{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:23:22Z","timestamp":1787271802882,"version":"build-2736575974"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T00:00:00Z","timestamp":1784505600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000},"content-version":"vor","delay-in-days":32,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP22tm0424223, JP22ek0410099, JP23tm0524005, JP25ek0410139, JP22ama121015 and JP223fa627010"],"award-info":[{"award-number":["JP22tm0424223, JP22ek0410099, JP23tm0524005, JP25ek0410139, JP22ama121015 and JP223fa627010"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"MEXT | Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["22H03114, 21K20647"],"award-info":[{"award-number":["22H03114, 21K20647"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005927","name":"Daiichi Sankyo Foundation of Life Science","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100005927","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005865","name":"Mochida Memorial Foundation for Medical and Pharmaceutical Research","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100005865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008732","name":"Uehara Memorial Foundation","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100008732","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Keio University Academic Development Funds, GSK Japan Research Grant and Takeda COCKPI-T Funding"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"DOI":"10.1038\/s41467-026-75767-2","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T05:04:01Z","timestamp":1784523841000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq"],"prefix":"10.1038","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2245-943X","authenticated-orcid":false,"given":"Michihiro","family":"Kono","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Hatano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenichiro","family":"Asahara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Nakano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reza","family":"Bagherzadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsugumi","family":"Kawashima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7061-5196","authenticated-orcid":false,"given":"Takahiro","family":"Arakawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miho","family":"Sato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hajime","family":"Inokuchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takahiro","family":"Nishino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1020-0108","authenticated-orcid":false,"given":"Takahiro","family":"Itamiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haruka","family":"Takahashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bunki","family":"Natsumoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akari","family":"Suzuki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiko","family":"Yamamoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2881-0657","authenticated-orcid":false,"given":"Kazuyoshi","family":"Ishigaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"75767_CR1","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.1038\/s41588-021-00931-x","volume":"53","author":"S Sakaue","year":"2021","unstructured":"Sakaue, S. et al. A cross-population atlas of genetic associations for 220 human phenotypes. Nat. Genet. 53, 1415\u20131424 (2021).","journal-title":"Nat. Genet."},{"key":"75767_CR2","doi-asserted-by":"publisher","first-page":"1640","DOI":"10.1038\/s41588-022-01213-w","volume":"54","author":"K Ishigaki","year":"2022","unstructured":"Ishigaki, K. et al. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat. Genet. 54, 1640\u20131651 (2022).","journal-title":"Nat. Genet."},{"key":"75767_CR3","doi-asserted-by":"publisher","first-page":"D977","DOI":"10.1093\/nar\/gkac1010","volume":"51","author":"E Sollis","year":"2023","unstructured":"Sollis, E. et al. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51, D977\u2013D985 (2023).","journal-title":"Nucleic Acids Res."},{"key":"75767_CR4","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nature06758","volume":"452","author":"V Emilsson","year":"2008","unstructured":"Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423\u2013428 (2008).","journal-title":"Nature"},{"key":"75767_CR5","doi-asserted-by":"publisher","first-page":"1217","DOI":"10.1038\/ng2142","volume":"39","author":"BE Stranger","year":"2007","unstructured":"Stranger, B. E. et al. Population genomics of human gene expression. Nat. Genet. 39, 1217\u20131224 (2007).","journal-title":"Nat. Genet."},{"key":"75767_CR6","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/ni1008-1091","volume":"9","author":"TSP Heng","year":"2008","unstructured":"Heng, T. S. P. & Painter, M. W. & Immunological Genome Project Consortium. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091\u20131094 (2008).","journal-title":"Nat. Immunol."