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Noack, F. ; Vangelisti, S. ; Ditzer, N.* ; Chong, F. ; Albert, M.* ; Bonev, B.

Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids.

Nat. Cell Biol. 12, 1873-1883 (2023)
Verlagsversion DOI PMC
Open Access Hybrid
Creative Commons Lizenzvertrag
Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomics methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a method—3D genome, RNA, accessibility and methylation sequencing (3DRAM-seq)—that simultaneously interrogates spatial genome organization, chromatin accessibility and DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA sequencing in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay to profile cell-type-specific enhancer activity in organoids and to functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Transcription Factors; Cerebral Organoids; Dna Methylation; Open Chromatin; Binding; Genome; Organization; Principles; Landscape; Dynamics
Sprache englisch
Veröffentlichungsjahr 2023
HGF-Berichtsjahr 2023
ISSN (print) / ISBN 1465-7392
e-ISSN 1476-4679
Zeitschrift Nature Cell Biology
Quellenangaben Band: 12, Heft: 12, Seiten: 1873-1883 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort Heidelberger Platz 3, Berlin, 14197, Germany
Begutachtungsstatus Peer reviewed
Institut(e) Helmholtz Pioneer Campus (HPC)
POF Topic(s) 30204 - Cell Programming and Repair
Forschungsfeld(er) Pioneer Campus
PSP-Element(e) G-510004-001
Förderungen EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
Deutsche Forschungsgemeinschaft (German Research Foundation)
DOI 10.1038/s41556-023-01296-5
WOS ID 001158641000014
WOS ID 001107215100001
Scopus ID 85177634151
PubMed ID 37996647
Erfassungsdatum 2023-12-11
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