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For: Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J, He A. CoBATCH for High-Throughput Single-Cell Epigenomic Profiling. Mol Cell 2019;76:206-216.e7. [DOI: 10.1016/j.molcel.2019.07.015] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/17/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022]
Number Cited by Other Article(s)
1
Qin F, Wang Y, Yang C, Ren Y, Wei Q, Tang Y, Xu J, Wang H, Luo F, Luo Q, Luo X, Liu X, Yang D, Zuo X, Yang Y, Cheng C, Xu J, Wang W, Liu T, Yi P. hnRNPL phase separation activates PIK3CB transcription and promotes glycolysis in ovarian cancer. Nat Commun 2025;16:4828. [PMID: 40413189 PMCID: PMC12103590 DOI: 10.1038/s41467-025-60115-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 05/13/2025] [Indexed: 05/27/2025]  Open
2
Fu M, Pang L, Wu Z, Wang M, Jin J, Ai S, Li X. Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation. BMC Genomics 2025;26:454. [PMID: 40340740 PMCID: PMC12060302 DOI: 10.1186/s12864-025-11619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Accepted: 04/21/2025] [Indexed: 05/10/2025]  Open
3
Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X, Xia Q, Xu Z, Fu Y, Zhang G, Wu H, Guo G, Guo H, Ruan Y, Wang Y, Xing D, Xu X, Zhang Z. Advances and applications in single-cell and spatial genomics. SCIENCE CHINA. LIFE SCIENCES 2025;68:1226-1282. [PMID: 39792333 DOI: 10.1007/s11427-024-2770-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 10/10/2024] [Indexed: 01/12/2025]
4
Liu M, Yue Y, Chen X, Xian K, Dong C, Shi M, Xiong H, Tian K, Li Y, Zhang QC, He A. Genome-coverage single-cell histone modifications for embryo lineage tracing. Nature 2025;640:828-839. [PMID: 40011786 PMCID: PMC12003199 DOI: 10.1038/s41586-025-08656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/16/2025] [Indexed: 02/28/2025]
5
Tian J, Zhang T, Zhang R, Hao S, Dong J, Chen Y, Zhou J, Tian Y. Lactylation in CNS disorders: mechanisms, cellular function, and disease relevance. Front Cell Dev Biol 2025;13:1566921. [PMID: 40226593 PMCID: PMC11985781 DOI: 10.3389/fcell.2025.1566921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Accepted: 03/05/2025] [Indexed: 04/15/2025]  Open
6
Zhong J, Gao RR, Zhang X, Yang JX, Liu Y, Ma J, Chen Q. Dissecting endothelial cell heterogeneity with new tools. CELL REGENERATION (LONDON, ENGLAND) 2025;14:10. [PMID: 40121354 PMCID: PMC11929667 DOI: 10.1186/s13619-025-00223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 02/20/2025] [Accepted: 02/22/2025] [Indexed: 03/25/2025]
7
Song D, Luo J, Duan X, Jin F, Lu YJ. Identification of G-quadruplex nucleic acid structures by high-throughput sequencing: A review. Int J Biol Macromol 2025;297:139896. [PMID: 39818384 DOI: 10.1016/j.ijbiomac.2025.139896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 01/04/2025] [Accepted: 01/13/2025] [Indexed: 01/18/2025]
8
Chovanec P, Yin Y. Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility. Nucleic Acids Res 2025;53:gkaf101. [PMID: 39997216 PMCID: PMC11851118 DOI: 10.1093/nar/gkaf101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 12/28/2024] [Accepted: 02/05/2025] [Indexed: 02/26/2025]  Open
9
Womersley HJ, Muliaditan D, DasGupta R, Cheow LF. Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression. Genome Res 2025;35:162-177. [PMID: 39622638 PMCID: PMC11789629 DOI: 10.1101/gr.279105.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025]
10
Yu X, Zheng G, Xu L, Guo W, Chen G, Zhu Y, Li T, Rao M, Wang L, Cong R, Pei H. MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets. Mol Omics 2025;21:32-37. [PMID: 39513632 DOI: 10.1039/d4mo00111g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
11
Bai D, Zhang X, Xiang H, Guo Z, Zhu C, Yi C. Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq. Nat Biotechnol 2025;43:85-96. [PMID: 38336903 DOI: 10.1038/s41587-024-02148-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
12
Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025;68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
13
Moreno-Gonzalez M, Sierra I, Kind J. A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research. Int J Cancer 2024. [PMID: 39711032 DOI: 10.1002/ijc.35307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 12/04/2024] [Accepted: 12/10/2024] [Indexed: 12/24/2024]
14
Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024;19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]  Open
15
Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci 2024;27:2292-2309. [PMID: 39627587 PMCID: PMC11999325 DOI: 10.1038/s41593-024-01806-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 09/23/2024] [Indexed: 12/13/2024]
16
Li Y, Wang X, Huang M, Wang X, Li C, Li S, Tang Y, Yu S, Wang Y, Song W, Wu W, Liu Y, Chen YG. BMP suppresses Wnt signaling via the Bcl11b-regulated NuRD complex to maintain intestinal stem cells. EMBO J 2024;43:6032-6051. [PMID: 39433900 PMCID: PMC11612440 DOI: 10.1038/s44318-024-00276-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 09/22/2024] [Accepted: 10/02/2024] [Indexed: 10/23/2024]  Open
