NPAC Controls Pre-mRNA Splicing in Mouse Embryonic Stem Cells

Akiko Ximeng^*
*Correspondence: Akiko Ximeng, Department of Integrative Oncology, Fudan University, China, Email:

Introduction

Pre-mRNA splicing is a fundamental process in eukaryotic gene expression, ensuring the precise removal of introns and the joining of exons to produce mature mRNAs. This process is especially crucial in stem cells, which require tight regulation of their transcriptome to maintain pluripotency, enable differentiation, and respond to environmental cues. Among the myriad of regulators involved in splicing, NPAC (Nucleosome Positioning and Chromatin Remodeling Protein) has emerged as a significant player in mouse Embryonic Stem Cells (mESCs). Recent studies have shed light on how NPAC influences pre-mRNA splicing and, by extension, the broader landscape of stem cell biology. NPAC, also known as GLYR1, is primarily recognized for its role in chromatin regulation, where it modulates nucleosome positioning and interacts with chromatin remodeling complexes. However, its influence extends beyond chromatin to encompass post-transcriptional processes such as RNA splicing. In mESCs, where precise spatiotemporal control of gene expression is critical, NPAC appears to act as a bridge between chromatin state and the splicing machinery, ensuring that transcripts are processed accurately and efficiently. This dual functionality underscores NPAC’s pivotal role in integrating transcriptional and post-transcriptional regulation in stem cells. In the context of pre-mRNA splicing, NPAC’s activity is closely linked to its ability to interact with splicing factors and chromatin-associated proteins. Recent research has demonstrated that NPAC is recruited to gene bodies during transcription, where it co-localizes with RNA polymerase II and splicing factors. This positioning allows NPAC to influence the recruitment and assembly of the spliceosome, the multi-protein complex responsible for executing splicing. By acting as a scaffold or adaptor protein, NPAC facilitates the efficient processing of nascent transcripts, particularly those encoding proteins essential for stem cell identity and function.

Description

One of the most striking aspects of NPAC’s role in splicing is its ability to influence alternative splicing, a process that generates multiple transcript variants from a single gene. Alternative splicing is a key mechanism by which mESCs achieve the transcriptomic diversity necessary for their pluripotency and differentiation potential. Studies have shown that loss of NPAC leads to widespread changes in splicing patterns, affecting genes involved in key stem cell pathways such as cell cycle regulation, signal transduction, and metabolic control. For example, transcripts encoding components of the Wnt/β-catenin signaling pathway, a crucial regulator of pluripotency, exhibit aberrant splicing in NPAC-deficient cells. These findings highlight NPAC’s role as a critical regulator of transcript isoform diversity in stem cells. The molecular mechanisms underlying NPAC’s influence on splicing are beginning to be elucidated. One proposed model suggests that NPAC’s interaction with chromatin remodeling complexes alters nucleosome positioning at splice sites, thereby affecting the accessibility of these regions to the splicing machinery. Nucleosome positioning has been shown to influence splice site recognition, as tightly packed chromatin can hinder the binding of spliceosomal components. By modulating chromatin structure, NPAC may create a more favorable environment for splicing to occur. Additionally, NPAC’s interactions with splicing factors such as SR proteins and hnRNPs likely contribute to its role in regulating alternative splicing decisions [1,2].

