science Advances , 2020, 6 (35), pp.eabb5820. ⟨10.1126/sciadv.abb5820⟩
Article dans une revue hal-03015005 v1
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Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

Alexy Promonet , Ismaël Padioleau , Yaqun Liu , Lionel A. Sanz , Anna Biernacka et al.
Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-020-17858-2⟩
Article dans une revue hal-02931000 v1
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Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation.

Aurore Sanchez , Céline Adam , Felix Rauh , Yann Duroc , Lepakshi Ranjha et al.
Proceedings of the National Academy of Sciences of the United States of America, 2020, ⟨10.1073/pnas.2013012117⟩
Article dans une revue hal-03020386 v1
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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 Yang et al.
European Urology, 2019, 76 (1), pp.9-13. ⟨10.1016/j.eururo.2019.03.032⟩
Article dans une revue hal-02369388 v1
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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 Schmidt et al.
Nature Communications, 2019, 10, pp.5693. ⟨10.1038/s41467-019-13674-5⟩
Article dans une revue hal-02430920 v1
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Replication landscape of the human genome

Nataliya Petryk , Malik Kahli , Yves d'Aubenton-Carafa , Yan Jaszczyszyn , Yimin Shen et al.
Nature Communications, 2016, 7, ⟨10.1038/ncomms10208⟩
Article dans une revue hal-01412672 v1

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 Petryk et al.
New Journal of Physics, 2014, 16 (11), pp.115014. ⟨10.1088/1367-2630/16/11/115014⟩
Article dans une revue cea-01120311 v1
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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 Guilbaud et al.
Nature Protocols, 2013, 8 (1), pp.98-110. ⟨10.1038/nprot.2012.145⟩
Article dans une revue hal-01557077 v1

From Simple Bacterial and Archaeal Replicons to Replication N/U-Domains

Olivier Hyrien , Aurélien Rappailles , Guillaume Guilbaud , Antoine Baker , Chun-Long Chen et al.
Journal of Molecular Biology, 2013, 425 (23), pp.4673-4689. ⟨10.1016/j.jmb.2013.09.021⟩
Article dans une revue istex hal-01557075 v1

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-Carafa et 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-01557084 v1

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-Carafa et 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-01557082 v1
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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 Leleu et al.
PLoS Computational Biology, 2012, 8 (4), pp.e1002443. ⟨10.1371/journal.pcbi.1002443⟩
Article dans une revue inserm-00706043 v1

Replication-Associated Mutational Asymmetry in the Human Genome

C. L. Chen , L. Duquenne , B. Audit , G. Guilbaud , A. Rappailles et al.
Molecular Biology and Evolution, 2011, 28 (8), pp.2327-2337. ⟨10.1093/molbev/msr056⟩
Article dans une revue hal-01557088 v1
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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 Arneodo et al.
PLoS Computational Biology, 2011, 7 (12), pp.e1002322. ⟨10.1371/journal.pcbi.1002322⟩
Article dans une revue inserm-00691534 v1

Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes.

Chun-Long Chen , Aurélien Rappailles , Lauranne Duquenne , Maxime Huvet , Guillaume Guilbaud et al.
Genome Research, 2010, 20 (4), pp.447-57. ⟨10.1101/gr.098947.109⟩
Article dans une revue ensl-00517756 v1

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-00413942 v1

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 Karpowicz et al.
Science, 2007, 318 (5848), pp.245-50. ⟨10.1126/science.1143609⟩
Article dans une revue hal-00198837 v1

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. Karpowicz et al.
Science, 2007, 318, pp.245-250
Article dans une revue hal-00188075 v1