ARGV: 3D genome structure exploration using augmented reality.
3D genome browser
3D genome organization
Augmented reality AR
Mobile app
Virtual reality VR
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
27 Aug 2024
27 Aug 2024
Historique:
received:
09
12
2023
accepted:
25
07
2024
medline:
28
8
2024
pubmed:
28
8
2024
entrez:
27
8
2024
Statut:
epublish
Résumé
Over the past two decades, scientists have increasingly realized the importance of the three-dimensional (3D) genome organization in regulating cellular activity. Hi-C and related experiments yield 2D contact matrices that can be used to infer 3D models of chromosome structure. Visualizing and analyzing genomes in 3D space remains challenging. Here, we present ARGV, an augmented reality 3D Genome Viewer. ARGV contains more than 350 pre-computed and annotated genome structures inferred from Hi-C and imaging data. It offers interactive and collaborative visualization of genomes in 3D space, using standard mobile phones or tablets. A user study comparing ARGV to existing tools demonstrates its benefits.
Identifiants
pubmed: 39192184
doi: 10.1186/s12859-024-05882-8
pii: 10.1186/s12859-024-05882-8
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
277Informations de copyright
© 2024. The Author(s).
Références
Bonev B, Cavalli G. Organization and function of the 3D genome. Nat Rev Genet. 2016;17(11):661–78.
pubmed: 27739532
doi: 10.1038/nrg.2016.112
Hsieh T-HS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ, Tjian R, Darzacq X. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol Cell. 2020;78(3):539–53.
pubmed: 32213323
pmcid: 7703524
doi: 10.1016/j.molcel.2020.03.002
Kim K, Jang I, Kim M, Choi J, Kim M-S, Lee B, Jung I. 3div update for 2021: a comprehensive resource of 3D genome and 3D cancer genome. Nucleic Acids Res. 2021;49(D1):D38–46.
pubmed: 33245777
doi: 10.1093/nar/gkaa1078
Ahmed M, Soares F, Xia J-H, Yang Y, Li J, Guo H, Peiran S, Tian Y, Lee HJ, Wang M, et al. Crispri screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer. Nat Commun. 2021;12(1):1781.
pubmed: 33741908
pmcid: 7979745
doi: 10.1038/s41467-021-21867-0
Dubois F, Sidiropoulos N, Weischenfeldt J, Beroukhim R. Structural variations in cancer and the 3D genome. Nat Rev Cancer. 2022;22(9):533–46.
pubmed: 35764888
pmcid: 10423586
doi: 10.1038/s41568-022-00488-9
Beagan JA, Phillips-Cremins JE. On the existence and functionality of topologically associating domains. Nat Genet. 2020;52(1):8–16.
pubmed: 31925403
pmcid: 7567612
doi: 10.1038/s41588-019-0561-1
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bradley Bernstein MA, Bender MG, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289–93.
pubmed: 19815776
pmcid: 2858594
doi: 10.1126/science.1181369
Beagrie RA, Scialdone A, Schueler M, Kraemer DCA, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas L-M, Branco MR, et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature. 2017;543(7646):519–24.
pubmed: 28273065
pmcid: 5366070
doi: 10.1038/nature21411
Hsieh T-HS, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping nucleosome resolution chromosome folding in yeast by Micro-C. Cell. 2015;162(1):108–19.
pubmed: 26119342
pmcid: 4509605
doi: 10.1016/j.cell.2015.05.048
Bintu B, Mateo LJ, Jun-Han S, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science. 2018;362(6413):eaau1783.
pubmed: 30361340
pmcid: 6535145
doi: 10.1126/science.aau1783
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Ming H, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80.
pubmed: 22495300
pmcid: 3356448
doi: 10.1038/nature11082
Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–80.
pubmed: 25497547
pmcid: 5635824
doi: 10.1016/j.cell.2014.11.021
Jerkovic I, Cavalli G. Understanding 3D genome organization by multidisciplinary methods. Nat Rev Mol Cell Biol. 2021;22(8):511–28.
pubmed: 33953379
doi: 10.1038/s41580-021-00362-w
MacKay K, Kusalik A. Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data. Brief Funct Genom. 2020;19(4):292–308.
doi: 10.1093/bfgp/elaa004
Varoquaux N, Ay F, Noble WS, Vert J-P. A statistical approach for inferring the 3D structure of the genome. Bioinformatics. 2014;30(12):i26–33.
