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Marker genes reveal dynamic features of cell evolving processes.

作者信息

Cao Wenjie, Zhang Bengong, Zhou Tianshou

机构信息

School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China.

School of Mathematics & Statistics, Wuhan Textile University, Wuhan 430200, China.

出版信息

Bioinform Adv. 2025 Aug 5;5(1):vbaf185. doi: 10.1093/bioadv/vbaf185. eCollection 2025.


DOI:10.1093/bioadv/vbaf185
PMID:40896714
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12396811/
Abstract

MOTIVATION: Embryonic cells finally evolve into various types of mature cells, where cell fate determinations play pivotal roles, but dynamic features of this process remain elusive. RESULTS: We analyze four single-cell RNA sequencing datasets on mouse embryo cells, mouse embryonic fibroblasts, human bone marrow, and intestine organoid. We show that key (high expression) genes of each organism exhibit different statistical features and expression patterns before and after branch, e.g. for mouse embryo cells, the mRNA distribution of gene Gata3 is bimodal before branch, unimodal at branching point and trimodal for one branch but bimodal for the other branch. Moreover, there is a distribution mode such that it is the same before and after branch, and this fact would account for maintenance of the genetic information in a complex cell evolving process. Machine learning reveal that along the cell pseudo-time trajectory, the strength that one key gene regulates another is fundamentally increasing before branch but is always monotonically increasing after branch; burst size and frequency of key genes are always monotonically decreasing before branch but monotonically increasing for one branch and monotonically decreasing for another branch. Our results unveil the essential features of dynamic cell processes and can be taken as a supplement for accurately screening marker genes of cell fate determination on basis of the existed methods. AVAILABILITY AND IMPLEMENTATION: The implementation of CFD is available at https://github.com/cellwj/CFD and the preprocessed data is available at https://zenodo.org/records/14367638.Cell fate determination, single-cell RNA sequencing data, marker gene, cell process, developmental branch.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/1b7f993e7e8d/vbaf185f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/f987957d4b9a/vbaf185f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/068082f66ba3/vbaf185f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/db8943c62c55/vbaf185f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/108bf2011bd1/vbaf185f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/449e705fee89/vbaf185f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/b054a7a319ef/vbaf185f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/1b7f993e7e8d/vbaf185f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/f987957d4b9a/vbaf185f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/068082f66ba3/vbaf185f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/db8943c62c55/vbaf185f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/108bf2011bd1/vbaf185f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/449e705fee89/vbaf185f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/b054a7a319ef/vbaf185f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0d86/12396811/1b7f993e7e8d/vbaf185f7.jpg

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本文引用的文献

[1]
Exact burst-size distributions for gene-expression models with complex promoter structure.

Biosystems. 2024-12

[2]
Edge-relational window-attentional graph neural network for gene expression prediction in spatial transcriptomics analysis.

Comput Biol Med. 2024-5

[3]
Gene trajectory inference for single-cell data by optimal transport metrics.

Nat Biotechnol. 2025-2

[4]
Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features.

Genome Res. 2023-8

[5]
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells.

Genome Res. 2023-8

[6]
Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics.

Bioinformatics. 2023-7-1

[7]
Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.

Nucleic Acids Res. 2023-1-11

[8]
Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids.

Nat Commun. 2021-12-15

[9]
Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data.

Brief Bioinform. 2021-11-5

[10]
Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics.

Nat Commun. 2021-7-23

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