Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale

  • Rao, SSP et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. cell 1591665–1680 (2014).

    CAS Article Google Scholar

  • Dixon, JR et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485376–380 (2012).

    CAS Article Google Scholar

  • Nora, EP et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485381–385 (2012).

    CAS Article Google Scholar

  • van Steensel, B. & Furlong, EEM The role of transcription in shaping the spatial organization of the genome. Wet. Rev. mole. Cell Biol. 20327–337 (2019).

    PubMed PubMed Central Google Scholar

  • Kosak, ST et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. science 296158–162 (2002).

    CAS Article Google Scholar

  • Dixon, JR et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518331–336 (2015).

    CAS Article Google Scholar

  • Amat, R. et al. Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock. Genome Res. 2918–28 (2019).

    CAS Article Google Scholar

  • Sima, J. et al. Identifying cis elements for spatiotemporal control of mammalian DNA replication. cell 176816–830.e18 (2019).

    CAS Article Google Scholar

  • Alipour, E. & Marko, JF Self-organization of domain structures by DNA loop-extruding enzymes. Nucleic Acids Res. 4011202–11212 (2012).

    CAS Article Google Scholar

  • Fudenberg, G., Abdennur, N., Imakaev, M., Goloborodko, A. & Mirny, LA Emerging evidence of chromosome folding by loop extrusion. Cold Spring Harb. Symp. Quant. bio. 8245–55 (2017).

    Article Google Scholar

  • Fudenberg, G. et al. Formation of chromosomal domains by loop extrusion. Cell Rep. 152038–2049 (2016).

    CAS Article Google Scholar

  • Sanborn, AL et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. proc. Natl Acad. sci. USA 112E6456–E6465 (2015).

    CAS PubMed PubMed Central Google Scholar

  • Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. science 2951306–1311 (2002).

    CAS Article Google Scholar

  • Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. science 326289–293 (2009).

    CAS Article Google Scholar

  • Krietenstein, N. et al. Ultrastructural details of mammalian chromosome architecture. mole. cell 78554–565.e7 (2020).

    CAS Article Google Scholar

  • Zhou, J. & Troyanskaya, OG Predicting effects of noncoding variants with deep learning–based sequence model. Wet. Methods 12931–934 (2015).

    CAS Article Google Scholar

  • Alipanahi, B., Delong, A., Weirauch, MT & Frey, BJ Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Wet. biotechnology. 33831–838 (2015).

    CAS Article Google Scholar

  • Kelley, DR, Snoek, J. & Rinn, JL Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res† https://doi.org/10.1101/gr.200535.115 (2016).

  • Zhou, J. et al. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Wet. Genet† https://doi.org/10.1038/s41588-018-0160-6 (2018).

  • Kelley, DR et al. Sequential regulatory activity prediction across chromosomes with convolutional neural networks. Genome Res. 28739–750 (2018).

    CAS Article Google Scholar

  • Chen, KM, Cofer, EM, Zhou, J. & Troyanskaya, OG Selene: a PyTorch-based deep learning library for sequence data. Wet. Methods† https://doi.org/10.1038/s41592-019-0360-8 (2019).

  • Avsec, Ž. et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Wet. Genet. 53354–366 (2021).

    CAS Article Google Scholar

  • Fudenberg, G., Kelley, D.R. & Pollard, K.S. Predicting 3D genome folding from DNA sequence with Akita. Wet. Methods 171111–1117 (2020).

    Article Google Scholar

  • Schwessinger, R. et al. DeepC: predicting 3D genome folding using megabase-scale transfer learning. Wet. Methods 171118–1124 (2020).

    CAS Article Google Scholar

  • Durand, NC et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell System. 399–101 (2016).

    CAS Article Google Scholar

  • Abdennur, N. & Mirny, LA Cooler: scalable storage for Hi-C data and other genomically labeled arrays. bioinformatics 36311–316 (2020).

    CAS Article Google Scholar

  • Chiang, C. et al. The impact of structural variation on human gene expression. Wet. Genet† https://doi.org/10.1038/ng.3834 (2017).

  • Zhang, D. et al. Alteration of genome folding via contact domain boundary insertion. Wet. Genet. 521076–1087 (2020).

    Article Google Scholar

  • Suzukawa, K. et al. Identification of a breakpoint cluster region 3′ of the ribophorin I gene at 3q21 associated with the transcriptional activation of the EVI1 gene in acute myelogenous leukemias with inv (3)(q21q26). blood. 842681–2688 (1994).

    CAS Article Google Scholar

  • Gröschel, S. et al. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. cell 157369–381 (2014).

    Article Google Scholar

  • Lupiáñez, DG et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. cell 1611012–1025 (2015).

    Article Google Scholar

  • Franke, M. et al. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 538265–269 (2016).

    CAS Article Google Scholar

  • Croft, B. et al. Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9. Wet. Communion. 95319 (2018).

    CAS Article Google Scholar

  • Young, RA Control of the embryonic stem cell state. cell 144940–954 (2011).

    CAS Article Google Scholar

  • Vierbuchen, T. et al. AP-1 transcription factors and the BAF complex mediate signal-dependent enhancer selection. mole. cell 681067–1082.e12 (2017).

    CAS Article Google Scholar

  • Rao, SSP et al. Cohesin loss eliminates all loop domains. cell† https://doi.org/10.1016/j.cell.2017.09.026 (2017).

  • Belaghzal, H. et al. Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Wet. Genet† https://doi.org/10.1038/s41588-021-00784-4 (2021).

  • Meuleman, W. et al. Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. Genome Res. 23270–280 (2013).

    CAS Article Google Scholar

  • Miga, KH et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature 58579–84 (2020).

    CAS Article Google Scholar

  • Logsdon, GA, Vollger, MR & Eichler, EE Long-read human genome sequencing and its applications. Wet. Rev. Genet. 21597–614 (2020).

    CAS Article Google Scholar

  • Vierstra, J. et al. Global reference mapping of human transcription factor footprints. Nature 583729–736 (2020).

    CAS Article Google Scholar

  • Chen, KM, Wong, AK, Troyanskaya, OG & Zhou, J. A sequence-based global map of regulatory activity for deciphering human genetics. preprint at bioRxiv† https://doi.org/10.1101/2021.07.29.454384 (2021).

  • Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Wet. Methods 9999–1003 (2012).

    CAS Article Google Scholar

  • Izmailov, P., Podoprikhin, D., Garipov, T., Vetrov, D. & Wilson, AG Averaging weights leads to wider optima and better generalization. Preprint at https://arxiv.org/abs/1803.05407 (2018).

  • Chen, T., Xu, B., Zhang, C. & Guestrin, C. Training deep nets with sublinear memory cost. Preprint at https://arxiv.org/abs/1604.06174 (2016).

  • Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46D1284 (2018).

    Article Google Scholar

  • Boix, CA, James, BT, Park, YP, Meuleman, W. & Kellis, M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature 590300–307 (2021).

    CAS Article Google Scholar

  • Leave a Reply

    Your email address will not be published.