Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes

Abstract

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 Arabidopsis thaliana 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.

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

“…Chromatin patterning after allopolyploidization is well established (Wendel et al 2018), but relatively little is known about the effects of autopolyploidization. Ploidy-induced chromatin accessibility changes have been reported in Arabidopsis (Karaaslan et al 2020) and wheat (Lu et al 2020). Similarly, during Arabidopsis somatic polyploidization, 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 the light response (Karaaslan et al 2020).…”

“…Ploidy-induced chromatin accessibility changes have been reported in Arabidopsis (Karaaslan et al 2020) and wheat (Lu et al 2020). Similarly, during Arabidopsis somatic polyploidization, 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 the light response (Karaaslan et al 2020). In the allopolyploid wheat genome, chromatin of the smaller D genome is more accessible than that of the larger A and B genomes.…”

Characterization of a Plant Nuclear Matrix Constituent Protein in Liverwort

“…DNA FISH in Marchantia nuclei was adapted from Bi et al (2017). Around 5,000 nuclei were sorted with a Beckman Coulter MofFlo XDP as described in Karaaslan et al (2020a). The sorted nuclei were centrifuged for 3,000 × g at 4 • C for 7 min.…”

Distinct guard cell specific remodeling of chromatin accessibility during abscisic acid and CO2 dependent stomatal regulation

“…Plant hormones are key signaling molecules controlling numerous aspects of plant life that coordinate genome activity with environmental conditions (4,5). Recent studies have provided insight into how chromatin structure changes during plant development (6)(7)(8)(9)(10)(11)(12) and in response to environmental and hormonal stimuli (13)(14)(15).…”