Whole-mount Clearing and Staining of Arabidopsis Flower Organs and Siliques

Pseudouridine guides germline small RNA transport and epigenetic inheritance

Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes1. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation2,3. In C. elegans, these inherited small RNAs have poly (UG) tails4, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop novel assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors. We also detect substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and piwi-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are localized to sperm cells, and we found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ and is required for transport of easiRNAs into sperm cells from the vegetative nucleus. We further show that Exportin-t is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, Ψ has a conserved role in marking inherited small RNAs in the germline.

A Novel Imaging Protocol for Investigating Arabidopsis thaliana Siliques and Seeds Using X-rays

Understanding silique and seed morphology is essential to developmental biology. Arabidopsis thaliana is one of the best-studied plant models for understanding the genetic determinants of seed count and size. However, the small size of its seeds, and their encasement in a pod known as silique, makes investigating their numbers and morphology both time consuming and tedious. Researchers often report bulk seed weights as an indicator of average seed size, but this overlooks individual seed details. Removal of the seeds and subsequent image analysis is possible, but automated counts are often impossible due to seed pigmentation and shadowing. Traditional ways of analyzing seed count and size, without their removal from the silique, involve lengthy histological processing (24-48 h) and the use of toxic organic solvents. We developed a method that is non-invasive, requires minimal sample processing, and obtains data in a short period of time (1-2 h). This method uses a custom X-ray imaging system to visualize Arabidopsis siliques at different stages of their growth. We show that this process can be successfully used to analyze the overall topology of Arabidopsis siliques and seed size and count. This new method can be easily adapted for other plant models. Key features • No requirement for organic solvents for imaging siliques. • Easy image capture and rapid turnaround time for obtaining data. • Protocol may be easily adapted for other plant models.

MAX: a simple, affordable, and rapid tissue clearing reagent for 3D imaging of wide variety of biological specimens

Transparency of biological specimens is crucial to obtaining detailed 3-dimensional images and understanding the structure and function of biological specimens. This transparency or tissue clearing can be achieved by adjusting the refractive index (RI) with embedding media and removing light barriers such as lipids, inorganic deposits, and pigments. Many currently available protocols consist of multiple steps to achieve sufficient transparency, making the process complex and time-consuming. Thus, in this study, we tailored the recipe for RI adjustment media named MAX based on the recently reported MACS protocol to achieve a single-step procedure, especially for ECM-rich tissues. This was achieved by the improvement of the tissue penetrability of the RI-matching reagent by combining MXDA with sucrose or iodixanol. While this was sufficient for the 3D imaging in many applications, MAX can also be combined with modular processes for de-lipidation, de-coloration, and de-calcification to further maximize the transparency depending on the special features of the tissues. Our approach provides an easy alternative for tissue clearing and 3D imaging.

From Microscopy to Nanoscopy: Defining an Arabidopsis thaliana Meiotic Atlas at the Nanometer Scale

Visualization of meiotic chromosomes and the proteins involved in meiotic recombination have become essential to study meiosis in many systems including the model plant Arabidopsis thaliana. Recent advances in super-resolution technologies changed how microscopic images are acquired and analyzed. New technologies enable observation of cells and nuclei at a nanometer scale and hold great promise to the field since they allow observing complex meiotic molecular processes with unprecedented detail. Here, we provide an overview of classical and advanced sample preparation and microscopy techniques with an updated Arabidopsis meiotic atlas based on super-resolution microscopy. We review different techniques, focusing on stimulated emission depletion (STED) nanoscopy, to offer researchers guidance for selecting the optimal protocol and equipment to address their scientific question.

Laser-Assisted Microdissection of Plant Embryos for Transcriptional Profiling

Transcriptomic studies have proven powerful and effective as a tool to study the molecular underpinnings of plant development. Still, it remains challenging to disentangle cell- or tissue-specific transcriptomes in complex structures like the plant seed. In particular, the embryo of flowering plants is embedded in the endosperm, a nurturing tissue, which, in turn, is enclosed by the maternal seed coat. Here, we describe laser-assisted microdissection (LAM) to isolate highly pure embryo tissue from whole seeds. This technique is applicable to virtually any plant seed, and we illustrate the use of LAM to isolate embryos from species of the Boechera and Solanum genera. LAM is a tool that will greatly help to increase the repertoires of tissue-specific transcriptomes, including those of embryos and parts thereof, in nonmodel plants.