RNA Regulation in Stem Cells and Host-Pathogen Interactions 

We are broadly interested in RNA regulation and its role in stem cell biology and in host-pathogen interactions. We combine biochemical, structural, and high throughput sequencing-based global analyses in our research.

The 3′ ends of most eukaryotic mRNAs are formed by an endonucleolytic cleavage and the subsequent addition of a string of adenosines. Interestingly, the transcripts of ~70% of genes in all eukaryotes have alternative 3′ ends that are formed by cleavage/polyadenylation at different sites, a phenomenon called mRNA alternative polyadenylation (APA). APA not only expands the proteomic and functional diversity, but also plays important roles in gene regulation. Deregulation of mRNA 3′ processing and APA have been implicated in a wide spectrum of human diseases. However, it remains poorly understood how poly(A) sites are recognized and how their recognition is regulated. Our goal is to decipher the rules that govern poly(A) site choice, or the “polyadenylation code”, by using a combination of biochemical, genomic, and genetic approaches. Our studies aim to provide novel insights into the basic mechanisms of post-transcriptional gene regulation as well as its role in many physiological and pathological processes..

  • mRNA APA regulation in cell fate decisions.

We have recently developed a high throughput sequencing-based method called PAS-seq for quantitatively RNA polyadenylation profiling at the transcriptome level. Using this method, we detected extensive changes in the global APA profile during stem cell differentiation to neurons that, in most cases, lead to 3′ UTR lengthening (Shepard et al., RNA 2011). We have identified the protein Fip1 as a critical regulator of the global APA profile and we have demonstrated that Fip1-mediated APA regulation is essential for embryonic stem cell self-renewal and for somatic reprogramming (Lackford et al., EMBO J 2014). We have identified the APA regulator CFIm25 as a key roadblock factor that prevents somatic reprogramming and characterized the underlying mechanisms (Brumbaugh et al, Cell 2018; Zhu et al, Mol Cell 2018). These studies revealed an unexpected role for APA regulation in cell fate decisions. Given the similarities between stem cells and cancer cells, we are also investigating whether and how APA regulation may contribute to cancer development.


Fip1 is essential for embryonic stem cell self-renewal. (Lackford et al., EMBO J. 2014)

  • Characterization of the mRNA 3′ processing machinery.

Previously we have purified the human mRNA 3′ processing complex in its active and intact form (Shi et al., Mol Cell 2009). Surprisingly, this complex consists of more than 85 proteins, including the core 3′ processing factors and many peripheral factors that may couple mRNA 3′ end formation to other cellular processes. To understand how the mRNA 3′ processing machinery recognizes specific poly(A) sites, we have systematically studied the key protein-RNA interactions for the core mRNA 3′ processing factors (Yao et al., PNAS 2012; Yao et al., RNA 2013; Chan et al. Genes & Dev 2014). Our recent studies have revealed the mechanisms for poly(A) signal recognition and significantly reshaped our understanding of mRNA 3′ processing (Chan et al. Genes & Dev 2014; Sun et al, PNAS 2018). Finally we have shown that mRNA 3′ processing and splicing share a similar activation mechanism despite the fact that they require distinct sets of trans acting factors, and provided evidence for a unified mechanism for RNA processing regulation (Zhu et al, Mol Cell 2018).

Electron microscopy images of purified human mRNA 3′ processing complex (Shi et al., Mol Cell 2009)

  • mRNA 3′ processing and host-pathogen interactions.

A new project in the lab is to investigate how Herpes Simplex virus influences host mRNA 3′ processing and how such interactions impact viral replication.

Our research is funded by: