Dr. Oguzhan Begik

Dr. Oguzhan Begik, a recent PhD graduate from the University of New South Wales (Sydney, Australia) is busy quantifying the RNA world one molecule at a time. Dr. Begik has been interested in RNA research since first completing his MSc degree focusing on deciphering alternative polyadenylation patterns in cancer patients at the Middle East Technical University (Ankara, Turkey). He then jumped into the ever-expanding world of RNA quantification methods and went on to complete his PhD with Dr. John Mattick and Dr. Eva Novoa, where he worked on developing methods to map RNA modifications at single molecule resolution. Most recently he developed Nano3P-Seq, a method that relies on direct cDNA sequencing to quantify RNA abundance, tail composition, and tail length dynamics of individual transcripts (now on bioRxiv). Nano3P-Seq employs a template-switching reverse transcriptase, thereby eliminating the need for a 3’ adaptor ligation step to allow for direct cDNA sequencing of coding and non-coding transcripts. Describing the benefits of Nano3P-Seq, Dr. Begik said, “I believe it will be a very useful tool to study transcriptomic regulation at single molecule resolution in a much less biased way.” With such an impressive array of RNA mapping tools, Dr. Begik was selected as the inaugural graduate student winner of the RNA Society’s Eclipse Award for Innovation in High Throughput Biology.

Dr. Begik was fortunate in that he was mentored by two prominent leaders in RNA biology during his PhD studies. Dr. Eva Novoa was a postdoctoral researcher transitioning to a group leader when Dr. Begik began his PhD with Dr. John Mattick in Sydney. This presented the unique opportunity for Dr. Begik to receive training from both Dr. Mattick and Dr. Novoa, both of whom he counts among his scientific inspirations. Dr. Begik soon moved with Dr. Novoa to the Centre for Genomic Regulation (CRG) in Barcelona, Spain to continue his PhD studies. On the move, he said, “I feel very privileged to have taken part in the progress of the Novoa lab becoming a recognized leader in the RNA modification field.” Beyond his PhD mentors, Dr. Begik credits his excitement for research to Dr. Carl Sagan and Dr. Richard Feynman. On Dr. Sagan, Dr. Begik said, “I was really moved by how excited he was about simply anything around him”. He also describes being inspired by Dr. Feynman’s view “that curiosity, doubt, and skepticism are major driving forces in science.” In an effort to inspire the same curiosity and passion in others, Dr. Begik led the organizing committee of the Aykut Kence Evolution conference, the largest evolutionary biology conference in Turkey. He recalled, “It was an amazing experience in terms of team building and leading aspects. I’d like to believe that these conferences inspired many people.”

“It’s amazing to see that studies on RNA modifications brought us to the point where we use them in vaccines to improve their efficiency and target them to fight against disease!”

Although it’s undeniable that Dr. Begik has already left his mark on the RNA world (one might say an epitranscriptomic mark), he admits that it wasn’t easy. He shares that he experienced both burnout and subsequent depression towards the end of his PhD studies. “It took me a very long time and a lot of determination to overcome [the burnout and depression]” he said. “The most significant thing that helped was to go out there and share my feelings with other people.” In line with this, his advice to graduate students, new or veteran, is to communicate openly with other scientists. “As someone who has personally suffered a great deal from impostor syndrome during my PhD, I can say that this is very common in academia, and you are not alone. The best thing you can do is to share your thoughts with other people because you will realize that you are not the only one.” Importantly, he noted that although it should not be, impostor syndrome is very common in academia. “I think that this is something that needs to be addressed and fixed. If we keep having more people in academia who think that impostor syndrome is “normal” and PhD students should just work more to overcome this, it will get even worse. I think that, just like any other profession, one should not define themselves based on their ‘success’ in their work.” He also cautions new trainees to establish a good work-life balance. “In the earlier years of my PhD study, I thought I wouldn’t succeed unless I worked at least 12 hours a day. Then I realized that overworking comes with a little surprise: burnout.”

As one of the scientists at the forefront of the race to map the epitranscriptome, Dr. Begik reflected, “The thing I was surprised and impressed the most about the RNA modification field was how incredibly fast it expanded since the discovery of their reversibility and consequent development of tools to detect them transcriptome-wide.” It should therefore come as little surprise that one of Dr. Begik’s favourite RNA Journal articles is “The RNA modification landscape in human diseases”, by his former colleague Nicky Jonkhout. Dr. Begik, always a fan of RNA modifications, said, “This paper beautifully illustrated how important RNA modifications are in human diseases.” While Dr. Begik is open to many areas of research for his postdoctoral studies, it is safe to say we can look forward to additional innovative findings from him in the future.

Looking back, Dr. Begik has fond memories from the 2017 RNA Society meeting in Prague. “I made friends with Martin Smith, who was soon to be my lab mate. As we were having beers after the talks, I told him that although I drank more than 5 bottles, I did not feel tipsy at all. That’s when he pointed out the fact that I was drinking alcohol-free beer all along!” You can talk to Dr. Begik at the 2022 RNA Society Meeting in Boulder, Colorado, where he will be accepting the Eclipse award—and hopefully celebrating with real beer this time.

Dr. Begik’s favorite RNA is the S. cerevisiae 15S ribosomal RNA because it was the seed of his first scientific breakthrough, the detection of pseudouridine using nanopore sequencing. “It was an especially exciting discovery because this modification is the result of a single nucleotide mutation in its neighboring position specifically in the Saccharomycetaceae family. It showed me how specific RNA modifications can be!” You can find him on Twitter @oguzhanbegik.