Alternative splicing in stem cells and development: research progress and emerging technologies

Yan Jin^{1

2

3}, XiaoLin Liang^{4

5

6}, Xiangting Wang^{7

8

9

10}

Affiliations

¹ Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China. jiny58@ustc.edu.cn.
² The RNA Institute, University of Science and Technology of China, Hefei, Anhui, 230026, China. jiny58@ustc.edu.cn.
³ MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, 230026, China. jiny58@ustc.edu.cn.
⁴ Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China.
⁵ The RNA Institute, University of Science and Technology of China, Hefei, Anhui, 230026, China.
⁶ MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, 230026, China.
⁷ Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.
⁸ The RNA Institute, University of Science and Technology of China, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.
⁹ Centre for Leading Medicine and Advanced Technologies of IHM, University of Science and Technology of China, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.
¹⁰ MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.

PMID: 40465008
PMCID: PMC12137872
DOI: 10.1186/s13619-025-00238-w

Review

Alternative splicing in stem cells and development: research progress and emerging technologies

Yan Jin et al. Cell Regen. 2025.

. 2025 Jun 4;14(1):20.

doi: 10.1186/s13619-025-00238-w.

Authors

Yan Jin^{1

2

3}, XiaoLin Liang^{4

5

6}, Xiangting Wang^{7

8

9

10}

Affiliations

¹ Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China. jiny58@ustc.edu.cn.
² The RNA Institute, University of Science and Technology of China, Hefei, Anhui, 230026, China. jiny58@ustc.edu.cn.
³ MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, 230026, China. jiny58@ustc.edu.cn.
⁴ Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China.
⁵ The RNA Institute, University of Science and Technology of China, Hefei, Anhui, 230026, China.
⁶ MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, 230026, China.
⁷ Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.
⁸ The RNA Institute, University of Science and Technology of China, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.
⁹ Centre for Leading Medicine and Advanced Technologies of IHM, University of Science and Technology of China, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.
¹⁰ MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, 230026, China. wangxt11@ustc.edu.cn.

PMID: 40465008
PMCID: PMC12137872
DOI: 10.1186/s13619-025-00238-w

Abstract

Alternative splicing is a key regulatory mechanism that generates transcriptomic diversity by selectively splicing pre-RNA molecules in different ways, leading to the production of multiple RNA isoforms from a single gene. This process is crucial for the fine-tuning of gene expression and is tightly regulated during various biological processes. Recent studies have highlighted how alternative splicing contributes to stem cells self-renewal and differentiation, as well as how dysregulation of splicing factors can impact stem cells behavior and lead to developmental abnormalities or diseases. This review summarizes the current understanding of alternative splicing in stem cells and development, focusing on the molecular mechanisms that govern alternative splicing regulation, the role of splicing factors, and the impact of splicing isoforms on stem cell fate determination and developmental processes. We also discuss emerging technologies, such as CRISPR/Cas-based tools, single-cell long-read RNA sequencing, imaging technologies and 3D culture systems, which are advancing our ability to study alternative splicing in vitro and in vivo. Overall, this field is rapidly evolving, revealing new insights into how alternative splicing shapes the molecular landscape and functions of stem cells and developmental processes.

Keywords: Alternative splicing; Development; Differentiation; Splicing factor; Stem Cells.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: All authors declare that they have no competing interests.

Figures

**Fig. 1**
Splicing factors and specific AS events in brain development. A Neuron-enriched splicing factor protein families co-regulate brain development. B Nova2 represses exon inclusion and Ptbp2-mediated intron retention to control specifically development of laminar structure in cortical excitatory neurons (Green dots) as well as proper motor coordination and synapse formation in cerebellar inhibitory Purkinje cells (Red dots). C Ptbp2, identified by transcriptome profiling, promotes exon skipping in *Shtn1* during axonogenesis. D The long noncoding RNA *Gm2694* undergoes AS to generate multiple isoforms in the cerebellum, including PM and *Synage*. PM is enriched in cerebellar granule cells. It associates with the Pax6/Mll1 complex to enhance transcription of *Cbln1* and synapse integrity in the nucleus of granule cells. *Synage* is predominantly expressed in cerebellar Purkinje cells. It regulates synapse stability and neuronal function by acting both as a scaffold for the Lrp1-Hsp90aa-Psd95 complex in postsynaptic terminals of Purkinje cells and as a miRNA sponge in presynaptic terminals of granule cells

**Fig. 2**
Splicing factors and specific AS events in heart development. A Various splicing factors mediate specific AS events to co-regulate heart development. B Rbm24 prevents PTB- and hnRNP A1/A2-mediated suppression of exon inclusion. Rbm24 facilitates exon inclusion in genes such as *Actn2*, *Myh10*, *Abcc9*, and *Slc25a3* to control cardiogenesis and sarcomere assembly

**Fig. 3**
Emerging technologies in AS research

See this image and copyright information in PMC

References

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Alternative splicing in stem cells and development: research progress and emerging technologies

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Alternative splicing in stem cells and development: research progress and emerging technologies

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