{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T12:21:03Z","timestamp":1762604463435,"version":"3.41.2"},"reference-count":79,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T00:00:00Z","timestamp":1715126400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Topologically associating domain (TAD) reorganization commonly occurs in the cell nucleus and contributes to gene activation and inhibition through the separation or fusion of adjacent TADs. However, functional genes impacted by TAD alteration and the underlying mechanism of TAD reorganization regulating gene transcription remain to be fully elucidated. Here, we first developed a novel approach termed Inter3D to specifically identify genes regulated by TAD reorganization. Our study revealed that the segregation of TADs led to the disruption of intrachromosomal looping at the myosin light chain 12B (MYL12B) locus, via the meticulous reorganization of TADs mediating epigenomic landscapes within tumor cells, thereby exhibiting a significant correlation with the down-regulation of its transcriptional activity. Conversely, the fusion of TADs facilitated intrachromosomal interactions, suggesting a potential association with the activation of cytochrome P450 family 27 subfamily B member 1 (CYP27B1). Our study provides comprehensive insight into the capture of TAD rearrangement-mediated gene loci and moves toward understanding the functional role of TAD reorganization in gene transcription. The Inter3D pipeline developed in this study is freely available at https:\/\/github.com\/bm2-lab\/inter3D and https:\/\/ngdc.cncb.ac.cn\/biocode\/tool\/BT7399.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae034","type":"journal-article","created":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T18:19:37Z","timestamp":1715192377000},"source":"Crossref","is-referenced-by-count":3,"title":["Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9092-0262","authenticated-orcid":false,"given":"Tianyi","family":"Ding","sequence":"first","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1707-5474","authenticated-orcid":false,"given":"Shaliu","family":"Fu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0242-8118","authenticated-orcid":false,"given":"Xiaoyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5444-1621","authenticated-orcid":false,"given":"Fan","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-5520-4229","authenticated-orcid":false,"given":"Jixing","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2303-5532","authenticated-orcid":false,"given":"Haowen","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6331-9148","authenticated-orcid":false,"given":"Jiaqi","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-3762-1840","authenticated-orcid":false,"given":"Chaoqun","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1549-0553","authenticated-orcid":false,"given":"Yibing","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-5606-7270","authenticated-orcid":false,"given":"Yiran","family":"Bai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6232-6345","authenticated-orcid":false,"given":"Wannian","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2804-6463","authenticated-orcid":false,"given":"Xindi","family":"Chang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7287-3642","authenticated-orcid":false,"given":"Shanjin","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6418-8370","authenticated-orcid":false,"given":"Chao","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2578-1221","authenticated-orcid":false,"given":"Qi","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9954-4451","authenticated-orcid":false,"given":"He","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University , Shanghai 200092,","place":["China"]},{"name":"Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Medical Department of Jinggangshan University, Ji'an 343009,","place":["China"]},{"name":"School of Life Science, Jinggangshan University, Ji'an 343009,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2024,5,8]]},"reference":[{"key":"2024101204455385700_qzae034-B1","doi-asserted-by":"crossref","first-page":"eaaw9498","DOI":"10.1126\/science.aaw9498","article-title":"Molecular basis and biological function of variability in spatial genome organization","volume":"365","author":"Finn","year":"2019","journal-title":"Science"},{"key":"2024101204455385700_qzae034-B2","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1016\/j.cell.2019.01.020","article-title":"Extensive heterogeneity and intrinsic variation in spatial genome organization","volume":"176","author":"Finn","year":"2019","journal-title":"Cell"},{"key":"2024101204455385700_qzae034-B3","doi-asserted-by":"crossref","first-page":"e25776","DOI":"10.7554\/eLife.25776","article-title":"CTCF and cohesin regulate chromatin loop stability with distinct dynamics","volume":"6","author":"Hansen","year":"2017","journal-title":"Elife"},{"key":"2024101204455385700_qzae034-B4","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/s41576-019-0195-2","article-title":"Methods