RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing

References

[1] Roy, Sushmita, Alireza Fotuhi Siahpirani, Deborah Chasman, Sara Knaack, Ferhat Ay, Ron Stewart, Michael Wilson, and Rupa Sridharan. 2015. “A Predictive Modeling Approach for Cell Line-Specific Long-Range Regulatory Interactions.” Nucleic Acids Research 43: 8694-8712. https://doi.org/10.1093/nar/gkv865

[2] Dowen, Jill M., Zi Peng Fan, Denes Hnisz, Gang Ren, Brian J. Abraham, Lyndon N. Zhang, Abraham S. Weintraub, et al. 2014. “Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes.” Cell 159: 374-387. https://doi.org/10.1016/j.cell.2014.09.030

[3] Fullwood, Melissa J., Meihui Liu, Youfu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L. Orlov, et al. 2009. “An Oestrogen-Receptor-α-Bound Human Chromatin Interactome.” Nature 462: 58-64. https://doi.org/10.1038/nature08497

[4] Lieberman-Aiden, Erez, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, et al. 2009. “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.” Science 326: 289-293. https://doi.org/10.1126/science.1181369

[5] Mifsud, Borbala, Filipe Tavares-Cadete, Alice N. Young, Robert Sugar, Stefan Schoenfelder, Lauren Ferreira, Steven W. Wingett, et al. 2015. “Mapping Long-Range Promoter Contacts in Human Cells With High-Resolution Capture Hi-C.” Nature Genetics 47: 598-606. https://doi.org/10.1038/ng.3286

[6] Ma, Wenxiu, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, et al. 2015. “Fine-Scale Chromatin Interaction Maps Reveal the Cis-Regulatory Landscape of Human lincRNA Genes.” Nature Methods 12: 71-78. https://doi.org/10.1038/nmeth.3205

[7] Whalen, Sean, Rebecca M. Truty, and Katherine S. Pollard. 2016. “Enhancer-Promoter Interactions Are Encoded by Complex Genomic Signatures on Looping Chromatin.” Nature Genetics 48: 488-496. https://doi.org/10.1038/ng.3539

[8] Kai, Yan, Jaclyn Andricovich, Zhouhao Zeng, Jun Zhu, Alexandros Tzatsos, and Weiqun Peng. 2018. “Predicting CTCF-Mediated Chromatin Interactions by Integrating Genomic and Epigenomic Features.” Nature Communications 9: 4221. https://doi.org/10.1038/s41467-018-06664-6

[9] Cao, Fan, Yu Zhang, Yichao Cai, Sambhavi Animesh, Ying Zhang, Semih Can Akincilar, Yan Ping Loh, et al. 2021. “Chromatin Interaction Neural Network (ChINN): A Machine Learning-Based Method for Predicting Chromatin Interactions From DNA Sequences.” Genome Biology 22: 226. https://doi.org/10.1186/s13059-021-02453-5

[10] Fudenberg, Geoff, David R. Kelley, and Katherine S. Pollard. 2020. “Predicting 3D Genome Folding From DNA Sequence With Akita.” Nature Methods 17: 1111-1117. https://doi.org/10.1038/s41592-020-0958-x

[11] Zhou, Jian. 2022. “Sequence-Based Modeling of Three-Dimensional Genome Architecture From Kilobase to Chromosome Scale.” Nature Genetics 54: 725-734. https://doi.org/10.1038/s41588-022-01065-4

[12] Zhang, Ruochi, and Jian Ma. 2020. “MATCHA: Probing Multi-Way Chromatin Interaction With Hypergraph Representation Learning.” Cell Systems 10: 397-407.e5. https://doi.org/10.1016/j.cels.2020.04.004

[13] Marchal, Claire, Jiao Sima, and David M. Gilbert. 2019. “Control of DNA Replication Timing in the 3D Genome.” Nature Reviews Molecular Cell Biology 20: 721-737. https://doi.org/10.1038/s41580-019-0162-y

[14] Rao, Suhas S. P., Miriam H. Huntley, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, et al. 2014. “A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.” Cell 159: 1665-1680. https://doi.org/10.1016/j.cell.2014.11.021

[15] Tang, Zhonghui, Oscar Junhong Luo, Xingwang Li, Meizhen Zheng, Jacqueline Jufen Zhu, Przemyslaw Szalaj, Pawel Trzaskoma, et al. 2015. “CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.” Cell 163: 1611-1627. https://doi.org/10.1016/j.cell.2015.11.024

[16] Liu, Shuai, Yaqiang Cao, Kairong Cui, Qingsong Tang, and Keji Zhao. 2022. “Hi-TrAC Reveals Division of Labor of Transcription Factors in Organizing Chromatin Loops.” Nature Communications 13: 6679. https://doi.org/10.1038/s41467-022-34276-8

[17] Sanyal, Amartya, Bryan R. Lajoie, Gaurav Jain, and Job Dekker. 2012. “The Long-Range Interaction Landscape of Gene Promoters.” Nature 489: 109-113. https://doi.org/10.1038/nature11279

[18] Ryba, Tyrone, Dana Battaglia, Bill H. Chang, James W. Shirley, Quinton Buckley, Benjamin D. Pope, Meenakshi Devidas, Brian J. Druker, and David M. Gilbert. 2012. “Abnormal Developmental Control of Replication-Timing Domains in Pediatric Acute Lymphoblastic Leukemia.” Genome Research 22: 1833-1844. https://doi.org/10.1101/gr.138511.112

[19] Ranieri, Roberta, Giulia Pianigiani, Sofia Sciabolacci, Vincenzo Maria Perriello, Andrea Marra, Valeria Cardinali, Sara Pierangeli, et al. 2022. “Current Status and Future Perspectives in Targeted Therapy of NPM1-Nutated AML.” Leukemia 36: 2351-2367. https://doi.org/10.1038/s41375-022-01666-2

[20] Liu, Zhiyuan, Yujie Chen, Qimin Xia, Menghan Liu, Heming Xu, Yi Chi, Yujing Deng, and Dong Xing. 2023. “Linking Genome Structures to Functions by Simultaneous Single-Cell Hi-C and RNA-seq.” Science 380: 1070-1076. https://doi.org/10.1126/science.adg3797

RIGHTS & PERMISSIONS

2025 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.