Thomas Gonatopoulos-Pournatzis, Ph.D.
- Center for Cancer Research
- National Cancer Institute
- Building 560, Room 21-102B
- Frederick, MD, 21702-1201
Thomas Gonatopoulos-Pournatzis studies the regulatory pathways and functional roles of alternative splicing and other pre-mRNA processing events in mammalian cells. Towards this, he has developed several CRISPR-based screening platforms which are coupled to high-throughput phenotyping and enable systematic exploration of the regulatory and functional complexity of pre-mRNA processing. Dr. Gonatopoulos-Pournatzis’ team combines these functional genomics tools with molecular and biochemical approaches as well as animal models to identify alternative exons and other genetic segments that underlie phenotypes related to normal physiology and disease states. The long-term goal of his research is to contribute to the functional annotation of all exons in the human genome and to map the gene regulatory networks that underlie the complexity of the mammalian transcriptome.
Areas of Expertise
Advances in next-generation sequencing have revealed that cancer and neurological disorders are often associated with distinct transcriptomic signatures, including widespread alterations in alternative splicing, a process that vastly expands the coding potential of the genome. Loss- or gain-of-function mutations in RNA binding proteins impact entire networks of coordinated RNA processing events, which play critical roles in cell fate decisions and impact processes such as cell cycle control, neurogenesis and synaptic transmission. However, given that the function of the overwhelming majority of such events, including alternative cassette exons, remains unexplored, Thomas Gonatopoulos-Pournatzis’ research program aims to identify individual events that control these fundamental biological processes, reveal how their disruption contributes to disease- or disorder-related phenotypes, and explore the regulatory networks that control RNA processing.
1. Exon-resolution functional genomics
To advance the systematic mapping of genetic interactions and interrogation of the functions of sizeable genomic segments, we have developed a CRISPR-based screening system for combinatorial genetic perturbations, named CHyMErA. CHyMErA employs co-expression of Cas9 and Cas12a nucleases and libraries of hybrid Cas9-Cas12a guide RNAs that can be employed for multi-targeted genome editing. We have applied CHyMErA in human cells to uncover novel genetic interactions between paralogous gene pairs. Importantly, we have also used CHyMErA to systematically target thousands of alternative splicing events, identifying dozens of exons underlying cell fitness. CHyMErA thus represents an effective screening approach for genetic interaction mapping and the functional analysis of sizeable genomic regions, such as alternative exons.
Functional Exomics: Future application of CHyMErA screens coupled to high-throughput phenotyping will enable the efficient functional characterization of alternative exons in the human genome and the identification of novel targets for precision medicine applications using high resolution phenotypic profilling.
Technology Development: A major goal of the Gonatopoulos-Pournatzis team is to continue developing cutting-edge technologies that will enable the systematic and efficient functional characterization of transcript isoform diversity and genetic interactions using phenotypically rich screening readouts.
2. Mapping gene regulatory networks that control alternative splicing
An important challenge in biomedical research is to elucidate the gene regulatory networks that underlie the establishment of complex transcript isoform expression patterns in a cell-type specific manner, and understand how their disruption contributes to disease-states. We have previously developed a CRISPR-based screening platform that allows the systematic identification of regulatory factors that control alternative splicing. CRISPR-Cas9 loss-of-function genome wide screens in neural cells expressing dual-fluorescent splicing reporters uncovered hundreds of splicing regulators and have shed light on how very short neuronal exons, linked to autism spectrum disorders, are recognized and spliced. The aforementioned strategy represents a highly effective approach for the comprehensive definition of splicing regulatory pathways. Future studies using this tool will systematically delineate regulatory pathways that control the splicing of alternative exons with critical roles in mammalian cells.
3. Uncover microexons that impact animal behavior and cognitive functioning
A program of neuronal-specific, highly conserved microexons is frequently disrupted in the brains of patients with autism spectrum disorder (ASD). We have started to identify individual microexons that contribute to ASD-associated phenotypes by characterizing a set of neuronal microexons in the translation initiation factors eIF4G1 and eIF4G3. The eIF4G microexons selectively up-regulate synaptic proteins that control neuronal activity and plasticity, and mice lacking the Eif4g1 microexon display social behavior as well as learning and memory deficits. Future studies are focused on uncovering additional alternative exons with such critical roles for animal behavior and cognitive functioning.
Diversity and Inclusion Statement
Our group strives to create and maintain a welcoming and equitable environment. We welcome all qualified individuals regardless of race, color, religion, sex (including pregnancy, sexual orientation, and gender identity), national origin, age, disability, and genetic information.
Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening
Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform
Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions
Thomas Gonatopoulos-Pournatzis, Ph.D.
Dr. Gonatopoulos-Pournatzis obtained his Bachelor’s degree in Biology from the National & Kapodistrian University of Athens, Greece in 2007 before moving to King’s College London in England to earn his Master’s degree in 2008. In 2013, Dr. Gonatopoulos-Pournatzis obtained his Ph.D. from the University of Dundee in Scotland where he worked in Prof. Victoria Cowling’s laboratory studying mechanisms underlying mRNA cap methylation and gene expression. For his postdoctoral research, he joined Prof. Ben Blencowe’s laboratory at the University of Toronto in Canada to study the regulation and function of splicing regulatory networks in neurons with the support of postdoctoral fellowships from the European Molecular Biology Organization (EMBO), Canadian Institutes of Health Research (CIHR) and Ontario Institute of Regenerative Medicine (OIRM). Dr. Gonatopoulos-Pournatzis has received multiple awards and recognitions, including the Baxter Prize (2012), the Donnelly Centre Research Excellence Award (2018) and his is also a recipient of the 2020 NIH Distinguished Scholar Program. In 2020, Dr. Gonatopoulos-Pournatzis joined the RNA Biology Laboratory at the National Cancer Institute to establish the Functional Transcriptomics Section, which integrates functional genomics and RNA biology. His lab focuses on developing and applying CRISPR tools to systematically uncover transcript variants that play critical roles in normal physiology and disease state.
Opportunities to Join Our Team
If you are interested applying for a postdoctoral fellowship in our group please send an email to firstname.lastname@example.org including your CV, stating your research interests and motivation to join our team as well as the contact details of three referees. Applicants should hold a PhD in molecular biology from a reputable academic institution and have at least one peer-reviewed first author publication. Experience in RNA biology, functional genomics or computational biology is very much welcomed.
What we offer:
We are based at the RNA Biology Laboratory of the NCI’s Center for Cancer Research, part of the NIH Intramural Research Program, which is one of the largest biomedical institutes in the world. We have access to state-of-the-art equipment and research facilities. The Gonatopoulos-Pournatzis group is dedicated to performing high quality science and providing strong mentoring in a welcoming and equitable environment. We offer fully funded long-term positions with generous stipends, relocation cost and benefits covering health insurance premiums.