for mapping 3D chromosome architecture","volume":"21","author":"Kempfer","year":"2020","journal-title":"Nat Rev Genet"},{"key":"2024101204455385700_qzae034-B5","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/s41580-021-00362-w","article-title":"Understanding 3D genome organization by multidisciplinary methods","volume":"22","author":"Jerkovic","year":"2021","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024101204455385700_qzae034-B6","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s13059-022-02687-x","article-title":"3D genome organization in the epithelial-mesenchymal transition spectrum","volume":"23","author":"Pang","year":"2022","journal-title":"Genome Biol"},{"key":"2024101204455385700_qzae034-B7","first-page":"97","article-title":"Altered expression of the retinoblastoma gene product in human high grade non-Hodgkin\u2019s lymphomas","volume":"8","author":"Weide","year":"1994","journal-title":"Leukemia"},{"key":"2024101204455385700_qzae034-B8","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","article-title":"Disruptions of topological chromatin domains cause pathogenic rewiring of gene\u2013enhancer interactions","volume":"161","author":"Lupianez","year":"2015","journal-title":"Cell"},{"key":"2024101204455385700_qzae034-B9","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1016\/j.stem.2021.04.023","article-title":"Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions","volume":"28","author":"Wang","year":"2021","journal-title":"Cell Stem Cell"},{"key":"2024101204455385700_qzae034-B10","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/s41586-021-04081-2","article-title":"Cell-type specialization is encoded by specific chromatin topologies","volume":"599","author":"Winick-Ng","year":"2021","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B11","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B12","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2024101204455385700_qzae034-B13","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.tig.2022.12.003","article-title":"Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains","volume":"39","author":"Yeo","year":"2023","journal-title":"Trends Genet"},{"key":"2024101204455385700_qzae034-B14","doi-asserted-by":"crossref","first-page":"110601","DOI":"10.1016\/j.celrep.2022.110601","article-title":"Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states","volume":"38","author":"Esposito","year":"2022","journal-title":"Cell Rep"},{"key":"2024101204455385700_qzae034-B15","doi-asserted-by":"crossref","first-page":"3082","DOI":"10.1016\/j.molcel.2021.06.008","article-title":"Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression","volume":"81","author":"Vos","year":"2021","journal-title":"Mol Cell"},{"key":"2024101204455385700_qzae034-B16","doi-asserted-by":"crossref","first-page":"10524","DOI":"10.1093\/nar\/gkab249","article-title":"Suppression of liquid\u2013liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells","volume":"49","author":"Ulianov","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024101204455385700_qzae034-B17","doi-asserted-by":"crossref","first-page":"eaau1783","DOI":"10.1126\/science.aau1783","article-title":"Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells","volume":"362","author":"Bintu","year":"2018","journal-title":"Science"},{"key":"2024101204455385700_qzae034-B18","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.15252\/embj.201798004","article-title":"Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins","volume":"36","author":"Wutz","year":"2017","journal-title":"EMBO J"},{"key":"2024101204455385700_qzae034-B19","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1038\/s41586-019-1910-z","article-title":"The structural basis for cohesin-CTCF-anchored loops","volume":"578","author":"Li","year":"2020","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B20","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2017.04.013","article-title":"The cohesin release factor WAPL restricts chromatin loop extension","volume":"169","author":"Haarhuis","year":"2017","journal-title":"Cell"},{"key":"2024101204455385700_qzae034-B21","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/nature09380","article-title":"Mediator and cohesin connect gene expression and chromatin architecture","volume":"467","author":"Kagey","year":"2010","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B22","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/s41580-021-00349-7","article-title":"Genome folding through loop extrusion by SMC complexes","volume":"22","author":"Davidson","year":"2021","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024101204455385700_qzae034-B23","doi-asserted-by":"crossref","first-page":"msac216","DOI":"10.1093\/molbev\/msac216","article-title":"Mode and tempo of 3D genome evolution in Drosophila","volume":"39","author":"Torosin","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2024101204455385700_qzae034-B24","doi-asserted-by":"crossref","first-page":"eade0090","DOI":"10.1126\/sciadv.ade0090","article-title":"Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements","volume":"9","author":"Kahn","year":"2023","journal-title":"Sci