Spatial profiling of chromatin accessibility in mouse and human tissues.

Autor: Deng Y; Department of Biomedical Engineering, Yale University, New Haven, CT, USA.; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA., Bartosovic M; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden., Ma S; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Zhang D; Department of Biomedical Engineering, Yale University, New Haven, CT, USA., Kukanja P; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden., Xiao Y; Department of Biomedical Engineering, Columbia University, New York, NY, USA., Su G; Department of Biomedical Engineering, Yale University, New Haven, CT, USA.; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA., Liu Y; Department of Biomedical Engineering, Yale University, New Haven, CT, USA.; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA., Qin X; Department of Biomedical Engineering, Yale University, New Haven, CT, USA.; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA., Rosoklija GB; Department of Psychiatry, Columbia University, New York, NY, USA.; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA.; Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia., Dwork AJ; Department of Psychiatry, Columbia University, New York, NY, USA.; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA.; Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia.; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA., Mann JJ; Department of Psychiatry, Columbia University, New York, NY, USA.; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA.; Department of Radiology, Columbia University, New York, NY, USA., Xu ML; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA., Halene S; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.; Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA., Craft JE; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA., Leong KW; Department of Biomedical Engineering, Columbia University, New York, NY, USA.; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA., Boldrini M; Department of Psychiatry, Columbia University, New York, NY, USA.; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA., Castelo-Branco G; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. goncalo.castelo-branco@ki.se.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden. goncalo.castelo-branco@ki.se., Fan R; Department of Biomedical Engineering, Yale University, New Haven, CT, USA. rong.fan@yale.edu.; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA. rong.fan@yale.edu.; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA. rong.fan@yale.edu.; Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA. rong.fan@yale.edu.
Jazyk: angličtina
Zdroj: Nature [Nature] 2022 Sep; Vol. 609 (7926), pp. 375-383. Date of Electronic Publication: 2022 Aug 17.
DOI: 10.1038/s41586-022-05094-1
Abstrakt: Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context 1 . The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping 2-5 , but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry 6 and microfluidic deterministic barcoding 5 . Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.
(© 2022. The Author(s).)
Databáze: MEDLINE
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