Systematic mapping of nuclear domain-associated transcripts

Rasim Barutcu, PhD
Postdoctoral fellow
Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

This conference is part of the the IRCM Early-Career Scientist Seminar Series (ECS³), a groundbreaking initiative whose mission is to showcase early career scientists. This is a great opportunity to discover the exciting projects of these researchers in training in front of a multidisciplinary audience.

Zoom Link: https://zoom.us/j/95269762104
ID: 952 6976 2104
Code: 476372

About the conference:
The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains, yet the composition and function of many of these structures is not well understood. Using APEX2-mediated proximity labelling and RNA sequencing, we surveyed transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, and enriched for functional sites of RNA binding proteins that are concentrated in these domains. They are also highly differentially regulated across diverse cellular contexts, including the cell cycle. Our study thus provides a rich resource of nuclear domain-associated transcripts and further reveals speckles and lamina as hubs of distinct populations of retained introns linked to gene regulation and cell cycle progression.

About Rasim Barutcu : 
Dr. Rasim Barutcu obtained his PhD in the Cell and Development Biology Program of the University of Massachusetts and then pursued a first postdoctoral fellowship at Harvard University under the mentorship of Dr. John Rinn. Now a postdoctoral fellow in the lab of Dr. Benjamin Blencowe at the University of Toronto, his work focuses on investigating the RNA components of nuclear condensates. Dr. Barutcu has an extensive publishing record, with 23 manuscripts accepted in highly respected journals such as Molecular Cell, Nature Communications and EMBO Journal, and over 1000 citations. His postdoctoral training is supported by prestigious agencies such as CIHR and NSERC.

Please tell us about your career path, leading up to your application to the ECS³ program:
I have a long-standing expertise in investigating the role of higher-order nuclear structure in cellular processes. During my PhD training at University of Massachusetts Medical School with Drs. Gary Stein and Anthony Imbalzano, I became an expert on the chromosome conformation capture (3C)-based methods, such as Hi-C, in collaboration with Dr. Job Dekker who is a frontier in the field. By using Hi-C, I performed one of the first global comparisons of genome-wide chromosomal interactions between normal and breast cancer cells and identified large-scale differences associated with oncogenic gene expression (Genome Biology). Furthermore, I characterized the architectural roles of a key transcription factor (RUNX1), the SWI/SNF chromatin remodeling complex (BRG1) and profiled the local chromatin structure of the bone-associated Runx2 gene (BBA Gene Regulatory Mechanisms, Genome Research, Nucleic Acids Research). 

During my first postdoctoral position at Harvard University with Dr. John Rinn, a leader in the long non-coding (lnc)RNA field, I studied the requirement of lncRNAs and the binding of CTCF, a key chromatin organizer, in genome structure (Nature Communications). Importantly, I acquired extensive skills using high-resolution microscopy methods involving CRISPR live-cell imaging, where DNA regions of interest can be visualized in real time in living cells. Next, I characterized the global and differential roles of pre-transcribed RNA and the act of transcription in chromosome organization (EMBO Reports). 

To further my postdoctoral training on RNA biology, nuclear organization and splicing, I joined Dr. Benjamin Blencowe’s laboratory, a world leader in the field of alternative splicing, at University of Toronto. I systemically mapped the RNA-protein associations of different subnuclear compartments using novel proximity labelling methods. This study is currently in-press as a Resource Article at Molecular Cell. During this time, I was awarded a highly competitive and prestigious Banting Fellowship and a subsequent CIHR Fellowship in 2018 and 2020, respectively.

Please tell us about your passion for research. What motivates you most about your work?
One of the most motivating aspects of studying the organization of the nucleus is that it regulates several important genomic processes, such as gene expression or splicing, that underlies cellular outcomes. For instance, one of the hallmarks of cancer is the alteration of the nuclear morphology, which has remained as the 'gold-standard' for diagnosis of cancer for over 150 years. The morphology of the nucleus also undergoes drastic changes during cellular differentiation. Although the importance of RNA in shaping nuclear structure has been known for decades, and we have considerable knowledge about the folding of the chromosomes, the specific contribution of RNA (i.e. long non-coding RNAs) in shaping nuclear architecture remains less-understood. Thus, understanding the functional relationships between the three-dimensional organization of the chromosomes simultaneously with RNA and protein content of sub-nuclear compartments will be very exciting to fully uncover the regulation of gene expression and splicing, which would lead to identification of novel pathways and targets in development and disease.

Please tell us about the next steps of your career. How will participating in the ECS³ program help you progress as a researcher?
Building on my previous expertise, I aim to establish my own independent laboratory and build a robust research program where the mechanistic relationship among RNA localization, chromosome folding, transcriptional and splicing networks and cellular outcomes (i.e. in cancer or during development) will be investigated. Therefore, participating in the ECS³ program will provide a unique opportunity for me to network with world-renowned experts on RNA biology, chromatin and other related fields in a cutting-edge research environment.

Please tell us about your professional goals. What do you hope to accomplish as a scientist?
As a scientist, I aim to identify and characterize novel mechanisms and molecules that regulate nuclear architecture and ultimately cellular outcomes, which can potentially be targeted for therapeutic purposes. While doing so, I aspire to train young scientists and establish both national and international collaborations to tackle these complex biological questions in a multi-disciplinary manner.