Adv"},{"key":"2024101204455385700_qzae034-B25","doi-asserted-by":"crossref","first-page":"eade1085","DOI":"10.1126\/sciadv.ade1085","article-title":"CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles","volume":"9","author":"Cavalheiro","year":"2023","journal-title":"Sci Adv"},{"key":"2024101204455385700_qzae034-B26","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1038\/s41586-022-04803-0","article-title":"Cohesin-mediated loop anchors confine the locations of human replication origins","volume":"606","author":"Emerson","year":"2022","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B27","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.cell.2012.01.010","article-title":"Three-dimensional folding and functional organization principles of the Drosophila genome","volume":"148","author":"Sexton","year":"2012","journal-title":"Cell"},{"key":"2024101204455385700_qzae034-B28","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/s41588-019-0561-1","article-title":"On the existence and functionality of topologically associating domains","volume":"52","author":"Beagan","year":"2020","journal-title":"Nat Genet"},{"key":"2024101204455385700_qzae034-B29","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/s41467-018-03017-1","article-title":"Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries","volume":"9","author":"Gong","year":"2018","journal-title":"Nat Commun"},{"key":"2024101204455385700_qzae034-B30","doi-asserted-by":"crossref","first-page":"852","DOI":"10.15252\/msb.20156492","article-title":"Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation","volume":"11","author":"Fraser","year":"2015","journal-title":"Mol Syst Biol"},{"key":"2024101204455385700_qzae034-B31","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-021-04246-z","article-title":"Targeting SWI\/SNF ATPases in enhancer-addicted prostate cancer","volume":"601","author":"Xiao","year":"2022","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B32","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/gkab1242","article-title":"CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates","volume":"50","author":"Lee","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024101204455385700_qzae034-B33","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41586-021-03662-5","article-title":"Phase separation drives aberrant chromatin looping and cancer development","volume":"595","author":"Ahn","year":"2021","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B34","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1016\/j.ccell.2021.04.001","article-title":"STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and\u00a0EWSR1\u2013FLI1\u00a0activity in Ewing sarcoma","volume":"39","author":"Surdez","year":"2021","journal-title":"Cancer Cell"},{"key":"2024101204455385700_qzae034-B35","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.molcel.2018.05.032","article-title":"Polycomb-dependent chromatin looping contributes to gene silencing during Drosophila development","volume":"71","author":"Ogiyama","year":"2018","journal-title":"Mol Cell"},{"key":"2024101204455385700_qzae034-B36","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1126\/science.aau0320","article-title":"Developmental enhancers and chromosome topology","volume":"361","author":"Furlong","year":"2018","journal-title":"Science"},{"key":"2024101204455385700_qzae034-B37","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nmeth.4396","article-title":"An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues","volume":"14","author":"Corces","year":"2017","journal-title":"Nat Methods"},{"key":"2024101204455385700_qzae034-B38","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2024101204455385700_qzae034-B39","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024101204455385700_qzae034-B40","doi-asserted-by":"crossref","first-page":"9354","DOI":"10.1038\/s41598-019-45839-z","article-title":"The ENCODE blacklist: identification of problematic regions of the genome","volume":"9","author":"Amemiya","year":"2019","journal-title":"Sci Rep"},{"key":"2024101204455385700_qzae034-B41","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2024101204455385700_qzae034-B42","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol"},{"key":"2024101204455385700_qzae034-B43","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1214\/11-AOAS466","article-title":"Measuring reproducibility of high-throughput experiments","volume":"5","author":"Li","year":"2011","journal-title":"Ann Appl Stat"},{"key":"2024101204455385700_qzae034-B44","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2024101204455385700_qzae034-B45","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2024101204455385700_qzae034-B46","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2024101204455385700_qzae034-B47","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"HiC-Pro: an optimized and flexible pipeline for Hi-C data processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biol"},{"key":"2024101204455385700_qzae034-B48","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1101\/gr.220640.117","article-title":"HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient","volume":"27","author":"Yang","year":"2017","journal-title":"Genome Res"},{"key":"2024101204455385700_qzae034-B49","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1038\/s41586-020-2493-4","article-title":"Expanded encyclopaedias of DNA elements in the human and mouse genomes","volume":"583","author":"ENCODE Project Consortium","year":"2020","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B50","doi-asserted-by":"crossref","first-page":"i474","DOI":"10.1093\/bioinformatics\/btaa403","article-title":"TopicNet: a framework for measuring transcriptional regulatory network change","volume":"36","author":"Lou","year":"2020","journal-title":"Bioinformatics"},{"key":"2024101204455385700_qzae034-B51","doi-asserted-by":"crossref","first-page":"4826","DOI":"10.1038\/s41467-020-18527-0","article-title":"A predictable conserved DNA base composition signature defines human core DNA replication origins","volume":"11","author":"Akerman","year":"2020","journal-title":"Nat Commun"},{"key":"2024101204455385700_qzae034-B52","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res"},{"key":"2024101204455385700_qzae034-B53","doi-asserted-by":"crossref","first-page":"2368","DOI":"10.1093\/molbev\/msw108","article-title":"Spatial colocalization of human ohnolog pairs acts to maintain dosage-balance","volume":"33","author":"Xie","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2024101204455385700_qzae034-B54","doi-asserted-by":"crossref","first-page":"11184","DOI":"10.1093\/nar\/gky753","article-title":"Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers","volume":"46","author":"Fu","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024101204455385700_qzae034-B55","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1007\/s00125-017-4254-y","article-title":"Hyperglycaemic memory affects the neurovascular unit of the retina in a diabetic mouse model","volume":"60","author":"Friedrichs","year":"2017","journal-title":"Diabetologia"},{"key":"2024101204455385700_qzae034-B56","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1210\/er.2016-1070","article-title":"Vitamin D-mediated hypercalcemia: mechanisms, diagnosis, and treatment","volume":"37","author":"Tebben","year":"2016","journal-title":"Endocr Rev"},{"key":"2024101204455385700_qzae034-B57","doi-asserted-by":"crossref","first-page":"e1008278","DOI":"10.1371\/journal.pgen.1008278","article-title":"Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates","volume":"15","author":"Eres","year":"2019","journal-title":"PLoS Genet"},{"key":"2024101204455385700_qzae034-B58","doi-asserted-by":"crossref","first-page":"e2203452119","DOI":"10.1073\/pnas.2203452119","article-title":"3D chromatin remodeling potentiates transcriptional programs driving cell invasion","volume":"119","author":"Lebeau","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024101204455385700_qzae034-B59","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1016\/j.apsb.2021.09.010","article-title":"The generation of PD-L1 and PD-L2 in cancer cells: from nuclear chromatin reorganization to extracellular presentation","volume":"12","author":"Fan","year":"2022","journal-title":"Acta Pharm Sin B"},{"key":"2024101204455385700_qzae034-B60","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/ng.3722","article-title":"Pan-cancer analysis of somatic copy-number alterations implicates\u00a0IRS4\u00a0and\u00a0IGF2\u00a0in enhancer hijacking","volume":"49","author":"Weischenfeldt","year":"2017","journal-title":"Nat Genet"},{"key":"2024101204455385700_qzae034-B61","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/s41588-022-01117-9","article-title":"In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation","volume":"54","author":"Anania","year":"2022","journal-title":"Nat Genet"},{"key":"2024101204455385700_qzae034-B62","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1038\/s41588-019-0466-z","article-title":"Functional dissection of the Sox9\u2013Kcnj2 locus identifies nonessential and instructive roles of TAD architecture","volume":"51","author":"Despang","year":"2019","journal-title":"Nat Genet"},{"key":"2024101204455385700_qzae034-B63","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1016\/j.cell.2017.05.004","article-title":"Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization","volume":"169","author":"Nora","year":"2017","journal-title":"Cell"},{"key":"2024101204455385700_qzae034-B64","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1016\/j.annonc.2020.02.002","article-title":"Epigenetic modulations and lineage plasticity in advanced prostate cancer","volume":"31","author":"Ge","year":"2020","journal-title":"Ann Oncol"},{"key":"2024101204455385700_qzae034-B65","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1038\/s41580-022-00464-z","article-title":"Pioneer factors as master regulators of the epigenome and cell