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In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei.
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- Additional Information
- Source:
Publisher: Oxford University Press Country of Publication: United States NLM ID: 0374636 Publication Model: Print Cited Medium: Internet ISSN: 1943-2631 (Electronic) Linking ISSN: 00166731 NLM ISO Abbreviation: Genetics Subsets: MEDLINE
- Publication Information:
Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Austin, Tex. [etc.]
- Subject Terms:
- Abstract:
The chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein. The perinuclear space-localized KASH domain anchors GFP to the outer nuclear membrane, and expression of UAS-GFPKASH can be controlled by tissue-specific Gal4 drivers. Using this protocol, we profiled chromatin accessibility using an improved version of Assay for Transposable Accessible Chromatin followed by sequencing (ATAC-seq), called Omni-ATAC. In addition, we examined the distribution of histone marks using Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) in adult photoreceptor neurons. We show that the chromatin landscape of photoreceptors reflects the transcriptional state of these cells, demonstrating the quality and reproducibility of our approach for profiling the transcriptome and epigenome of specific cell types in Drosophila.
(© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email:
[email protected].)
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- Grant Information:
R01 EY024905 United States EY NEI NIH HHS; UL1 TR002529 United States TR NCATS NIH HHS
- Contributed Indexing:
Keywords: Drosophila; ATAC-seq; cell type; chromatin; photoreceptor; transcription
- Accession Number:
0 (Chromatin)
147336-22-9 (Green Fluorescent Proteins)
- Publication Date:
Date Created: 20210522 Date Completed: 20220317 Latest Revision: 20220317
- Publication Date:
20231215
- Accession Number:
PMC8864739
- Accession Number:
10.1093/genetics/iyab079
- Accession Number:
34022041
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