An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis

Summary

We provide here an efficient and reliable protocol for immunostaining, Fluorescence in situ Hybridization, DNA staining followed by quantitative, high-resolution imaging in whole-mount Arabidopsis thaliana ovules. This method was successfully used to analyze chromatin modifications and nuclear architecture.

Abstract

In flowering plants, the somatic-to-reproductive cell fate transition is marked by the specification of spore mother cells (SMCs) in floral organs of the adult plant. The female SMC (megaspore mother cell, MMC) differentiates in the ovule primordium and undergoes meiosis. The selected haploid megaspore then undergoes mitosis to form the multicellular female gametophyte, which will give rise to the gametes, the egg cell and central cell, together with accessory cells. The limited accessibility of the MMC, meiocyte and female gametophyte inside the ovule is technically challenging for cytological and cytogenetic analyses at single cell level. Particularly, direct or indirect immunodetection of cellular or nuclear epitopes is impaired by poor penetration of the reagents inside the plant cell and single-cell imaging is demised by the lack of optical clarity in whole-mount tissues.

Thus, we developed an efficient method to analyze the nuclear organization and chromatin modification at high resolution of single cell in whole-mount embedded Arabidopsis ovules. It is based on dissection and embedding of fixed ovules in a thin layer of acrylamide gel on a microscopic slide. The embedded ovules are subjected to chemical and enzymatic treatments aiming at improving tissue clarity and permeability to the immunostaining reagents. Those treatments preserve cellular and chromatin organization, DNA and protein epitopes. The samples can be used for different downstream cytological analyses, including chromatin immunostaining, fluorescence in situ hybridization (FISH), and DNA staining for heterochromatin analysis. Confocal laser scanning microscopy (CLSM) imaging, with high resolution, followed by 3D reconstruction allows for quantitative measurements at single-cell resolution.

Introduction

In flowering plants, the establishment of reproductive lineages begins with the differentiation of SMCs, female MMC and male microspore mother cell. The MMC develops from a sub-epidermal nucellar cell at the distal tip of the ovule primordium, and the microspore mother cell develops from sporogenous tissue in the anther locule, which are located deep inside the floral organs¹. SMCs undergo meiosis to produce haploid spores, which then give rise to the gametophytes upon mitosis. The female gametophyte, or embryo sac, consists of one egg cell, one central cell, two synergids and three antipodals. The male gametophyte, or pollen, is composed of one vegetative ....

Protocol

The procedure is described in the workflow in Figure 1, and the setup for dissection and embedding of tissues are presented in Figure 2.

1. Tissue Fixation

1. Collect 20-30 carpels in a microfuge tube containing freshly made BVO fixative buffer on ice.
2. Fix the tissue 30 min with gentle shaking at room temperature.
3. Spin the tubes containing the carpels in fixative in a benchtop microcentrifuge 1 min at 400 x g.
4. Remove carefully the fixative buffer and add 1 ml of PBT, place the tubes on ice.

2. Dissection and Embedding

1. Prep....

Results

We provide a robust protocol for large-scale preparation and processing of Arabidopsis ovules suitable for cytological staining in whole-mount. Thanks to the embedding, the ovules retain a 3-dimensional structure (Figure 3). Furthermore, the tissue processing including optical clarification enables imaging subcellular structures at high-resolution. Figure 4 shows DNA staining in whole-mount ovule primordia where heterochromatin appears as bright, well defined conspicuous foci (n.......

Discussion

In flowering plants, the female reproductive lineage is surrounded by several cell layers including the nucellus and the ovule teguments, thus rendering cytological staining in whole-mount technically challenging. Here we present an efficient protocol enabling the preparation and processing of a large number of ovules suitable for cytological staining such as immunostaining, DNA staining and fluorescence in situ hybridization in whole-mount. We successfully used it for the analysis of the female reproductive ger.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Solutions
BVO Fixation Buffer (based on32)			2 mM EGTA, pH 7.5, 1% (v/v) formaldehyde, 10% DMSO, 1x PBS, 0.1% Tween-20
PBT			1x PBS, 0.1% Tween-20
PBT-F			1x PBT, 2.5% (v/v) formaldehyde
30% acrylamide:bisacrylamide			3 g acrylamide, 0.33 g bisacrylamide, 1x PBS (prepare 10 ml, store at 4 °C)
200 ml 5% acrylamide mix in PBS			34 ml 30% acrylamide:bisacrylamide, 166 ml 1x PBS (make fresh from 30% stock)
20% ammoniumpersulfte			0.2 g ammoniumpersulfte, 1 ml sterile water (prepare aliquots with 1 ml and store at -20 °C)
20% sodium sulfite			0.2 g sodium sulfite, 1 ml sterile water (prepare aliquots with 1 ml and store at -20 °C)
Cell wall enzyme mix			0.5% (w/v) cellulase, 1% (w/v) driselase, 0.5% (w/v) pectolyase
Reagents and Materials
Formaldehyde	Sigma-Aldrich	F1635
DMSO	Sigma	D5879
Tris	Amaresco	0497
Ethanol	Schaurlau	ET00102500
Methanol	Schaurlau	ME03062500
Xylene	ROTH	4436.1
Cellulase	Sigma	1794
Driselase	Sigma	D8037
pectolyase	Sigma	P5936
Tween-20	Merck	8.22184.0500
EGTA	Sigma	E-4378
acrylamide	Sigma	A-3553
bisacrylamide	Sigma	M2022	toxic
ammoniumpersulfate	Sigma	A9164
Sodium sulfite	Fluka	71988
Anti-trimethyl-Histone H3 (Lys4)	Upstate	07-473
Anti- monomethyl-Histone H3 (Lys27)	Upstate	07-448
Alexa Fluor 488~goat ~anti ~rabbit (H+L)	Molecular Probe	A11008
ProlongGold	Invitrogen	P36934
Propidium iodide	Sigma	P4170	toxic
DAPI	Sigma	D9542	toxic
RNAse A	Roche	10109169001
Coplin jar	Huber & CO	10.055
Forceps	DUMONT BIOLOGY
Shaker	Heidolph	543-12310-00-0
Moist chamber			A plastic box with damp paper towel inside, a plastic support is put into the box for supporting the slides and keep slides from the water.
Superfrost Plus slide	Thermo Fisher	J1800AMNZ	Menzel-Gläser
FISH Tag DNA KIt	Invitrogen	F32947
GFP booster	Chromotek