Benjamin Blencowe has been studying alternative splicing since the 1990s. There’s still so much to learn.

When the first draft sequence of the human genome was published in 2001, scientists began to redirect their research questions to better reflect new understandings. Among them was Benjamin Blencowe, PI at the Donnelly Centre and professor in the Department of Molecular Genetics. 

“The draft sequence revealed we have a similar number of protein coding genes as far less complex species,” explains Blencowe. “C. Elegans—the nematode worm—only has 200 neurons, whereas with a comparable number of protein coding genes the human genome specifies over 80 billion neurons capable of forming more than 100 trillion synaptic connections. Our attention turned towards trying to figure out mechanisms driving that complexity.” 

Since then, the Blencowe Lab has focused on the contribution of a key step in gene regulation to biological complexity: alternative splicing.  

ALTERNATIVE SPLICING AND THE BLENCOWE LAB 

If the genetic code can be understood as a long list of life-building instructions, alternative RNA splicing is the process that includes or omits specific instructional segments. 

“After genes are copied into RNA, the process of splicing acts to remove non-coding segments and paste together different coding regions,” says Blencowe. “Alternative splicing allows this to happen in different combinations, such that a single gene can encode multiple different messenger RNAs that direct protein synthesis.” 

This diversity of messenger RNAs results in expanded repertoires of proteins that carry out different functions. 

RNA splicing captured Blencowe’s attention during his PhD thesis research in the early 1990s and has grown into the keystone of his career-long investigation into biological complexity. In the early 2000s, the Blencowe Lab developed the first quantitative microarray system capable of monitoring alternative splicing events in mammalian systems. This enabled his team to identify thousands of new tissue-regulated splicing events. But Blencowe was still pushing for more, and with powerful developments by the sequencing instrument company Illumina, a truly global-scale analysis was becoming a possibility. 

That goal was reached in late 2008, with the publication of “Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing”. Earlier that year, Blencowe had reached out to Illumina for access to their RNA sequencing datasets from human tissues, only to find out that his colleague Christopher Burge at MIT had contacted them for the same data two weeks before. Coordinating his lab’s efforts with Burge’s, Blencowe’s team developed a new computational pipeline, analyzed the Illumina data for splicing patterns, and published their paper within a rapid eight-month timeline. 

“This paper was our first glimpse into the complexity of human splicing when looking at all expressed genes across different tissue types,” Blencowe says. “We were able to demonstrate that approximately 95% of human protein-coding genes have exons that undergo alternative splicing. This process is the rule, not the exception.” 

With more than 4,800 citations, the paper grew to become Blencowe’s most referenced work. It laid the foundation for subsequent studies, leading to insights into how alternative splicing impacts the evolution of biological complexity in vertebrate species, as well as the discovery that this process is frequently disrupted in brain disorders. 

 “Our discoveries have led us to a new understanding of the role of alternative splicing in brain development and disorders,” says Blencowe, “which we’re currently leveraging as a basis for new therapeutic strategies.” 

Since their milestone publication in 2008, Blencowe’s team has developed increasingly advanced computational and experimental approaches to discover and characterize programs of regulated alternative splicing, with a focus on the nervous system. These subsequent discoveries have revealed novel insights into brain-specific “microexons”, which his group, in collaboration with researcher Sabine Cordes and others, have shown are frequently dysregulated in autism and play important roles in cognitive functioning.  

After decades of research, Blencowe is still investigating how RNA regulation impacts life. As he gathers more answers, more questions emerge, sending his team in unexpected research directions. The Blencowe Lab’s initial focus on tackling a very deep question about biological complexity yielded some important insights. But, by Blencowe's own admittance, the field is probably still scratching the surface. 

“Our 2008 paper was the beginning of a new wave of research in our group,” Blencowe says, smiling. “It led to some interesting answers and approaches that opened-up exciting new discoveries that we’re still exploring.”