17
Zhang X, Liang SB, Yi Z, Qiao Z, Xu B, Geng H, Wang H, Yin X, Tang M, Ge W, Xu YZ, Liang K, Fan YJ, Chen L. Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila. Nucleic Acids Res 2024;52:13110-13127. [PMID: 39470713 PMCID: PMC11602159 DOI: 10.1093/nar/gkae933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 09/30/2024] [Accepted: 10/08/2024] [Indexed: 10/30/2024]  Open
18
Li Q, Guo Y, Wu Z, Xu X, Jiang Z, Qi S, Liu Z, Wen L, Tang F. scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells. Nat Methods 2024;21:2044-2057. [PMID: 39375575 DOI: 10.1038/s41592-024-02453-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 09/08/2024] [Indexed: 10/09/2024]
19
Li M, Na X, Lin F, Liang S, Huang Y, Song J, Xu X, Yang C. DMF-ChIP-seq for Highly Sensitive and Integrated Epigenomic Profiling of Low-Input Cells. ACS APPLIED MATERIALS & INTERFACES 2024;16:52047-52058. [PMID: 39303213 DOI: 10.1021/acsami.4c11280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
20
Dong C, Meng X, Zhang T, Guo Z, Liu Y, Wu P, Chen S, Zhou F, Ma Y, Xiong H, Shu S, He A. Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome. Nat Methods 2024;21:1624-1633. [PMID: 39025969 PMCID: PMC11399096 DOI: 10.1038/s41592-024-02360-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
21
Stuart T. Progress in multifactorial single-cell chromatin profiling methods. Biochem Soc Trans 2024;52:1827-1839. [PMID: 39023855 PMCID: PMC11668300 DOI: 10.1042/bst20231471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
22
Fu M, Jia S, Xu L, Li X, Lv Y, Zhong Y, Ai S. Single-cell multiomic analysis identifies macrophage subpopulations in promoting cardiac repair. J Clin Invest 2024;134:e175297. [PMID: 39190625 PMCID: PMC11444165 DOI: 10.1172/jci175297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 08/15/2024] [Indexed: 08/29/2024]  Open
23
Pepin AS, Schneider R. Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins. EMBO Rep 2024;25:3202-3220. [PMID: 39095610 PMCID: PMC11316037 DOI: 10.1038/s44319-024-00199-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/10/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024]  Open
24
Rhaman MS, Ali M, Ye W, Li B. Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae026. [PMID: 38996445 PMCID: PMC11423859 DOI: 10.1093/gpbjnl/qzae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 07/14/2024]
25
Chen Y, Ye X, Zhong Y, Kang X, Tang Y, Zhu H, Pang C, Ning S, Liang S, Zhang F, Li C, Li J, Gu C, Cheng Y, Kuang Z, Qiu J, Jin J, Luo H, Fu M, Hui HX, Li L, Ruan D, Liu P, Chen X, Sun L, Ai S, Gao X. SP6 controls human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements. Dev Cell 2024;59:1506-1522.e11. [PMID: 38582082 DOI: 10.1016/j.devcel.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/14/2023] [Accepted: 03/12/2024] [Indexed: 04/08/2024]
26
Xu Q, Zhang Y, Xu W, Liu D, Jin W, Chen X, Hong N. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. Nucleic Acids Res 2024;52:3106-3120. [PMID: 38364856 PMCID: PMC11014328 DOI: 10.1093/nar/gkae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024]  Open
27
Bárcenas-Walls JR, Ansaloni F, Hervé B, Strandback E, Nyman T, Castelo-Branco G, Bartošovič M. Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution. Nat Protoc 2024;19:791-830. [PMID: 38129675 DOI: 10.1038/s41596-023-00932-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
28
Sichani AS, Khoddam S, Shakeri S, Tavakkoli Z, Jafroodi AR, Dabbaghipour R, Sisakht M, Fallahi J. Partial Reprogramming as a Method for Regenerating Neural Tissues in Aged Organisms. Cell Reprogram 2024;26:10-23. [PMID: 38381402 DOI: 10.1089/cell.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]  Open
29
Xiong H, Wang Q, Li CC, He A. Single-cell joint profiling of multiple epigenetic proteins and gene transcription. SCIENCE ADVANCES 2024;10:eadi3664. [PMID: 38170774 PMCID: PMC10796078 DOI: 10.1126/sciadv.adi3664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
30
Han Y, Huang C, Pan Y, Gu X. Single Cell Sequencing Technology and Its Application in Alzheimer's Disease. J Alzheimers Dis 2024;97:1033-1050. [PMID: 38217599 DOI: 10.3233/jad-230861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
31
Janssens DH, Greene JE, Wu SJ, Codomo CA, Minot SS, Furlan SN, Ahmad K, Henikoff S. Scalable single-cell profiling of chromatin modifications with sciCUT&Tag. Nat Protoc 2024;19:83-112. [PMID: 37935964 PMCID: PMC11229882 DOI: 10.1038/s41596-023-00905-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/18/2023] [Indexed: 11/09/2023]
32
Gaza HV, Bhardwaj V, Zeller P. Single-Cell Histone Modification Profiling with Cell Enrichment Using sortChIC. Methods Mol Biol 2024;2846:215-241. [PMID: 39141239 DOI: 10.1007/978-1-0716-4071-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
33