pubmed: 24931992
pmcid: 4229903
doi: 10.1093/bioinformatics/btu268
Boninsegna L, Yildirim A, Polles G, Zhan Y, Quinodoz SA, Finn EH, Guttman M, Zhou XJ, Alber F. Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods. 2022;19(8):938–49.
pubmed: 35817938
pmcid: 9349046
doi: 10.1038/s41592-022-01527-x
Varoquaux N, Noble WS, Vert J-P. Inference of 3D genome architecture by modeling overdispersion of Hi-C data. Bioinformatics. 2023;39(1):btac838.
pubmed: 36594573
pmcid: 9857972
doi: 10.1093/bioinformatics/btac838
Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Stanley Fields C, Blau A, Noble WS. A three-dimensional model of the yeast genome. Nature. 2010;465(7296):363–7.
pubmed: 20436457
pmcid: 2874121
doi: 10.1038/nature08973
Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert J-P, Noble WS, Le Roch KG. Three-dimensional modeling of the p. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res. 2014;24(6):974–88.
pubmed: 24671853
pmcid: 4032861
doi: 10.1101/gr.169417.113
Rieber L, Mahony S. minimds: 3D structural inference from high-resolution Hi-C data. Bioinformatics. 2017;33(14):i261–6.
pubmed: 28882003
pmcid: 5870652
doi: 10.1093/bioinformatics/btx271
Zhang Y, Weiwei Liu Yu, Lin YK, Ng SL. Large-scale 3D chromatin reconstruction from chromosomal contacts. BMC Genom. 2019;20(2):129–41.
Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M. Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinform. 2011;12(1):1–16.
doi: 10.1186/1471-2105-12-414
Ming H, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol. 2013;9(1): e1002893.
doi: 10.1371/journal.pcbi.1002893
Zou C, Zhang Y, Ouyang Z. HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure. Genome Biol. 2016;17:1–14.
doi: 10.1186/s13059-016-0896-1
Butyaev A, Mavlyutov R, Blanchette M, Cudré-Mauroux P, Waldispühl J. A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data. Nucleic Acids Res. 2015;43(16): e103.
pubmed: 25990738
pmcid: 4652742
doi: 10.1093/nar/gkv476
Zhu X, Zhang Y, Wang Y, Tian D, Belmont AS, Swedlow JR, Ma J. Nucleome browser: an integrative and multimodal data navigation platform for 4d nucleome. Nat Methods. 2022;19(8):911–3.
pubmed: 35864167
pmcid: 9357120
doi: 10.1038/s41592-022-01559-3
Li D, Harrison JK, Purushotham D, Wang T. Exploring genomic data coupled with 3D chromatin structures using the Washu epigenome browser. Nat Methods. 2022;19(8):909–10.
pubmed: 35864166
doi: 10.1038/s41592-022-01550-y
Marti-Renom MA, Mirny LA. Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput Biol. 2011;7(7):1–6.
doi: 10.1371/journal.pcbi.1002125
Goodstadt NM, Marti-Renom MA. Challenges for visualizing three-dimensional data in genomic browsers. FEBS Lett. 2017;591(17):2505–19.
pubmed: 28771695
pmcid: 5638070
doi: 10.1002/1873-3468.12778
Goodstadt NM, Marti-Renom MA. Communicating genome architecture: biovisualization of the genome, from data analysis and hypothesis generation to communication and learning. J Mol Biol. 2019;431(6):1071–87.
pubmed: 30419242
doi: 10.1016/j.jmb.2018.11.008
Waldispühl J, Zhang E, Butyaev A, Nazarova E, Cyr Y. Storage, visualization, and navigation of 3D genomics data. Methods. 2018;142(74–80):06.
Ganapathy A. Virtual reality and augmented reality driven real estate world to buy properties. Asian J Humanit Art Lit. 2016;3(2):137–46.
doi: 10.18034/ajhal.v3i2.567
Farshid M, Paschen J, Eriksson T, Kietzmann J. Go boldly!: Explore augmented reality (AR), virtual reality (VR), and mixed reality (MR) for business. Bus Horiz. 2018;61(5):657–63.
doi: 10.1016/j.bushor.2018.05.009
Dhar P, Rocks T, Samarasinghe RM, Stephenson G, Smith C. Augmented reality in medical education: students’ experiences and learning outcomes. Med Educ Online. 2021;26(1):1953953.
pubmed: 34259122
pmcid: 8281102
doi: 10.1080/10872981.2021.1953953
Alsop T. Number of mobile augmented reality (AR) active user devices worldwide from 2019 to 2024. 02 2021.