fate","volume":"23","author":"Balsalobre","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024101204455385700_qzae034-B66","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/s13578-019-0347-2","article-title":"CTCF and cellular heterogeneity","volume":"9","author":"Ren","year":"2019","journal-title":"Cell Biosci"},{"key":"2024101204455385700_qzae034-B67","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/s41573-020-0077-5","article-title":"Targeting the epigenetic regulation of antitumour immunity","volume":"19","author":"Hogg","year":"2020","journal-title":"Nat Rev Drug Discov"},{"key":"2024101204455385700_qzae034-B68","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1016\/j.molcel.2018.06.044","article-title":"Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data","volume":"71","author":"Pliner","year":"2018","journal-title":"Mol Cell"},{"key":"2024101204455385700_qzae034-B69","first-page":"e21529","article-title":"HBx-upregulated MAFG-AS1 promotes cell proliferation and migration of hepatoma cells by enhancing MAFG expression and stabilizing nonmuscle myosin IIA","volume":"35","author":"Zhang","year":"2021","journal-title":"FASEB J"},{"key":"2024101204455385700_qzae034-B70","doi-asserted-by":"crossref","first-page":"801","DOI":"10.3390\/nu12030801","article-title":"Single nucleotide polymorphisms in 25-hydroxyvitamin D3 1-alpha-hydroxylase (CYP27B1) gene: the risk of malignant tumors and other chronic diseases","volume":"12","author":"Latacz","year":"2020","journal-title":"Nutrients"},{"key":"2024101204455385700_qzae034-B71","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1002\/gcc.20122","article-title":"CDK4 is a probable target gene in a novel amplicon at 12q13.3\u2013q14.1 in lung cancer","volume":"42","author":"Wikman","year":"2005","journal-title":"Genes Chromosomes Cancer"},{"key":"2024101204455385700_qzae034-B72","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1038\/nature08456","article-title":"DNA demethylation in hormone-induced transcriptional derepression","volume":"461","author":"Kim","year":"2009","journal-title":"Nature"},{"key":"2024101204455385700_qzae034-B73","doi-asserted-by":"crossref","first-page":"105590","DOI":"10.1016\/j.jsbmb.2020.105590","article-title":"In silico identification of novel transcription factors associated with CYP27B1 transcriptional regulation in LPS-challenged mononuclear phagocytes","volume":"199","author":"Martinelli","year":"2020","journal-title":"J Steroid Biochem Mol Biol"},{"key":"2024101204455385700_qzae034-B74","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/s41580-019-0132-4","article-title":"The role of 3D genome organization in development and cell differentiation","volume":"20","author":"Zheng","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024101204455385700_qzae034-B75","doi-asserted-by":"crossref","first-page":"eaay1645","DOI":"10.1126\/science.aay1645","article-title":"Chromatin accessibility dynamics in a model of human forebrain development","volume":"367","author":"Trevino","year":"2020","journal-title":"Science"},{"key":"2024101204455385700_qzae034-B76","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1038\/s41588-020-0602-9","article-title":"Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia","volume":"52","author":"Kloetgen","year":"2020","journal-title":"Nat Genet"},{"key":"2024101204455385700_qzae034-B77","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/s41588-020-0665-7","article-title":"Cross-species chromatin interactions drive transcriptional rewiring in Epstein\u2013Barr virus-positive gastric adenocarcinoma","volume":"52","author":"Okabe","year":"2020","journal-title":"Nat Genet"},{"key":"2024101204455385700_qzae034-B78","doi-asserted-by":"crossref","first-page":"4154","DOI":"10.1038\/s41467-019-12079-8","article-title":"A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome","volume":"10","author":"Rhie","year":"2019","journal-title":"Nat Commun"},{"key":"2024101204455385700_qzae034-B79","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The Genome Sequence Archive Family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gpb\/advance-article-pdf\/doi\/10.1093\/gpbjnl\/qzae034\/57492881\/qzae034.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/22\/3\/qzae034\/59726154\/qzae034.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/22\/3\/qzae034\/59726154\/qzae034.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,12]],"date-time":"2024-10-12T04:46:16Z","timestamp":1728708376000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/doi\/10.1093\/gpbjnl\/qzae034\/7667293"}},"subtitle":[],"editor":[{"given":"Zhihua","family":"Zhang","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,5,8]]},"references-count":79,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,9,13]]}},"URL":"https:\/\/doi.org\/10.1093\/gpbjnl\/qzae034","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"type":"print","value":"1672-0229"},{"type":"electronic","value":"2210-3244"}],"subject":[],"published-other":{"date-parts":[[2024,6]]},"published":{"date-parts":[[2024,5,8]]},"article-number":"qzae034"}}