Avik Mukherjee

Meet Avik Mukherjee, a PhD student at Presidency University, Kolkata, India, whose research is uncovering fascinating insights into the post-transcriptional regulation of long non-coding RNAs (lncRNAs) in the lab of Dr. Chandrama Mukherjee. His research focuses on the cytoplasmic pool of mRNA capping enzyme (cCE) and its role in capping lncRNAs, adding yet another layer of complexity to the eukaryotic gene regulation network.

The 7-methylguanosine cap added to the 5’ end of all RNA polymerase II transcripts protects mRNA from degradation and is necessary for translation initiation. While most mRNA capping occurs in the nucleus, recent research has uncovered that a population of cytoplasmic capping enzyme assembles into a complex that can re-cap and methylate re-capped RNAs, plus localizes to stress granules upon stress, suggesting another layer of post-transcriptional RNA regulation. Avik’s research aims to uncover whether lncRNAs are also substrates for cytoplasmic capping. Recently, their team was the first to report that certain lncRNAs can exist in a stable uncapped form in the cytoplasm and can be recapped by the pool of mRNA capping enzymes that reside in the cytosol.  Interestingly, he found some cCE-targeted lncRNAs can harbor coding potential, which he is currently examining. "The coding potentiality of lncRNAs supports the emerging perspective of the complexity of the eukaryotic proteome contributed by ncRNA-derived peptides," he explains.

Mukherjee completed his bachelor’s degree in Chemistry at Seth Anandaram Jaipuria College in Kolkata, India. During his undergraduate training, a class called Bioinorganic Chemistry sparked his interest in biological sciences. This led him to pursue a Master's in Biochemistry at the University of Kalyani, India, to learn how atoms and molecules interact within cells. However, his lab experience there was limited: "All I had was the practical exposure to basic biochemistry (like amino acid titration and paper chromatography)." Things changed after his Master’s when he joined the National Institute of Technology Rourkela as a Junior Research Fellow. Under the mentorship of Prof. Samir Kumar Patra, who focuses on cancer epigenetics, Mukherjee’s passion for science truly blossomed, fuelling his motivation to pursue a PhD.

"I suggest young researchers to have patience and be calm whenever there is a backlash in doing experiments. I believe these are the keys to overcoming any harsh situation. Everyone makes mistakes but eventually becomes wiser from these experiences."

Mukherjee's scientific inspirations are Sir Jagadish Chandra Bose and Dr. APJ Abdul Kalam. "Bose was the first scientist to invent a methodology to detect the response of living organisms to external stimuli, and Dr. Kalam played a pivotal role in boosting India's defense sector and later became the President of India," he shares.

Mukherjee faced significant challenges at the beginning of his journey at Presidency University. The COVID-19 pandemic in early 2020 forced their lab to shut down for almost a year. "Our lab was new at that point, and the initial stages of all my experiments took a hit. When our lab re-opened, we were forced to resume all our experiments from scratch. Despite these setbacks, we identified some of the lncRNAs targeted by cCE and published our research in FEBS Letters," he recounts, an achievement he is very proud of.

His persistence paid off when he attended the RNA 2023 meeting in Singapore, his first international meeting. “I had the opportunity to go through excellent research posters and scientific talks. I interacted with peers globally, showcased my research findings, and received valuable suggestions that shaped my future research methodologies. I especially want to thank the RNA Society for organizing a unique mentor-mentee session at this meeting.”

Mukherjee advises young researchers to decide on their scientific interests before choosing a lab. "Sometimes young enthusiasts join a lab and later find that it doesn't align with their scientific interests," he advises. He also emphasizes patience and calmness when experiments face setbacks. "Everyone makes mistakes but eventually becomes wiser from these experiences."

Mukherjee’s favorite RNA is MIR663AHG, an hnRNA located at the centromere of human chromosome 20. The primary transcript of this gene can be simultaneously spliced into microRNA miR663a and lncRNA miR663AHG. "This is a prime example of how alternative splicing contributes to the complexity of the human transcriptome," he says. His favorite RNA Journal article is "Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)," which he believes can open new insights into the biological functions of cCE-targeted lncRNAs.

Connect with Avik Mukherjee on X at @AvikMuk64372658 or on LinkedIn!