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For: Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li Y, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 2023;382:eadf5357. [PMID: 37824674 PMCID: PMC10572106 DOI: 10.1126/science.adf5357] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Number Cited by Other Article(s)
1
Nobori T. Exploring the untapped potential of single-cell and spatial omics in plant biology. THE NEW PHYTOLOGIST 2025. [PMID: 40398874 DOI: 10.1111/nph.70220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Accepted: 04/24/2025] [Indexed: 05/23/2025]
2
Bougnères P, Le Stunff C. Revisiting the Pathogenesis of X-Linked Adrenoleukodystrophy. Genes (Basel) 2025;16:590. [PMID: 40428412 PMCID: PMC12111468 DOI: 10.3390/genes16050590] [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: 05/01/2025] [Revised: 05/11/2025] [Accepted: 05/15/2025] [Indexed: 05/29/2025]  Open
3
Sun Y, Li M, Ning C, Gao L, Liu Z, Zhong S, Lv J, Ke Y, Wang X, Ma Q, Liu Z, Wu S, Yu H, Zhao F, Zhang J, Gong Q, Liu J, Wu Q, Wang X, Chen X. Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development. Cell Discov 2025;11:50. [PMID: 40374600 DOI: 10.1038/s41421-025-00798-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 02/21/2025] [Indexed: 05/17/2025]  Open
4
Wu Y, Wu BZ, Ellenbogen Y, Kant JBY, Yu P, Li X, Caloren L, Sotov V, Tran C, Restrepo M, Kushida M, Ayyadhury S, Kossinna P, Lau R, Habibi P, Mansouri S, Regala J, Durbic T, Aboualizadeh F, Tsao J, Ketela T, Pugh T, Butler MO, Wang BX, Dirks PB, Gao A, Zadeh G, Gaiti F. Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration. Dev Cell 2025:S1534-5807(25)00260-6. [PMID: 40381621 DOI: 10.1016/j.devcel.2025.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 02/06/2025] [Accepted: 04/25/2025] [Indexed: 05/20/2025]
5
Konstantinides N, Desplan C. Neuronal Circuit Evolution: From Development to Structure and Adaptive Significance. Cold Spring Harb Perspect Biol 2025;17:a041493. [PMID: 38951021 PMCID: PMC11688512 DOI: 10.1101/cshperspect.a041493] [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] [Indexed: 07/03/2024]
6
Chai H, Huang X, Xiong G, Huang J, Pels KK, Meng L, Han J, Tang D, Pan G, Deng L, Xiao Q, Wang X, Zhang M, Banecki K, Plewczynski D, Wei CL, Ruan Y. Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan. Nat Methods 2025;22:994-1007. [PMID: 40301621 DOI: 10.1038/s41592-025-02658-7] [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: 11/14/2024] [Accepted: 03/13/2025] [Indexed: 05/01/2025]
7
Sugo N, Atsumi Y, Yamamoto N. Transcription and epigenetic factor dynamics in neuronal activity-dependent gene regulation. Trends Genet 2025;41:425-436. [PMID: 39875312 DOI: 10.1016/j.tig.2024.12.008] [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: 09/19/2024] [Revised: 12/20/2024] [Accepted: 12/20/2024] [Indexed: 01/30/2025]
8
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]
9
Papetti AV, Jin M, Ma Z, Stillitano AC, Jiang P. Chimeric brain models: Unlocking insights into human neural development, aging, diseases, and cell therapies. Neuron 2025:S0896-6273(25)00256-9. [PMID: 40300597 DOI: 10.1016/j.neuron.2025.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Revised: 03/07/2025] [Accepted: 03/31/2025] [Indexed: 05/01/2025]
10
Yuan Y, Biswas P, Zemke NR, Dang K, Wu Y, D’Antonio M, Xie Y, Yang Q, Dong K, Lau PK, Li D, Seng C, Bartosik W, Buchanan J, Lin L, Lancione R, Wang K, Lee S, Gibbs Z, Ecker J, Frazer K, Wang T, Preissl S, Wang A, Ayyagari R, Ren B. Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.28.630634. [PMID: 39764062 PMCID: PMC11703273 DOI: 10.1101/2024.12.28.630634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
11