Beyond its mechanistic roles, NPAC’s impact on mESC biology is evident from phenotypic studies. Knockdown or knockout of NPAC in mESCs results in impaired self-renewal and differentiation, phenotypes that can be attributed, at least in part, to defective splicing. Aberrant splicing of transcripts encoding transcription factors, signaling molecules, and chromatin regulators disrupts the regulatory networks that sustain pluripotency and guide lineage commitment. For instance, improper splicing of the Nanog transcript, a key pluripotency factor, has been observed in NPAC-deficient cells, leading to reduced expression and compromised stem cell identity. Similarly, defects in the splicing of differentiation-associated genes impair the ability of NPAC-deficient cells to transition to specialized cell types, underscoring the importance of NPAC-mediated splicing in developmental processes. The interplay between NPAC and the cellular stress response also warrants attention. mESCs are highly sensitive to environmental and metabolic stress, which can perturb transcription and splicing. NPAC has been implicated in mitigating the effects of such stress by stabilizing splicing machinery and ensuring the fidelity of transcript processing. For example, under conditions of oxidative stress, NPAC is recruited to stress-responsive genes, where it aids in the proper splicing of transcripts required for cellular adaptation. This protective role highlights NPAC’s function as a guardian of transcriptome integrity in the face of stress, further emphasizing its importance in stem cell biology [3].

The broader implications of NPAC’s role in splicing extend to developmental biology and regenerative medicine. As a key regulator of mESC transcriptomes, NPAC likely plays a similar role in other stem cell types and during early embryonic development. Understanding how NPAC-mediated splicing influences lineage specification and organogenesis could provide valuable insights into developmental disorders and congenital anomalies. Moreover, the ability to modulate NPAC activity or mimic its effects could have therapeutic applications in regenerative medicine, where reprogramming somatic cells to a pluripotent state or directing stem cell differentiation are key objectives. Emerging technologies such as single-cell RNA sequencing and high-resolution chromatin profiling are poised to accelerate our understanding of NPAC’s functions. These approaches will allow researchers to dissect NPAC’s contributions to splicing and chromatin regulation at unprecedented resolution, uncovering context-specific roles and potential interactions with other regulatory factors. Additionally, the development of targeted molecular tools, such as small molecules or CRISPR-based systems, could enable precise manipulation of NPAC activity, paving the way for experimental and therapeutic advancements [4,5].

Conclusion

Despite these exciting prospects, challenges remain in fully elucidating NPAC’s role in pre-mRNA splicing. The redundancy and complexity of splicing regulation in eukaryotic cells make it difficult to isolate the specific contributions of individual factors like NPAC. Furthermore, the dynamic nature of splicing and its integration with other layers of gene regulation necessitate a systems-level approach to study NPAC’s functions comprehensively. Advances in computational modeling and integrative data analysis will be critical in addressing these challenges and constructing a holistic view of NPAC’s role in stem cell biology. NPAC represents a key regulator of premRNA splicing in mouse embryonic stem cells, bridging chromatin dynamics and the splicing machinery to maintain transcriptome integrity and functional plasticity. Its influence on alternative splicing, pluripotency, and stress response underscores its multifaceted role in stem cell biology. Continued research into NPAC’s mechanisms and functions holds promise for advancing our understanding of gene regulation in development and unlocking new possibilities in regenerative medicine and disease modeling. As we uncover more about NPAC and its interplay with other regulatory networks, it becomes increasingly clear that this protein is indispensable for the intricate orchestration of stem cell identity and function.

Acknowledgement

None.

Conflict of Interest

None.

References

1. Evans, Martin J. and Matthew H. Kaufman. "Establishment in culture of pluripotential cells from mouse embryos." Nature 292 (1981): 154-156.

   Google Scholar, Crossref, Indexed at

2. Martin, Gail R. "Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells." Proc Natl Acad Sci 78 (1981): 7634-7638.

   Google Scholar, Crossref, Indexed at

3. Boyer, Laurie A., Tong Ihn Lee, Megan F. Cole and Sarah E. Johnstone, et al. "Core transcriptional regulatory circuitry in human embryonic stem cells." cell 122 (2005): 947-956.

   Google Scholar, Crossref, Indexed at

4. Nichols, Jennifer and Austin Smith. "Naive and primed pluripotent states." Cell Stem Cell 4 (2009): 487-492.

   Google Scholar, Crossref, Indexed at

5. Pan, Qun, Ofer Shai, Leo J. Lee and Brendan J. Frey, et al. "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing." Nat Genet 40 (2008): 1413-1415.

   Google Scholar, Crossref, Indexed at