},{"key":"75767_CR7","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1038\/s41588-021-00913-z","volume":"53","author":"U V\u00f5sa","year":"2021","unstructured":"V\u00f5sa, U. et al. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. Nat. Genet. 53, 1300\u20131310 (2021).","journal-title":"Nat. Genet."},{"key":"75767_CR8","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nature24277","volume":"550","author":"GTEx Consortium","year":"2017","unstructured":"GTEx Consortium et al. Genetic effects on gene expression across human tissues. Nature 550, 204\u2013213 (2017).","journal-title":"Nature"},{"key":"75767_CR9","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1126\/science.aaz1776","volume":"369","author":"GTEx Consortium","year":"2020","unstructured":"GTEx Consortium The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318\u20131330 (2020).","journal-title":"Science"},{"key":"75767_CR10","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1016\/j.cell.2018.10.022","volume":"175","author":"BJ Schmiedel","year":"2018","unstructured":"Schmiedel, B. J. et al. Impact of genetic polymorphisms on human immune cell gene expression. Cell 175, 1701\u20131715.e16 (2018).","journal-title":"Cell"},{"key":"75767_CR11","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1038\/s41588-020-00745-3","volume":"53","author":"V Chandra","year":"2021","unstructured":"Chandra, V. et al. Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants. Nat. Genet. 53, 110\u2013119 (2021).","journal-title":"Nat. Genet."},{"key":"75767_CR12","doi-asserted-by":"publisher","first-page":"3006","DOI":"10.1016\/j.cell.2021.03.056","volume":"184","author":"M Ota","year":"2021","unstructured":"Ota, M. et al. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell 184, 3006\u20133021.e17 (2021).","journal-title":"Cell"},{"key":"75767_CR13","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.74970","volume":"11","author":"NJ Connally","year":"2022","unstructured":"Connally, N. J. et al. The missing link between genetic association and regulatory function. eLife 11, e74970 (2022).","journal-title":"eLife"},{"key":"75767_CR14","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1038\/ng.3795","volume":"49","author":"S Chun","year":"2017","unstructured":"Chun, S. et al. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat. Genet. 49, 600\u2013605 (2017).","journal-title":"Nat. Genet."},{"key":"75767_CR15","doi-asserted-by":"publisher","first-page":"1866","DOI":"10.1038\/s41588-023-01529-1","volume":"55","author":"H Mostafavi","year":"2023","unstructured":"Mostafavi, H., Spence, J. P., Naqvi, S. & Pritchard, J. K. Systematic differences in discovery of genetic effects on gene expression and complex traits. Nat. Genet. 55, 1866\u20131875 (2023).","journal-title":"Nat. Genet."},{"key":"75767_CR16","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1126\/science.aay3983","volume":"369","author":"S Zhang","year":"2020","unstructured":"Zhang, S. et al. Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants. Science 369, 561\u2013565 (2020).","journal-title":"Science"},{"key":"75767_CR17","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/ng.3769","volume":"49","author":"J Xu","year":"2017","unstructured":"Xu, J. et al. Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nat. Genet. 49, 377\u2013386 (2017).","journal-title":"Nat. Genet."},{"key":"75767_CR18","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/s41588-020-0579-4","volume":"52","author":"M Gutierrez-Arcelus","year":"2020","unstructured":"Gutierrez-Arcelus, M. et al. Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nat. Genet. 52, 247\u2013253 (2020).","journal-title":"Nat. Genet."},{"key":"75767_CR19","doi-asserted-by":"publisher","first-page":"e64","DOI":"10.1093\/nar\/gkad332","volume":"51","author":"S Cooper","year":"2023","unstructured":"Cooper, S., Schwartzentruber, J., Coomber, E. L., Wu, Q. & Bassett, A. Screening for functional regulatory variants in open chromatin using GenIE-ATAC. Nucleic Acids Res. 51, e64 (2023).","journal-title":"Nucleic Acids Res."},{"key":"75767_CR20","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1038\/s41584-021-00637-8","volume":"17","author":"Y Baglaenko","year":"2021","unstructured":"Baglaenko, Y., Macfarlane, D., Marson, A., Nigrovic, P. A. & Raychaudhuri, S. Genome editing to define the function of risk loci and variants in rheumatic disease. Nat. Rev. Rheumatol. 17, 462\u2013474 (2021).","journal-title":"Nat. Rev. Rheumatol."},{"key":"75767_CR21","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213\u20131218 (2013).","journal-title":"Nat. Methods"},{"key":"75767_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms16021","volume":"8","author":"CD Langefeld","year":"2017","unstructured":"Langefeld, C. D. et al. Transancestral mapping and genetic load in systemic lupus erythematosus. Nat. Commun. 8, 16021 (2017).","journal-title":"Nat. Commun."},{"key":"75767_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-05328-9","volume":"9","author":"RC Pelikan","year":"2018","unstructured":"Pelikan, R. C. et al. Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. Nat. Commun. 9, 2905 (2018).","journal-title":"Nat. Commun."},{"key":"75767_CR24","doi-asserted-by":"publisher","first-page":"S65","DOI":"10.1101\/gr.3.4.S65","volume":"3","author":"MC Edwards","year":"1994","unstructured":"Edwards, M. C. & Gibbs, R. A. Multiplex PCR: advantages, development, and applications. PCR Methods Appl. 3, S65\u2013S75 (1994).","journal-title":"PCR Methods Appl."},{"key":"75767_CR25","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1654-y","volume":"20","author":"A Karabacak Calviello","year":"2019","unstructured":"Karabacak Calviello, A., Hirsekorn, A., Wurmus, R., Yusuf, D. & Ohler, U. Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling. Genome Biol. 20, 42 (2019).","journal-title":"Genome Biol."},{"key":"75767_CR26","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1016\/j.ajhg.2019.03.012","volume":"104","author":"T Amariuta","year":"2019","unstructured":"Amariuta, T. et al. IMPACT: genomic annotation of cell-state-specific regulatory elements inferred from the epigenome of bound transcription factors. Am. J. Hum. Genet. 104, 879\u2013895 (2019).","journal-title":"Am. J. Hum. Genet."},{"key":"75767_CR27","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1038\/ng.3404","volume":"47","author":"HK Finucane","year":"2015","unstructured":"Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228\u20131235 (2015).","journal-title":"Nat. Genet."},{"key":"75767_CR28","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/s41588-018-0081-4","volume":"50","author":"HK Finucane","year":"2018","unstructured":"Finucane, H. K. et al. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat. Genet. 50, 621\u2013629 (2018).","journal-title":"Nat. Genet."},{"key":"75767_CR29","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1038\/s41588-018-0278-6","volume":"51","author":"N Kumasaka","year":"2019","unstructured":"Kumasaka, N., Knights, A. J. & Gaffney, D. J. High-resolution genetic mapping of putative causal interactions between regions of open chromatin. Nat. Genet. 51, 128\u2013137 (2019).","journal-title":"Nat. Genet."},{"key":"75767_CR30","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1136\/annrheumdis-2020-219209","volume":"80","author":"X Yin","year":"2021","unstructured":"Yin, X. et al. Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus. Ann. Rheum. Dis. 80, 632\u2013640 (2021).","journal-title":"Ann. Rheum. Dis."},{"key":"75767_CR31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48620-7","volume":"15","author":"K Weinand","year":"2024","unstructured":"Weinand, K. et al. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nat. Commun. 15, 4650 (2024).","journal-title":"Nat. Commun."},{"key":"75767_CR32","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1038\/s41588-024-01682-1","volume":"56","author":"S Sakaue","year":"2024","unstructured":"Sakaue, S. et al. Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nat. Genet. 56, 615\u2013626 (2024).","journal-title":"Nat. Genet."},{"key":"75767_CR33","doi-asserted-by":"publisher","first-page":"e131","DOI":"10.1093\/nar\/gkaa960","volume":"48","author":"SE Cooper","year":"2020","unstructured":"Cooper, S. E., Schwartzentruber, J., Bello, E., Coomber, E. L. & Bassett, A. R. Screening for functional transcriptional and splicing regulatory variants with GenIE. Nucleic Acids Res. 48, e131 (2020).","journal-title":"Nucleic Acids Res."},{"key":"75767_CR34","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.12677","volume":"5","author":"MA Horlbeck","year":"2016","unstructured":"Horlbeck, M. A. et al. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 5, e12677 (2016).","journal-title":"eLife"},{"key":"75767_CR35","doi-asserted-by":"publisher","first-page":"9351","DOI":"10.1073\/pnas.1810062115","volume":"115","author":"RM Yarrington","year":"2018","unstructured":"Yarrington, R. M., Verma, S., Schwartz, S., Trautman, J. K. & Carroll, D. Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo. Proc. Natl. Acad. Sci. USA 115, 9351\u20139358 (2018).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"75767_CR36","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1093\/nar\/gkad1076","volume":"52","author":"Y Ito","year":"2024","unstructured":"Ito, Y. et al. Epigenetic profiles guide improved CRISPR\/Cas9-mediated gene knockout in human T cells. Nucleic Acids Res. 52, 141\u2013153 (2024).","journal-title":"Nucleic Acids Res."},{"key":"75767_CR37","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1016\/j.molcel.2021.12.026","volume":"82","author":"TS Nambiar","year":"2022","unstructured":"Nambiar, T. S., Baudrier, L., Billon, P. & Ciccia, A. CRISPR-based genome editing through the lens of DNA repair. Mol. Cell 82, 348\u2013388 (2022).","journal-title":"Mol. Cell"},{"key":"75767_CR38","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/nature13011","volume":"507","author":"SH Sternberg","year":"2014","unstructured":"Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62\u201367 (2014).","journal-title":"Nature"},{"key":"75767_CR39","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/nrm2651","volume":"10","author":"T Misteli","year":"2009","unstructured":"Misteli, T. & Soutoglou, E. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat. Rev. Mol. Cell Biol. 10, 243\u2013254 (2009).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"75767_CR40","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1016\/j.molcel.2012.06.002","volume":"46","author":"G Soria","year":"2012","unstructured":"Soria, G., Polo, S. E. & Almouzni, G. Prime, repair, restore: the active role of chromatin in the DNA damage response. Mol. Cell 46, 722\u2013734 (2012).","journal-title":"Mol. Cell"},{"key":"75767_CR41","doi-asserted-by":"publisher","first-page":"5635","DOI":"10.1016\/j.cell.2021.09.018","volume":"184","author":"PJ Chen","year":"2021","unstructured":"Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635\u20135652.e29 (2021).","journal-title":"Cell"},{"key":"75767_CR42","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1038\/s41587-021-01039-7","volume":"40","author":"JW Nelson","year":"2022","unstructured":"Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402\u2013410 (2022).","journal-title":"Nat. Biotechnol."},{"key":"75767_CR43","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2022.100234","volume":"3","author":"K Mouri","year":"2023","unstructured":"Mouri, K. et al. Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay. Cell Genomics 3, 100234 (2023).","journal-title":"Cell Genomics"},{"key":"75767_CR44","doi-asserted-by":"publisher","unstructured":"Kanai, M. et al. Population-scale multiome immune cell atlas reveals complex disease drivers. Preprint at https:\/\/doi.org\/10.1101\/2025.11.25.25340489 (2025).","DOI":"10.1101\/2025.11.25.25340489"},{"key":"75767_CR45","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2014562118","volume":"118","author":"F Li","year":"2021","unstructured":"Li, F. et al. TFH cells depend on Tcf1-intrinsic HDAC activity to suppress CTLA4 and guard B-cell help function. Proc. Natl. Acad. Sci. USA 118, e2014562118 (2021).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"75767_CR46","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/s41577-021-00563-6","volume":"22","author":"X Zhao","year":"2022","unstructured":"Zhao, X., Shan, Q. & Xue, H.-H. TCF1 in T cell immunity: a broadened frontier. Nat. Rev. Immunol. 22, 147\u2013157 (2022).","journal-title":"Nat. Rev. Immunol."},{"key":"75767_CR47","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1038\/ni.3226","volume":"16","author":"YS Choi","year":"2015","unstructured":"Choi, Y. S. et al. LEF-1 and TCF-1 orchestrate T(FH) differentiation by regulating differentiation circuits upstream of the transcriptional repressor Bcl6. Nat. Immunol. 16, 980\u2013990 (2015).","journal-title":"Nat. Immunol."},{"key":"75767_CR48","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/ni.2897","volume":"15","author":"FC Steinke","year":"2014","unstructured":"Steinke, F. C. et al. TCF-1 and LEF-1 act upstream of Th-POK to promote the CD4(+) T cell fate and interact with Runx3 to silence Cd4 in CD8(+) T cells. Nat. Immunol. 15, 646\u2013656 (2014).","journal-title":"Nat. Immunol."},{"key":"75767_CR49","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1111\/j.1365-2567.2008.02854.x","volume":"125","author":"MB Hossain","year":"2008","unstructured":"Hossain, M. B. et al. Lymphoid enhancer factor interacts with GATA-3 and controls its function in T helper type 2 cells. Immunology 125, 377\u2013386 (2008).","journal-title":"Immunology"},{"key":"75767_CR50","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1038\/nmeth.4380","volume":"14","author":"M Stoeckius","year":"2017","unstructured":"Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865\u2013868 (2017).","journal-title":"Nat. Methods"},{"key":"75767_CR51","doi-asserted-by":"publisher","first-page":"2130","DOI":"10.1002\/art.42642","volume":"75","author":"S Nakajima","year":"2023","unstructured":"Nakajima, S. et al. Synovial tissue heterogeneity in Japanese patients with rheumatoid arthritis elucidated using a cell-type deconvolution approach. Arthritis Rheumatol. 75, 2130\u20132136 (2023).","journal-title":"Arthritis Rheumatol."},{"key":"75767_CR52","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1007\/s10571-015-0290-7","volume":"36","author":"X Liu","year":"2016","unstructured":"Liu, X. et al. T-cell factor (TCF\/LEF1) binding elements (TBEs) of FasL (Fas ligand or CD95 ligand) bind and cluster Fas (CD95) and form complexes with the TCF-4 and b-catenin transcription factors in vitro and in vivo which result in triggering cell death and\/or cell activation. Cell. Mol. Neurobiol. 36, 1001\u20131013 (2016).","journal-title":"Cell. Mol. Neurobiol."},{"key":"75767_CR53","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature12873","volume":"506","author":"Y Okada","year":"2014","unstructured":"Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376\u2013381 (2014).","journal-title":"Nature"},{"key":"75767_CR54","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.adt3955","volume":"10","author":"Y Masuo","year":"2025","unstructured":"Masuo, Y. et al. Stem-like and effector peripheral helper T cells comprise distinct subsets in rheumatoid arthritis. Sci. Immunol. 