Zhou J, Wu Y, Liu H, Tian W, Castanon RG, Bartlett A, Zhang Z, Yao G, Shi D, Clock B, Marcotte S, Nery JR, Liem M, Claffey N, Boggeman L, Barragan C, Drigo RAE, Weimer AK, Shi M, Cooper-Knock J, Zhang S, Snyder MP, Preissl S, Ren B, O’Connor C, Chen S, Luo C, Dixon JR, Ecker JR. Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.23.644697. [PMID: 40196612 PMCID: PMC11974725 DOI: 10.1101/2025.03.23.644697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
12
Gao R, Ferraro TN, Chen L, Zhang S, Chen Y. Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model. BIOLOGY 2025;14:288. [PMID: 40136544 PMCID: PMC11940666 DOI: 10.3390/biology14030288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Revised: 03/01/2025] [Accepted: 03/10/2025] [Indexed: 03/27/2025]
13
Dougherty JD, Sarafinovska S, Chaturvedi SM, Law TE, Akinwe TM, Gabel HW. Single-cell technology grows up: Leveraging high-resolution omics approaches to understand neurodevelopmental disorders. Curr Opin Neurobiol 2025;92:102990. [PMID: 40036988 DOI: 10.1016/j.conb.2025.102990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/30/2025] [Accepted: 02/05/2025] [Indexed: 03/06/2025]
14
Liu Z, Gu A, Bao Y, Lin GN. Epigenetic Impacts of Non-Coding Mutations Deciphered Through Pre-Trained DNA Language Model at Single-Cell Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2413571. [PMID: 39888214 PMCID: PMC11924033 DOI: 10.1002/advs.202413571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 01/20/2025] [Indexed: 02/01/2025]
15
Sun W, Hewitt SM, Wright H, Keller C, Barr FG. DNA methylation patterns are influenced by Pax3::Foxo1 expression and developmental lineage in rhabdomyosarcoma tumours forming in genetically engineered mouse models. J Pathol 2025;265:316-329. [PMID: 39812007 PMCID: PMC11794984 DOI: 10.1002/path.6386] [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: 04/22/2024] [Revised: 10/21/2024] [Accepted: 11/28/2024] [Indexed: 01/16/2025]
16
O'Dea MR, Hasel P. Are we there yet? Exploring astrocyte heterogeneity one cell at a time. Glia 2025;73:619-631. [PMID: 39308429 PMCID: PMC11784854 DOI: 10.1002/glia.24621] [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: 05/13/2024] [Revised: 09/02/2024] [Accepted: 09/14/2024] [Indexed: 02/01/2025]
17
Liu S, Wang CY, Zheng P, Jia BB, Zemke NR, Ren P, Park HL, Ren B, Zhuang X. Cell type-specific 3D-genome organization and transcription regulation in the brain. SCIENCE ADVANCES 2025;11:eadv2067. [PMID: 40009678 PMCID: PMC11864200 DOI: 10.1126/sciadv.adv2067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 01/23/2025] [Indexed: 02/28/2025]
18
Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal MS, McAuliffe L, Majounie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Stojakovic J, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. Scalable Screening of Ternary-Code DNA Methylation Dynamics Associated with Human Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
19
Yan M, Zhang XM, Yang Z, Jia M, Liao R, Li J. Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus. Nat Commun 2025;16:1485. [PMID: 39929797 PMCID: PMC11811026 DOI: 10.1038/s41467-024-55582-3] [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: 05/16/2024] [Accepted: 12/09/2024] [Indexed: 02/13/2025]  Open
20
Zhou H, Clark E, Guan D, Lagarrigue S, Fang L, Cheng H, Tuggle CK, Kapoor M, Wang Y, Giuffra E, Egidy G. Comparative Genomics and Epigenomics of Transcriptional Regulation. Annu Rev Anim Biosci 2025;13:73-98. [PMID: 39565835 DOI: 10.1146/annurev-animal-111523-102217] [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: 11/22/2024]
21
Wu H, Wang M, Zheng Y, Xie XS. Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics. Cell Discov 2025;11:8. [PMID: 39837831 PMCID: PMC11751028 DOI: 10.1038/s41421-025-00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Accepted: 12/30/2024] [Indexed: 01/23/2025]  Open
22
Nichols RV, Rylaarsdam LE, O'Connell BL, Shipony Z, Iremadze N, Acharya SN, Adey AC. Atlas-scale single-cell DNA methylation profiling with sciMETv3. CELL GENOMICS 2025;5:100726. [PMID: 39719707 PMCID: PMC11770211 DOI: 10.1016/j.xgen.2024.100726] [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: 09/03/2024] [Revised: 10/25/2024] [Accepted: 11/26/2024] [Indexed: 12/26/2024]
