Behind the Paper

From microRNA to RBP: B Cell Biology Through the Lens of RNA

Pengda Chen Apr 02, 2025

 1. From microRNA to RBP: the beginning of our journey

Our journey into RNA biology began with the study of microRNAs (miRNAs). Throughout the twentieth century, the study of B cell biology focused primarily on transcription factors and signaling pathways. It was therefore striking when our mouse genetic studies at the beginning of this century revealed that these small RNAs play major roles in B cell biology, spanning lymphocyte development, differentiation, lymphoma, and autoimmune disease 1, 2, 3.

Motivated by these findings, we set out to uncover the mechanisms by which miRNAs regulate gene expression, and how they fit into the broader regulatory programs governing B cell biology. Our study demonstrated that the function of miRNA is highly cellular context-dependent, and that miRNA plays a crucial role in fine-tuning gene expression in a precise and quantitative manner, ultimately guiding immune cell fate decisions 4, 5, 6.

To fully understand RNA-level regulation in a cell type-specific context, we recognized that miRNAs are only part of the picture. Their function is not only determined by their own binding to mRNAs but also modulated by RNA-binding proteins (RBPs) 7. This insight expanded our interest to RBPs, which regulate a much broader spectrum of RNA biology, including RNA splicing, stability, translation, and localization. Understanding how RBPs coordinate immune cell function at the RNA level offers an opportunity to uncover novel regulatory mechanisms, complement miRNA-mediated control, and pave the way for innovative therapies to treat immune-related diseases.

 2. Mapping the B cell-specific RBP landscape

When we were committed to exploring RBPs in B cell biology, Changchun Xiao proposed a systematic investigation to identify all functional RBPs in B cells. A 2012 Cell paper 8 introduced a technique to experimentally identify mRNA-binding proteins and revealed that RNA-binding capability is highly cell type-specific and not limited to proteins with canonical RNA-binding domains. To explore this in the context of B cells, we employed mRNA interactome capture across different stages of B cell differentiation. Intriguingly, our experiments revealed a substantial number of non-canonical RBPs that are differentiation stage-specific. This dataset provided a solid foundation for further functional characterization of RBPs in B cell biology.

  3. Functional screening of RBPs

Transcription factors are well-known fate-determining regulators during cell fate decisions. We hypothesized that some RBPs might similarly control cell fate at the post-transcriptional level. Specifically, we asked whether certain RBPs could function analogously to Prdm1, the well known master regulator of plasma cell differentiation.To explore this, we performed a CRISPR-based high-throughput functional screen to identify RBPs involved in B cell differentiation toward plasma cells. Our screen identified Strap, Csde1 and Ythdf2 as key regulators. We also uncovered novel and functionally critical non-canonical RBPs, such as Gpi1 and Eral1, which had not previously been linked to RNA binding or plasma cell differentiation. Although we have yet to fully characterize these non-canonical RBPs, they present promising directions for future investigation.

  4. The Strap-Csde1 complex: a key regulator of plasma cell differentiation

To test our hypothesis, we focused on RBPs that specifically regulate plasma cell differentiation. Among 15 candidates validated through individual screening, Csde1 stood out for promoting differentiation with minimal impact on cell proliferation. Interestingly, another non-canonical RBP, Strap, showed a similar role and is known to tightly associate with Csde1. Yet, the biological function of the Strap-Csde1 complex had remained elusive.

We generated conditional knockout mice for Strap and Csde1 and crossed them with Cg1-Cre mice, in which the expression of Cre recombinase is turned on in activated B cells. Encouragingly, T cell-dependent immunization experiments revealed that both Strap and Csde1 are critical for the generation of antibody-secreting cells and for mounting effective antibody responses in vivo. These results further validated the robustness of our screening approach.

Additionally, our data suggest that while Strap and Csde1 are essential for plasma cell differentiation, Prdm1 remains the overarching master regulator. Mechanistically, our studies revealed how Strap and Csde1 act at the RNA level. Using a combination of eCLIP, mass spectrometry, and ribosome profiling, we mapped their downstream targets and assessed the impact of their loss on mRNA translation. We found that the Strap-Csde1 complex regulates Bach2 and Atp2a2 via translationally coupled mRNA decay. During the germinal center (GC) response, transient upregulation of Bach2 protein is necessary to promote GCB and memory B cell fates. However, its timely downregulation is crucial for initiating plasma cell differentiation. The Strap-Csde1 complex binds to Bach2 mRNA to enhance its translation upon T cell stimulation, and subsequently triggers its degradation to limit the magnitude and duration of Bach2 protein expression. In the absence of Strap or Csde1, this coupling is lost, resulting in prolonged and elevated Bach2 expression, ultimately impairing plasma cell differentiation (Figure 1).

     Figure1. A graphical abstract of Strap-Csde1 complex regulatory mechanism

 5. The RNA way in B cell biology

With a growing body of evidence and decades of experience studying miRNAs and RBPs in B cell biology, we have come to appreciate the significance of RNA-level regulation in shaping B cell programs. While mRNA-level control may not solely determine cell fate, it is definitely a vital layer of gene regulation.

Key target genes such as Pten, Bim and Bach2, regulated by the miR-17~92 cluster and the Strap-Csde1 complex, exhibit highly dynamic protein expression across B cell development and differentiation stages. This layer of post-transcriptional regulation enables rapid and precise responses to changing environmental cues and supports the flexible, stage-specific needs of B cell differentiation.

Notably, both Strap and Csde1 are multifunctional proteins that do not always act as a complex. Their interaction, and function, appears to be cell-context dependent, mirroring the cell context-specific nature of miRNA activity. This supports the broader idea that RNA-level regulators contribute to the complexity of B cell programs through fine-tuning core gene expression in a timely, spatial, and quantitative manner.

Compared to DNA-level regulation, especially transcriptional control, RNA-level regulation remains less understood, limited in part by current technological tools. As we continue to explore this field, it is important to remain humble and curious, avoiding the tendency to keep eyes only on well-characterized genes. For instance, although Atp2a2 emerged as a functional downstream target of Strap-Csde1, its function and mechanisms of actions in B cells remain largely unexplored.

Finally, RNA-level regulation in the contexts of human diseases, including disease initiation and progression, remains an exciting and largely unexplored area. Better understanding of regulatory mechanisms in the RNA level could offer novel insights and therapeutic avenues for many human diseases.

REFERENCE

 

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