10, eadt3955 (2025).","journal-title":"Sci. Immunol."},{"key":"75767_CR55","doi-asserted-by":"publisher","DOI":"10.1172\/JCI181034","volume":"135","author":"A Horisberger","year":"2025","unstructured":"Horisberger, A. et al. Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. J. Clin. Invest. 135, e181034 (2025).","journal-title":"J. Clin. Invest."},{"key":"75767_CR56","doi-asserted-by":"publisher","first-page":"2431","DOI":"10.1038\/s41596-022-00724-4","volume":"17","author":"JL Doman","year":"2022","unstructured":"Doman, J. L., Sousa, A. A., Randolph, P. B., Chen, P. J. & Liu, D. R. Designing and executing prime editing experiments in mammalian cells. Nat. Protoc. 17, 2431\u20132468 (2022).","journal-title":"Nat. Protoc."},{"key":"75767_CR57","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10\u201312 (2011).","journal-title":"EMBnet J."},{"key":"75767_CR58","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"75767_CR59","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"75767_CR60","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1038\/s42003-020-01403-4","volume":"3","author":"T Zhu","year":"2020","unstructured":"Zhu, T., Liao, K., Zhou, R., Xia, C. & Xie, W. ATAC-seq with unique molecular identifiers improves quantification and footprinting. Commun. Biol. 3, 675 (2020).","journal-title":"Commun. Biol."},{"key":"75767_CR61","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"75767_CR62","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"75767_CR63","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v067.i01","volume":"67","author":"D Bates","year":"2015","unstructured":"Bates, D., M\u00e4chler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1\u201348 (2015).","journal-title":"J. Stat. Softw."},{"key":"75767_CR64","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049","volume":"8","author":"GXY Zheng","year":"2017","unstructured":"Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).","journal-title":"Nat. Commun."},{"key":"75767_CR65","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573\u20133587.e29 (2021).","journal-title":"Cell"},{"key":"75767_CR66","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1038\/s41590-021-00933-1","volume":"22","author":"A Nathan","year":"2021","unstructured":"Nathan, A. et al. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nat. Immunol. 22, 781\u2013793 (2021).","journal-title":"Nat. Immunol."},{"key":"75767_CR67","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"75767_CR68","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aaq0305","volume":"10","author":"CY Fonseka","year":"2018","unstructured":"Fonseka, C. Y. et al. Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis. Sci. Transl. Med. 10, eaaq0305 (2018).","journal-title":"Sci. Transl. Med."},{"key":"75767_CR69","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"75767_CR70","doi-asserted-by":"publisher","first-page":"3048","DOI":"10.1093\/bioinformatics\/btab135","volume":"37","author":"A Graubert","year":"2021","unstructured":"Graubert, A., Aguet, F., Ravi, A., Ardlie, K. G. & Getz, G. RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts. Bioinformatics 37, 3048\u20133050 (2021).","journal-title":"Bioinformatics"},{"key":"75767_CR71","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","volume":"22","author":"J Harrow","year":"2012","unstructured":"Harrow, J. et al. GENCODE: the reference human genome annotation for the ENCODE Project. Genome Res. 22, 1760\u20131774 (2012).","journal-title":"Genome Res."},{"key":"75767_CR72","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"75767_CR73","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"75767_CR74","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010).","journal-title":"Mol. Cell"},{"key":"75767_CR75","doi-asserted-by":"publisher","unstructured":"Hatano, H. hhat\/UNIChro-seq-Analysis: v1.2. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.20423205 (2026).","DOI":"10.5281\/zenodo.20423205"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-75767-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-75767-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-75767-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T23:29:08Z","timestamp":1787268548000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-75767-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,20]]},"references-count":75,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["75767"],"URL":"https:\/\/doi.org\/10.1038\/s41467-026-75767-2","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,20]]},"assertion":[{"value":"20 September 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"RIKEN has filed a patent application related to this work (WO\/2024\/242037). K.I., M.K., and T.A. are inventors on this patent. The remaining authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"8807"}}