23
Mori FK, Shimosawa T. The Fetal Environment and the Development of Hypertension-The Epigenetic Modification by Glucocorticoids. Int J Mol Sci 2025;26:420. [PMID: 39796274 PMCID: PMC11720225 DOI: 10.3390/ijms26010420] [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: 11/23/2024] [Revised: 12/18/2024] [Accepted: 01/02/2025] [Indexed: 01/13/2025]  Open
24
Westphal M, Drexler R, Maire C, Ricklefs F, Lamszus K. Cancer neuroscience and glioma: clinical implications. Acta Neurochir (Wien) 2025;167:2. [PMID: 39752006 PMCID: PMC11698767 DOI: 10.1007/s00701-024-06406-2] [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: 11/19/2024] [Accepted: 12/19/2024] [Indexed: 01/04/2025]
25
Weymouth L, Smith AR, Lunnon K. DNA Methylation in Alzheimer's Disease. Curr Top Behav Neurosci 2025;69:149-178. [PMID: 39455499 DOI: 10.1007/7854_2024_530] [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: 10/28/2024]
26
Ma J, Qi R, Wang J, Berto S, Wang GZ. Human-unique brain cell clusters are associated with learning disorders and human episodic memory activity. Mol Psychiatry 2025;30:353-359. [PMID: 39227435 DOI: 10.1038/s41380-024-02722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024]
27
Davie JR, Sattarifard H, Sudhakar SRN, Roberts CT, Beacon TH, Muker I, Shahib AK, Rastegar M. Basic Epigenetic Mechanisms. Subcell Biochem 2025;108:1-49. [PMID: 39820859 DOI: 10.1007/978-3-031-75980-2_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] [Indexed: 01/19/2025]
28
Twa GM, Phillips RA, Robinson NJ, Day JJ. Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.29.626066. [PMID: 39677603 PMCID: PMC11642824 DOI: 10.1101/2024.11.29.626066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
29
Pressl C, Baffuto M, Darnell P, Wang C, Carroll TS, Heintz N, Mätlik K. Isolation and Molecular Profiling of Nuclei of Specific Neuronal Types from Human Cerebral Cortex and Striatum. Curr Protoc 2024;4:e70067. [PMID: 39651942 PMCID: PMC11627125 DOI: 10.1002/cpz1.70067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
30
Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy J, Melief EJ, Agrawal A, Kana O, Zhen X, Barlow ST, Brouner K, Campos J, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Cool J, Dalley R, Darvas M, Ding SL, Dolbeare T, Egdorf T, Esposito L, Ferrer R, Fleckenstein LE, Gala R, Gary A, Gelfand E, Gloe J, Guilford N, Guzman J, Hirschstein D, Ho W, Hupp M, Jarsky T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore MD, Kirkland A, Kunst M, Lee BR, Leytze M, Mac Donald CL, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Mena G, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus JK, Olsen PA, Pacleb M, Pagan CM, Peña N, Pham T, Pom CA, Postupna N, Rimorin C, Ruiz A, Saldi GA, Schantz AM, Shapovalova NV, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting JT, Torkelson A, Tran T, Valera Cuevas NJ, Walling-Bell S, Wang MQ, Waters J, Wilson AM, Xiao M, Haynor D, Gatto NM, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith KA, et alGabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy J, Melief EJ, Agrawal A, Kana O, Zhen X, Barlow ST, Brouner K, Campos J, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Cool J, Dalley R, Darvas M, Ding SL, Dolbeare T, Egdorf T, Esposito L, Ferrer R, Fleckenstein LE, Gala R, Gary A, Gelfand E, Gloe J, Guilford N, Guzman J, Hirschstein D, Ho W, Hupp M, Jarsky T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore MD, Kirkland A, Kunst M, Lee BR, Leytze M, Mac Donald CL, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Mena G, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus JK, Olsen PA, Pacleb M, Pagan CM, Peña N, Pham T, Pom CA, Postupna N, Rimorin C, Ruiz A, Saldi GA, Schantz AM, Shapovalova NV, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting JT, Torkelson A, Tran T, Valera Cuevas NJ, Walling-Bell S, Wang MQ, Waters J, Wilson AM, Xiao M, Haynor D, Gatto NM, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith KA, Close JL, Miller JA, Hodge RD, Larson EB, Grabowski TJ, Hawrylycz M, Keene CD, Lein ES. Integrated multimodal cell atlas of Alzheimer's disease. Nat Neurosci 2024;27:2366-2383. [PMID: 39402379 PMCID: PMC11614693 DOI: 10.1038/s41593-024-01774-5] [Show More Authors] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/28/2024] [Indexed: 10/19/2024]
