Sorting, storing and regulating messenger RNAs: the oocyte factory contributing to fertility

For a long time, the lipid membranes that surround cells and organelles were considered the main mechanism for keeping biological functions compartmentalized. More recently, research has shown how soluble biomolecules can condense into liquid droplets, like drops of vinegar separate from oil in a salad dressing, to create membrane-free organelles. The cell is like an emulsion, and these phase separations serve to organize the messengers of genetic information.

Messenger RNAs assemble in microdroplets like Russian dolls

RNA messengers can be soluble and diffused or repressed, condensed and stored in drops. They can even solidify pathologically. The condensation or dissolution of messengers not only controls the dissemination of information, but the mechanism by which drops assemble within drops, like Russian dolls, allows information to be classified into different compartments.

In an egg cell, a complete library encodes embryo development

The present study characterizes a new level of organization in the expression of genetic text. The DNA we inherit from our biological parents is a 4-letter code, A,T,C,G, encoding a dictionary of tens of thousands of genes along with the sequences that define their expression. For comparison, this corresponds to the number of words in a French dictionary. But the dictionary does not communicate a message. It is the order of the words placed in the right sequence at the right time that conveys a coherent text. A thick novel such as Victor Hugo's Les Misérables, contains 500,000 words. In an egg cell, tens of thousands of genes have been copied into tens of millions of messengers - a complete library encoding the embryo's early development. Like a book is organized at different levels, by the order of letters, words, sentences, paragraphs, chapters, book series, or libraries, the researchers who conducted this study show that messengers are organized at multiple scales. If the foundations A,T,G,C define the messenger, they show that the messengers self-assemble into nano-clusters, which co-assemble and divide into the different phases of a drop, among the many drops that form the cell emulsion.

Knowing the list of messenger RNAs is like having a list of words in a text without knowing where or when they were pronounced.

Using oocyte development in the nematode C. elegans as a model, the authors adapted imaging methods to count and locate copies of messenger RNAs. They also improved a method for sequencing RNAs condensed in drops. Conventional sequencing methods provide a list of the messenger RNAs in a cell, but do not differentiate between the number of disseminated copies and the number of copies stored and condensed in droplets. This is like knowing the list of words in a text, without knowing where or when they were pronounced. In the same way as words, sentences, paragraphs and chapters interact and contribute to make a text understandable, this study identifies a multi-scale organization of messengers: messengers self-assemble in clusters of a few dozen copies, which co-assemble in mesoscopic phases, forming macroscopic drops. The messengers temporarily stored in the drops are classified into chapters and sub-chapters before being released.

When too many copies of messenger RNA accumulate in a cell, they condense into droplets.

While a single author writes a text, the genetic messengers in a cell coordinate their own expression through a self-organizing mechanism. The message communicated emerges from this group of messengers that self-organize both autonomously and cooperatively. The researchers in this study have described two principles of self-organization. The first is the principle of saturation, by which a buffer stock of genetic information is stored. By way of comparison, water diffuses in the air, but when the air is saturated with water, the water molecules condense into drops that precipitate and fill water reservoirs such as lakes and oceans. Similarly, when too many copies of repressed messenger RNA accumulate in a cell, copies of identical messengers precipitate and condense in reservoir drops where they are stored.

A consequence of the saturation principle is the buffer effect. For example, when we add salt to a solution, the salt is soluble and diffuses, but beyond a certain threshold concentration (the saturation concentration), the excess salt precipitates. The salt concentration becomes buffered, any excess salt precipitates out, and the solution concentration remains unchanged. Researchers have shown that the same principle applies to information messengers: copies can be counted without being seen, and copies in excess, at saturation, self-aggregate to be stored in a reservoir drop.

A simple principle: birds of a feather flock together

The second self-organization principle described in the study is demixing, by which messenger copies organize themselves according to their identity. In a salad dressing, vinegar molecules assemble with vinegar molecules and oil molecules assemble with oil molecules: this is the principle of self-organization. If the cook shakes the salad dressing to mix it, the molecules self-organize just as quickly according to a simple principle: like attracts like. This second principle also applies to the messengers of genetic information. Together, the ability to store to saturation and to classify by demixing makes it possible for the flow of millions of genetic messengers to self-organize and develop a robust cellular identity that coordinates the cell’s expression with its activity and adapts to its environment. Dysregulation of these information flows is a source of infertility. Future applications also include the treatment of cancer, where these information flows are deregulated, of infections where the messenger machinery is taken hostage by viruses, and of degenerative diseases in which messengers solidify and are no longer active.

Press release CNRS, INSB

Pour en savoir plus :

Self-demixing of mRNA copies buffers mRNA:mRNA and mRNA:regulator stoichiometries.
Andrés H. Cardona, Szilvia Ecsedi, Mokrane Khier, Zhou Yi, Alia Bahri, Amira Ouertani, Florian Valero,
Margaux Labrosse, Sami Rouquet, Stéphane Robert, Agnès Loubat, Danielle Adekunle, and Arnaud
Hubstenberger, Cell 2023, sous presse

Contacts

Arnaud Hubstenberger
Chargé de Recherche CNRS - Institut de Biologie Valrose (Université Côte d'Azur, CNRS, Inserm)
+33 4 89 15 08 65 - Arnaud.HUBSTENBERGER@univ-cotedazur.fr

Illustration :
Les ARN messagers dont la traduction est réprimée s’autoassemblent dans des gouttes pour compacter et stocker
l’information. Ainsi, les copies de messagers en excès, à saturation, condensent, et la concentration de copies solubles
qui diffusent l’information est robustement fixée. Cet effet tampon contrôle le ratio entre messagers et regulateurs.
Un mécanisme de démixtion classent les ARNm en fonction de leur identité de séquence. Chaque messager autoregule ainsi son nombre de copies, en fonction de son activité et de son identité.
© Arnaud Hubstenberger et Andrés Cardona.