Bin Tian, Ph.D.

Cleavage and polyadenylation (CPA) is responsible for the 3′ end maturation of almost all protein-coding and long non-coding RNAs in eukaryotic cells. The CPA site, commonly known as polyA site or PAS, also plays a key role in termination of transcription. Over 70-80% of human genes harbor multiple PASs, resulting in expression of mRNA isoforms with different 3′ termini, a phenomenon known as alternative cleavage and polyadenylation (APA). APA isoforms can differ in coding sequences and/or 3’ untranslated regions (3’UTRs). The Tian lab has used a battery of sequencing tools, including short-read and long-read sequencing technologies, to comprehensively map PAS across species and understand APA site usage dynamics and evolution. They are also using single-cell RNA sequencing methods to examine cell type-specificity of APA isoform expression under physiological and pathology conditions. Moreover, using these technologies, the Tian lab is addressing how PAS choice is coupled with other events of mRNA biogenesis and processing, such as transcription, splicing and base modifications.

While most PAS in human genes are located in the 3′-most exon, a sizable fraction (~20%) of genes display APA in regions upstream of the last exon. Those APA events, commonly known as intronic polyadenylation, lead to early termination of transcription (ETT). ETT transcripts can encode proteins with different C-terminal sequences and hence have distinct functions and cellular properties, such as subcellular localization. Many of the ETT transcripts that harbor a 5′ splice site, however, are unstable in the cell, making ETT a powerful mechanism to inhibit gene expression. As such, regulation of ETT, often involving a balance among RNA polymerase II processivity, transcriptional elongation rate, splicing kinetics and CPA activities, can have substantial impacts on the gene expression program.  The Tian lab is examining how ETT plays a role in establishing the cell identity,  such as neuronal cells vs. blood cells, and how perturbations of ETT impacts neoantigen expression in cancer cells with the goal of enhancing cancer immunotherapies.

The 3’UTRs of protein-coding transcripts play regulatory roles in mRNA metabolism, including mRNA decay, translation and subcellular localization. Sequence and structural motifs embedded in 3’UTRs contribute to 3’UTR functions through interactions with their cognate RNA binding proteins (RBPs) and microRNAs (miRNAs). The Tian lab uncovered widespread translation-independent endoplasmic reticulum association (TiERA) of mRNAs, in which 3’UTRs play an important role in modulating mRNA interactions with the endomembrane system in the cell. The Tian lab is studying how TiERA could impact cell signaling through localized mRNA translation. In addition, the Tian lab has reported widespread transcript shortening in secretory cell differentiation. The phenomenon, named secretion-coupled APA (SCAP), was observed in multiple professional secretory cells. They are studying underlying mechanisms of SCAP and pursuing novel approaches to modulate protein secretion capacities through CPA-based engineering with the goal of augmenting mRNA and DNA-based vaccines.

Small molecule inhibitors of CPA (CPAi) have recently been found to be effective anti-cancer therapeutics.  The Tian lab has revealed multiple mechanisms by which CPAi can impact the transcriptome in a cell, including APA isoform changes and transcriptional readthrough. In addition, they found that cancer cells with a high CPA activity and a high proliferation rate are particularly vulnerable to CPAi, due to replication-transcript conflicts.  They are now developing novel, more potent CPAi compounds through medicinal chemistry and antisense oligonucleotides (ASOs) that are amenable to distinct therapeutic deliveries. In addition, they are studying cancer cell signatures that determine the effectiveness of CPAi in multiple cancer types. In addition, based on the observations that CPAi has been found to have anti-inflammation properties, the Tian lab is developing novel anti-inflammatory modalities using small molecules and biologics.