31
Aldridge AI, West AE. Epigenetics and the timing of neuronal differentiation. Curr Opin Neurobiol 2024;89:102915. [PMID: 39277975 PMCID: PMC11611672 DOI: 10.1016/j.conb.2024.102915] [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: 06/16/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/17/2024]
32
Li M, Flack N, Larsen PA. Multifaceted Role of Specialized Neuropeptide-Intensive Neurons on the Selective Vulnerability to Alzheimer's Disease in the Human Brain. Biomolecules 2024;14:1518. [PMID: 39766225 PMCID: PMC11673071 DOI: 10.3390/biom14121518] [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: 08/19/2024] [Revised: 10/11/2024] [Accepted: 11/21/2024] [Indexed: 01/11/2025]  Open
33
Shibata D. Human Brain Ancestral Barcodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.14.603450. [PMID: 39071290 PMCID: PMC11275915 DOI: 10.1101/2024.07.14.603450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
34
Chen ZJ, Das SS, Kar A, Lee SHT, Abuhanna KD, Alvarez M, Sukhatme MG, Gelev KZ, Heffel MG, Zhang Y, Avram O, Rahmani E, Sankararaman S, Heinonen S, Peltoniemi H, Halperin E, Pietiläinen KH, Luo C, Pajukanta P. Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.02.621694. [PMID: 39554055 PMCID: PMC11566006 DOI: 10.1101/2024.11.02.621694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
35
Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, Luo C. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature 2024;635:481-489. [PMID: 39385032 PMCID: PMC11560841 DOI: 10.1038/s41586-024-08030-7] [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: 10/24/2022] [Accepted: 09/06/2024] [Indexed: 10/11/2024]
36
Fan S, Dang D, Gao L, Zhang S. ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2406364. [PMID: 39264290 PMCID: PMC11558076 DOI: 10.1002/advs.202406364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 08/03/2024] [Indexed: 09/13/2024]
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Rahman S, Roussos P. The 3D Genome in Brain Development: An Exploration of Molecular Mechanisms and Experimental Methods. Neurosci Insights 2024;19:26331055241293455. [PMID: 39494115 PMCID: PMC11528596 DOI: 10.1177/26331055241293455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 10/08/2024] [Indexed: 11/05/2024]  Open
38
Gordon JA, Dzirasa K, Petzschner FH. The neuroscience of mental illness: Building toward the future. Cell 2024;187:5858-5870. [PMID: 39423804 PMCID: PMC11490687 DOI: 10.1016/j.cell.2024.09.028] [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: 09/13/2024] [Revised: 09/16/2024] [Accepted: 09/16/2024] [Indexed: 10/21/2024]
39
Zemke NR, Lee S, Mamde S, Yang B, Berchtold N, Maximiliano Garduño B, Indralingam HS, Bartosik WM, Lau PK, Dong K, Yang A, Tani Y, Chen C, Zeng Q, Ajith V, Tong L, Seng C, Li D, Wang T, Xu X, Ren B. Epigenetic and 3D genome reprogramming during the aging of human hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618338. [PMID: 39463924 PMCID: PMC11507755 DOI: 10.1101/2024.10.14.618338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
40
Pedrotti S, Castiglioni I, Perez-Estrada C, Zhao L, Chen JP, Crosetto N, Bienko M. Emerging methods and applications in 3D genomics. Curr Opin Cell Biol 2024;90:102409. [PMID: 39178735 DOI: 10.1016/j.ceb.2024.102409] [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: 05/13/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/26/2024]
41
