Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes
The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/11/1478 |
| _version_ | 1797549004344524800 |
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| author | Ezgi Süheyla Karaaslan Natalie Faiß Chang Liu Kenneth Wayne Berendzen |
| author_facet | Ezgi Süheyla Karaaslan Natalie Faiß Chang Liu Kenneth Wayne Berendzen |
| author_sort | Ezgi Süheyla Karaaslan |
| collection | DOAJ |
| description | The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from <i>Arabidopsis thaliana</i> by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response. |
| first_indexed | 2024-03-10T15:08:37Z |
| format | Article |
| id | doaj.art-fef12fc01426462693e13c14c7c77fe8 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T15:08:37Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-fef12fc01426462693e13c14c7c77fe82023-11-20T19:36:58ZengMDPI AGPlants2223-77472020-11-01911147810.3390/plants9111478Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility LandscapesEzgi Süheyla Karaaslan0Natalie Faiß1Chang Liu2Kenneth Wayne Berendzen3Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, GermanyCenter for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, GermanyCenter for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, GermanyCenter for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, GermanyThe capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from <i>Arabidopsis thaliana</i> by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response.https://www.mdpi.com/2223-7747/9/11/1478FANSendopolyploidyskotomorphogenesisphotomorphogenesisATAC-seqhypocotyl |
| spellingShingle | Ezgi Süheyla Karaaslan Natalie Faiß Chang Liu Kenneth Wayne Berendzen Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes Plants FANS endopolyploidy skotomorphogenesis photomorphogenesis ATAC-seq hypocotyl |
| title | Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes |
| title_full | Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes |
| title_fullStr | Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes |
| title_full_unstemmed | Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes |
| title_short | Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes |
| title_sort | isolation of lineage specific nuclei based on distinct endoreduplication levels and tissue specific markers to study chromatin accessibility landscapes |
| topic | FANS endopolyploidy skotomorphogenesis photomorphogenesis ATAC-seq hypocotyl |
| url | https://www.mdpi.com/2223-7747/9/11/1478 |
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