Wang K, Zhang X, Cheng H, Ma W, Bao G, Dong L, Gou Y, Yang J, Cai H. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining. BMC Bioinformatics 2023;24:463. [PMID: 38062357 PMCID: PMC10704760 DOI: 10.1186/s12859-023-05590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]  Open
34
Hu Y, Shen F, Yang X, Han T, Long Z, Wen J, Huang J, Shen J, Guo Q. Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity. Clin Epigenetics 2023;15:161. [PMID: 37821906 PMCID: PMC10568863 DOI: 10.1186/s13148-023-01574-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]  Open
35
Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
36
Zhang Y, Li X, Gao S, Liao Y, Luo Y, Liu M, Bian Y, Xiong H, Yue Y, He A. Genetic reporter for live tracing fluid flow forces during cell fate segregation in mouse blastocyst development. Cell Stem Cell 2023;30:1110-1123.e9. [PMID: 37541214 DOI: 10.1016/j.stem.2023.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/02/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023]
37
Chang L, Deng E, Wang J, Zhou W, Ao J, Liu R, Su D, Fan X. Single-cell third-generation sequencing-based multi-omics uncovers gene expression changes governed by ecDNA and structural variants in cancer cells. Clin Transl Med 2023;13:e1351. [PMID: 37517066 PMCID: PMC10387328 DOI: 10.1002/ctm2.1351] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023]  Open
38
Stuart T, Hao S, Zhang B, Mekerishvili L, Landau DA, Maniatis S, Satija R, Raimondi I. Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. Nat Biotechnol 2023;41:806-812. [PMID: 36536150 PMCID: PMC10272075 DOI: 10.1038/s41587-022-01588-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
39
Yu W, Wang HL, Zhang J, Yin C. The effects of epigenetic modifications on bone remodeling in age-related osteoporosis. Connect Tissue Res 2023;64:105-116. [PMID: 36271658 DOI: 10.1080/03008207.2022.2120392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
40
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat Methods 2023;20:363-374. [PMID: 36864196 DOI: 10.1038/s41592-023-01791-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/24/2023] [Indexed: 03/04/2023]
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Penkov D, Zubkova E, Parfyonova Y. Tn5 DNA Transposase in Multi-Omics Research. Methods Protoc 2023;6:mps6020024. [PMID: 36961044 PMCID: PMC10037646 DOI: 10.3390/mps6020024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]  Open
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Wang M, Li Q, Liu L. Factors and Methods for the Detection of Gene Expression Regulation. Biomolecules 2023;13:biom13020304. [PMID: 36830673 PMCID: PMC9953580 DOI: 10.3390/biom13020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]  Open
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Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nat Genet 2023;55:333-345. [PMID: 36539617 PMCID: PMC9925381 DOI: 10.1038/s41588-022-01260-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
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Wooten M, Takushi B, Ahmad K, Henikoff S. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523323. [PMID: 36712130 PMCID: PMC9882078 DOI: 10.1101/2023.01.09.523323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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scChIX-seq infers dynamic relationships between histone modifications in single cells. Nat Biotechnol 2023:10.1038/s41587-022-01560-3. [PMID: 36593403 DOI: 10.1038/s41587-022-01560-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/12/2022] [Indexed: 01/03/2023]
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Ouyang W, Li X. CUT&Tag for Mapping In Vivo Protein-DNA Interactions in Plants. Methods Mol Biol 2023;2698:109-117. [PMID: 37682472 DOI: 10.1007/978-1-0716-3354-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
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Martin BK, Qiu C, Nichols E, Phung M, Green-Gladden R, Srivatsan S, Blecher-Gonen R, Beliveau BJ, Trapnell C, Cao J, Shendure J. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nat Protoc 2023;18:188-207. [PMID: 36261634 PMCID: PMC9839601 DOI: 10.1038/s41596-022-00752-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/30/2022] [Indexed: 01/17/2023]
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Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023;24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
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Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. Nat Biotechnol 2022:10.1038/s41587-022-01535-4. [DOI: 10.1038/s41587-022-01535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
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Li C, Yin Z, Xiao R, Huang B, Cui Y, Wang H, Xiang Y, Wang L, Lei L, Ye J, Li T, Zhong Y, Guo F, Xia Y, Fang P, Liang K. G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes. Genome Biol 2022;23:259. [PMID: 36522639 PMCID: PMC9753424 DOI: 10.1186/s13059-022-02830-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/02/2022] [Indexed: 12/16/2022]  Open
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