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General Transcription Factors

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

Master Transcription Regulators

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

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Nuclear reprogramming is a process of transforming one cell type into an unrelated cell type by epigenetic changes that alter the cell’s original gene expression pattern. Such epigenetic changes force cells to express a different set of genes, which play a significant role in inducing transformation into other cell types. Nuclear reprogramming offers applications in reproductive cloning for livestock propagation and regenerative medicine — developing patient-specific cells for...

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Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

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SinCMat: A single-cell-based method for predicting functional maturation transcription factors.

Sybille Barvaux¹, Satoshi Okawa², Antonio Del Sol³

¹Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg.

Stem Cell Reports

|January 12, 2024

Summary

This study introduces SinCMat, a computational tool predicting transcription factors (TFs) for functional cell maturation. SinCMat aids regenerative medicine by identifying key TFs to engineer fully mature cells.

Keywords:

cell engineering cellular therapy functional cell maturation scRNA-seq transcription factors

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Area of Science:

Regenerative Medicine
Computational Biology
Genomics

Background:

Generating fully mature, functional cells remains a challenge in regenerative medicine.
Existing computational methods predict cell differentiation factors but not maturation factors.

Purpose of the Study:

To develop a computational method, SinCMat, for predicting transcription factors (TFs) crucial for functional cell maturation.
To address the gap in predicting TFs specifically involved in the cell maturation process.

Main Methods:

Developed SinCMat, a single-cell RNA sequencing (RNA-seq)-based computational method.
Modeled cell maturation to identify pairs of identity and signal-dependent TFs co-targeting maturation genes.
Applied SinCMat to large-scale datasets like the Mouse Cell Atlas and Tabula Sapiens.

Main Results:

SinCMat successfully recapitulated known cell maturation TFs.
Identified novel candidate TFs involved in functional cell maturation.
Demonstrated the method's accuracy and scalability on diverse datasets.

Conclusions:

SinCMat is a valuable computational resource for identifying TFs driving functional cell maturation.
This method complements existing tools, advancing the goal of producing fully mature cells for regenerative medicine applications.