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📰 Understanding gene regulation in the cell cycle through deep learning

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In a study published in the journal communications type, scientists are developing a new tool for studying the cell cycle: “DeepCycle”. The latter combines a method based on high-resolution single-cell sequencing and a deep learning approach to reconstruct gene expression maps of the cell cycle (The cell cycle is the set of phases through which a cell passes between two divisions …). In this way, DeepCycle helps to better understand the regulation (The term regulation refers in its concrete sense to a technical discipline, which is …) genes and the factors involved in this process. This technological advancement is a tool (A tool is a purposeful object used by a living being to increase its …) powerful that can be applied to a wide range of systems, from cell lines to human pathologies.

The cell cycle is the process by which the genome (The genome is all the genetic material of an individual or a …) of a cell is duplicated to allow the division (Division is a law of composition that associates the product of the first with two numbers …) and create new cells. It is a fundamental process, which requires a check (The word control can have several meanings. It can be used as a synonym for examination, for …) severe, mistakes can cause pathologies such as cancer. To better understand how it works, an understanding dynamic (The word dynamic is often used to designate or qualify what refers to movement. It …) quantitative gene regulation everything (The whole understood as the whole of what exists is often interpreted as the world or …) the whole cycle is still lacking. The DeepCycle tool developed here provides a method for reconstructing high-resolution cell cycle gene expression maps for mouse and human cell models at different cycle stages.

Currently, the tools used to observe the dynamics of gene expression during the cell cycle do not allow for studies inhabit, they disturb the cells and are not very generalizable. Bring data (In information technology (IT), data is an elementary description, often …) easier to interpret, the DeepCycle tool is based on a Net (A computer network is a set of equipment connected to each other to exchange information …) of deep neurons to learn the pathway (The trajectory is the line described by any point of a moving object, and …) gene expression during the cell cycle. Analyze for each embarrassed (A gene is a deoxyribonucleic acid (DNA) sequence that specifies the …) mRNA splicing dynamics (unspliced ​​/ spliced) and deduces a “speed (We stand out 🙂 of RNA “, predictive value of the state of the cells. In this way, DeepCycle allows to sort the cells according to the stage (A stadium (from the ancient Greek στ? Διον stadion, from the verb …) cell cycle and to follow its progress, providing very precise data.

To prove the power (The word power is used in several fields with a particular meaning 🙂 from DeepCycle, scientists generated single-celled data from sequencing (In biochemistry, sequencing consists of determining the linear order of …) RNA deepened from embryonic stem cells of mouse (The term topo is an ambiguous vulgar name that can designate, for French speakers, before …) and human fibroblasts. This allowed to develop high resolution gene expression dynamics, to discover transcription factors that coordinate cell cycle regulation and to highlight the link with pluripotency regulators. Scientists were able to characterize the point (graphics) branch point where human fibroblasts exit their cell cycle during phase (The word phase can have different meanings, it is used in different fields and …) G1 and enter cell cycle arrest (G0). They also identified novel marker genes and transcription factors that drive this process, paving the way for characterization systematic (In the life sciences and natural history, systematics is the science that has for …) of the G1-G0 transition in different cell models.

DeepCycle therefore constitutes a significant advance, producing more robust and generalizable data, for the fields of study of cell cycle regulation, gene expression dynamics and Research (Scientific research primarily refers to all actions undertaken with a view to …) biomedical in general.


Figure: DeepCycle is an autoencoder that, from unspliced ​​and spliced ​​reads of single-cell RNA sequencing experiments, is able to sort cells based on their progress through the cell cycle represented by θ.

To know more:

Dynamics of cell cycle gene regulation revealed by RNA velocity and deep learning.
Riba A, Oravecz A, Durik M, Jiménez S, Alumni V, Cerciat M, Jung M, Keime C, Keyes WM, Molina N.
Nature Communications. May 23, 2022 doi: 10.1038 / s41467-022-30545-8.

laboratory:
Institute of genetic (Genetics (from the Greek genno γεννώ = to give birth) is …), molecular biology (Molecular biology (sometimes abbreviated bio mol or BM) is a discipline …) and mobile-IGBMC (CNRS / Inserm / University of Strasbourg) – 1, Street (The street is a circulation space in the city that serves homes and places …) Laurent crisps. 76404 Ilkirch Cedex.

Contact:
Nacho Molina- Researcher (A researcher (female researcher) refers to a person whose job is to do research …) CNRS (The National Center for Scientific Research, better known by the acronym CNRS, is the largest …) to theInstitute (An institution is a permanent organization created for a specific purpose. It is …) genetics, biology (Biology, commonly called “bio”, is the science of life ….) molecular and cellular – IGBMC (CNRS / Inserm / University of Strasbourg) –
molinan on igbmc.fr

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