Melesse Nune

The eukaryotic DNA is beautifully organized into a nucleosome comprising 147 bp DNA wrapped around an octamer of core histone proteins H2A, H2B, H3 and H4. The nucleosome is the basic repeating unit of a chromatin. The chromatin is decorated with a wide range of reversible histone post-translational modifications that regulate all processes that require access to DNA. Monoubiquitination of histone H2B (H2B-Ub) plays a role in transcription and DNA replication, and is required for the function of a protein complex that is responsible for the assembly and disassembly of nucleosomes called FACT. Dysregulation of H2B-Ub or FACT is associated with a variety of cancers. In Cynthia Wolberger’s lab, my study focused on understanding how FACT and the deubiquitinating enzyme Ubp10 work in concert to govern histone H2B deubiquitination. My work demonstrated that Ubp10 preferentially cleaves free-standing H2A/H2B-Ub dimers much faster than intact ubiquitinated nucleosomes, but that the addition of FACT stimulates Ubp10 activity on nucleosomes. Importantly, my work also demonstrated that disrupting the functions of these proteins in cells leads to defects in transcription and DNA replication. To get a better understanding of the reason behind Ubp10’s low activity on the nucleosomes, I solved the cryogenic electron microscopy (cryoEM) structures of Ubp10 bound to a ubiquitinated nucleosome. The structures revealed that Ubp10 makes several contacts with histones, ubiquitin, and severely alters the nucleosomal DNA at the nucleosome entry/exit site. Ubp10 docks onto the nucleosome in many conformations suggesting that the enzyme doesn’t bind nucleosomes in the correct register that promotes H2B deubiquitination without the help of FACT. The findings from my work highlight novel relationships between H2B monoubiquitination and the role of FACT in destabilizing the nucleosome to assist Ubp10 in H2B deubiquitination.

Questions & Answers

Why did you choose Johns Hopkins for your work?

Hopkins is regarded as one of the best schools in the world for biomedical research. My decision to come to Johns Hopkins was largely based on two reasons. First, Hopkins has a great infrastructure for someone like me who wants to learn the techniques in structural biology. I wanted to be in an environment that has state-of-the-art facilities and world-renowned scientists to learn from. Second, I have always wanted to live in the D.C./Maryland/Virginia area. After being here for many years, my personal and scientific adventures have confirmed that coming to Hopkins was one of the best decisions I’ve made in my life.

What does receiving this award mean to you personally and professionally? Do you have any connection with the particular award you received?

I was made aware of the Young Investigators’ Day Award during my second year of graduate studies. Ever since then, I have been thinking about what it would take and what it would feel like to win this award. I’m deeply honored that I was chosen to receive the Alicia Showalter Reynolds Award. It also gave me a boost in my confidence as a researcher.

What contributed to your project’s success?

Besides pure hard work, I would not have been successful without the contributions from my scientific collaborators. A portion of my work was done through national and international collaborations with a geneticist at University of Utah (Tim Formosa), a chemist at Technion-Israel Institute of Technology in Israel (Ashraf Brik), a single-molecule microscopist at the Johns Hopkins University School of Medicine (Taekjip Ha), and a biochemist at UT Dallas (Sheena D’Arcy). In addition, the feedback I received about my work from my mentor, Cynthia, and everyone in the Wolberger lab had a great impact on my success.

What thoughts do you have about Young Investigators’ Day itself, as a celebration of the roles students and fellows play in research at Johns Hopkins?

I think it’s paramount to recognize trainees in events such as Young Investigators’ Day. It not only provides a platform for trainees to showcase their work to an interdisciplinary audience, it also gives them confidence to pursue greater things.

What has been your best/most memorable experience while at Johns Hopkins?

My most memorable experience at Hopkins was when I first operated (on my own) the newly installed Titan Krios, a state-of-the-art electron microscope used to look at the high-resolution 3D details of molecular machines in cells. On that day, I spent so many hours setting up cryoEM data collection. A few days later, I was able to determine the 3D structure of the protein complex that I was investigating. This was done with phenomenal speed. Before the Titan Krios was installed at Hopkins, it would take months to years to collect high-resolution data for protein structure determination.

What are your plans over the next year or so?

I plan to graduate within the next few months and start a postdoctoral position. I’m excited to expand upon my expertise in cryo-electron microscopy in my postdoctoral training.

Tell us something interesting about yourself.

I greatly enjoy learning about financial markets. I spend the majority of my free time analyzing stock portfolio and making buy/sell recommendations to family and friends. I also like photography. I’m enthusiastic about capturing my life’s events and freezing them to eternity. I hope someday my family and friends would enjoy seeing the pictures I captured over the years.