MnM detects replication states and genomic subpopulations in single-cell DNA data, enabling accurate replication timing profiles from heterogeneous samples.

bioRxiv · Dec 26, 2023 · PreprintGenomics

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 Meléndez García, Xia Wu, Yaqun Liu, Stefano Gnan, Sami El-Hilali, Olivier Brison, Filippo Rosselli, Chun-Long Chen, Michelle Debatisse

The paper shows that ATR and DDK control TopBP1-mediated locking of dormant origins at the pre-IC stage, with compensation involving both passive and active processes.

bioRxiv · Nov 29, 2023 · PreprintGenetics

OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Yaqun Liu, Xia Wu, Yves d’Aubenton-Carafa, Claude Thermes, Chun-Long Chen

OKseqHMM measures genome-wide replication fork directionality using OK-Seq data and related techniques to study transcription-replication conflicts and genome instability.

Nucleic Acids Research · Dec 20, 2022Peer-reviewedBioinformatics

Cohesin-mediated loop anchors confine the location of human replication origins

Daniel J. Emerson, Peiyao A Zhao, Ashley L. Cook, R. Jordan Barnett, Kyle N. Klein, Dalila Saulebekova, Chunmin Ge, Linda Zhou, Zoltán Simándi, Miriam K. Minsk, Katelyn R. Titus, Weitao Wang, Wanfeng Gong, Di Zhang, Liyan Yang, , Jennifer E. Phillips‐Cremins

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

Nature · Jun 8, 2022Peer-reviewedGenomics

Kronos scRT: a uniform framework for single-cell replication timing analysis

Stefano Gnan, Joseph M. Josephides, Xia Wu, Manuela Spagnuolo, Dalila Saulebekova, Mylène Bohec, Marie Dumont, Laura G. Baudrin, Daniele Fachinetti, Sylvain Baulande, Chun-Long Chen

Kronos scRT enables single-cell replication timing analysis without cell sorting, analyzing thousands of cells from mouse and human cell lines.

Nature Communications · Apr 28, 2022Peer-reviewedGenomics

GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium

Stefano Gnan, Mélody Matelot, Marion Weiman, Olivier Arnaiz, Frédéric Guèrin, Linda Sperling, Mireille Bétermier, Claude Thermes, Chun-Long Chen, Sandra Duharcourt

Genome Research · Apr 1, 2022Peer-reviewedGenomics

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, Xiaopeng Zhu, Tyler M. Borrman, Alex R. Hastie, Zhiping Weng, John Bechhoefer, Chun-Long Chen, David M. Gilbert, Nick Rhind

This study uses Optical Replication Mapping to map human DNA replication initiation sites and finds that replication initiation is stochastic and not confined to specific origins.

Molecular Cell · Jun 21, 2021Peer-reviewedGenomics

Mechanism of in vivo activation of the MutLγ-Exo1 complex for meiotic crossover formation

Aurore Sanchez, Céline Adam, Felix Rauh, Yann Duroc, Lepakshi Ranjha, Bérangère Lombard, Xiaojing Mu, Mélody Wintrebert, Damarys Loew, Alba Guarné, Stefano Gnan, Chun-Long Chen, Scott Keeney, Petr Ćejka, Raphaël Guérois, , Valérie Borde

The paper identifies the role of the MutLγ-Exo1 complex in meiotic crossover formation by showing Exo1 recruits Cdc5 to activate MutLγ and highlights its spatial regulation near DSB hotspots.

Proceedings of the National Academy of Sciences · Nov 16, 2020Peer-reviewedMolecular Biology

Fragile X Mental Retardation Protein regulates R-loop formation and prevents global chromosome fragility

Arijita Chakraborty, Piroon Jenjaroenpun, Jing Li, Sami El-Hilali, Andrew McCulley, Brian K. Haarer, Elizabeth A. Hoffman, Aimee Belak, Audrey Thorland, Heidi Hehnly, Carl L. Schildkraut, Chun-Long Chen, Vladimir A. Kuznetsov, Wenyi Feng

This study shows FMRP prevents chromosome fragility by reducing R-loop formation and identifies novel FXS-susceptible genes.

Cell Reports · Sep 1, 2020Peer-reviewedGenomics

TRANSCRIPTION-MEDIATED ORGANIZATION OF THE REPLICATION INITIATION PROGRAM ACROSS LARGE GENES SETS UP COMMON FRAGILE SITES GENOME-WIDE

Olivier Brison, Sami El-Hilali, Dana Azar, Stéphane Koundrioukoff, Mélanie Schmidt, Viola Nähse, Yan Jaszczyszyn, Anne-Marie Lachagès, Bernard Dutrillaux, Claude Thermes, Michelle Debatisse, Chun-Long Chen

The paper shows that transcription suppresses replication initiation in large genes, leading to delayed replication and instability at common fragile sites.

Nature Communications · Dec 13, 2019Peer-reviewedGenomics

Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping

Kyle N. Klein, Weitao Wang, Tyler M. Borrman, Saki Chan, Denghong Zhang, Zhiping Weng, Alex R. Hastie, Chun-Long Chen, David M. Gilbert, Nick Rhind

This study identifies early-firing human replication origins in HeLa cells using Optical Replication Mapping, revealing that initiation occurs across broad zones rather than confined to efficient origins.

bioRxiv · Nov 6, 2017 · PreprintGenomics