In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei
| Autor: | Kimaya Bakhle, Vikki M. Weake, Juan Jauregui-Lozano |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Cell type
Green Fluorescent Proteins ATAC-seq Transcriptome 03 medical and health sciences 0302 clinical medicine Genetics Animals 030304 developmental biology Cell Nucleus Investigation 0303 health sciences biology Epigenome biology.organism_classification Chromatin Cell biology Histone Code Histone Drosophila melanogaster Organ Specificity biology.protein Chromatin Immunoprecipitation Sequencing Chromatin immunoprecipitation 030217 neurology & neurosurgery |
| Zdroj: | Genetics |
| ISSN: | 1943-2631 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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