Asbury TM, Mitman M, Jijun Tang W, Zheng J. Genome3d: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinform. 2010;11:444.
doi: 10.1186/1471-2105-11-444
Nowotny J, Wells A, Oluwadare O, Lingfei X, Cao R, Trieu T, He C, Cheng J. GMOL: an interactive tool for 3D genome structure visualization. Sci Rep. 2016;6:20802.
pubmed: 26868282
pmcid: 4751627
doi: 10.1038/srep20802
Trieu T, Oluwadare O, Wopata J, Cheng J. GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. Bioinformatics. 2019;35(8):1416–8.
Li R, Liu Y, Li T, Li C. 3Disease browser: a web server for integrating 3D genome and disease-associated chromosome rearrangement data. Sci Rep. 2016;6:34651.
pubmed: 27734896
pmcid: 5062081
doi: 10.1038/srep34651
Serra F, Baù D, Goodstadt M, Castillo D, Filion GJ, Marti-Renom MA. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. PLoS Comput Biol. 2017;13(7): e1005665.
pubmed: 28723903
pmcid: 5540598
doi: 10.1371/journal.pcbi.1005665
Todd S, Todd P, McGowan SJ, Hughes JR, Kakui Y, Leymarie FF, Latham W, Taylor S. Csynth: an interactive modelling and visualization tool for 3D chromatin structure. Bioinformatics. 2021;37(7):951–5.
pubmed: 32866221
doi: 10.1093/bioinformatics/btaa757
Wolle P, Muller MP, Rauh D. Augmented reality in scientific publications-taking the visualization of 3D structures to the next level. ACS Chem Biol. 2018;13(3):496–9.
pubmed: 29544257
doi: 10.1021/acschembio.8b00153
Yiu C-PB, Chen YW. Molecular data visualization with augmented reality (AR) on mobile devices. In: Structural genomics. Springer; 2021. p. 347–56.
Tang B, Li X, Li G, Tian D, Li F, Zhang Z. Delta.AR: An augmented reality-based visualization platform for 3D genome. Innovation. 2021;2(3): 100149.
pubmed: 34557786
pmcid: 8454738
Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’shea CC, Park PJ, Ren B, et al. The 4D nucleome project. Nature. 2017;549(7671):219–26.
pubmed: 28905911
pmcid: 5617335
doi: 10.1038/nature23884
Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Syst. 2018;6(2):256–8.
pubmed: 29428417
pmcid: 6047755
doi: 10.1016/j.cels.2018.01.001
Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K, et al. New developments on the encyclopedia of DNA elements (encode) data portal. Nucleic Acids Res. 2020;48(D1):D882–9.
pubmed: 31713622
doi: 10.1093/nar/gkz1062
Oluwadare O, Highsmith M, Turner D, Aiden EL, Cheng J. GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data. BMC Mol Cell Biol. 2020;21(1):1–10.
Davis AP, Wiegers TC, Johnson RJ, Sciaky D, Wiegers J, Mattingly CJ. Comparative toxicogenomics database (CTD): update 2023. Nucleic Acids Res. 2023;51(D1):D1257–62.
pubmed: 36169237
doi: 10.1093/nar/gkac833
Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1):1–12.
doi: 10.1186/s13059-018-1486-1
Trieu T, Cheng J. 3D genome structure modeling by Lorentzian objective function. Nucleic Acids Res. 2017;45(3):1049–58.
pubmed: 28180292
doi: 10.1093/nar/gkw1155
Zhang É, Drogaris C, Gédon A, Sossin A, Faraj R, Chen H, Cyr Y, Majewski J, Blanchette M, Waldispühl J. 3DGV: Immersive exploration of 3d genome structures using virtual reality. bioRxiv. 2019;page 855379.
open2c. open2c/distiller-nf: a modular hi-c mapping pipeline. GitHub, 2019.
Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012;9(10):999.
pubmed: 22941365
pmcid: 3816492
doi: 10.1038/nmeth.2148
Abdennur N, Mirny LA. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–6.
pubmed: 31290943
doi: 10.1093/bioinformatics/btz540
Cameron CJF, Dostie J, Blanchette M. HIFI: estimating DNA–DNA interaction frequency from Hi-C data at restriction-fragment resolution. Genome Biol. 2020;21(1):1–15.
doi: 10.1186/s13059-019-1913-y
Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, Zhou XJ. TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res. 2016;44(7):e70–e70.
pubmed: 26704975
doi: 10.1093/nar/gkv1505
Kruse K, Hug CB, Vaquerizas JM. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol. 2020;21(1):1–19.
doi: 10.1186/s13059-020-02215-9