Sullivan PF, Yao S, Hjerling-Leffler J. Schizophrenia genomics: genetic complexity and functional insights. Nat Rev Neurosci 2024;25:611-624. [PMID: 39030273 DOI: 10.1038/s41583-024-00837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2024] [Indexed: 07/21/2024]
42
Marumo T, Yoshida N, Inoue N, Yamanouchi M, Ubara Y, Urakami S, Fujii T, Takazawa Y, Ohashi K, Kawarazaki W, Nishimoto M, Ayuzawa N, Hirohama D, Nagae G, Fujimoto M, Arai E, Kanai Y, Hoshino J, Fujita T. Aberrant proximal tubule DNA methylation underlies phenotypic changes related to kidney dysfunction in patients with diabetes. Am J Physiol Renal Physiol 2024;327:F397-F411. [PMID: 38961842 DOI: 10.1152/ajprenal.00124.2024] [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: 04/22/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]  Open
43
Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. Cell-type-specific effects of age and sex on human cortical neurons. Neuron 2024;112:2524-2539.e5. [PMID: 38838671 DOI: 10.1016/j.neuron.2024.05.013] [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: 11/29/2023] [Revised: 03/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
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Wei X, Li J, Cheng Z, Wei S, Yu G, Olsen ML. Decoding the Epigenetic Landscape: Insights into 5mC and 5hmC Patterns in Mouse Cortical Cell Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602342. [PMID: 39026756 PMCID: PMC11257419 DOI: 10.1101/2024.07.06.602342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
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Chen R, Nie P, Wang J, Wang GZ. Deciphering brain cellular and behavioral mechanisms: Insights from single-cell and spatial RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024;15:e1865. [PMID: 38972934 DOI: 10.1002/wrna.1865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 07/09/2024]
46
Tian W, Ding W, Shen J, Li D, Wang T, Ecker JR. BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data. Bioinformatics 2024;40:btae404. [PMID: 38905499 PMCID: PMC11216754 DOI: 10.1093/bioinformatics/btae404] [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: 09/22/2023] [Revised: 03/27/2024] [Accepted: 06/20/2024] [Indexed: 06/23/2024]  Open
47
Pletenev I, Bazarevich M, Zagirova D, Kononkova A, Cherkasov A, Efimova O, Tiukacheva E, Morozov K, Ulianov K, Komkov D, Tvorogova A, Golimbet V, Kondratyev N, Razin S, Khaitovich P, Ulianov S, Khrameeva E. Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome. Nucleic Acids Res 2024;52:6234-6252. [PMID: 38647066 PMCID: PMC11194087 DOI: 10.1093/nar/gkae271] [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: 11/07/2023] [Revised: 03/21/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]  Open
48
Outeiro TF, Kalia LV, Bezard E, Ferrario J, Lin CH, Salama M, Standaert DG, Taiwo L, Takahashi R, Vila M, Mollenhauer B, Svenningsson P. Basic Science in Movement Disorders: Fueling the Engine of Translation into Clinical Practice. Mov Disord 2024;39:929-933. [PMID: 38576081 DOI: 10.1002/mds.29802] [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: 02/21/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024]  Open
49
Zhang L, Bartosovic M. Single-cell mapping of cell-type specific chromatin architecture in the central nervous system. Curr Opin Struct Biol 2024;86:102824. [PMID: 38723561 DOI: 10.1016/j.sbi.2024.102824] [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: 12/13/2023] [Revised: 03/22/2024] [Accepted: 04/08/2024] [Indexed: 05/19/2024]
50
Zagirova D, Kononkova A, Vaulin N, Khrameeva E. From compartments to loops: understanding the unique chromatin organization in neuronal cells. Epigenetics Chromatin 2024;17:18. [PMID: 38783373 PMCID: PMC11112951 DOI: 10.1186/s13072-024-00538-6] [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: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024]  Open
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