OUR CREATIVE TEAM
Jamie Lane
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Max Johnson
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Jesse Neimus
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Drew Carlyle
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CENTER FOR GENOMIC INFORMATION ENCODED
BY RNA NUCLEOTIDE MODIFICATIONS
About:
The Center for Genomic Information Encoded by RNA Nucleotide Modifications seeks to fundamentally advance our understanding of gene expression regulation in the cell. We are focusing on the powerful ability of the translating ribosome to control gene expression. The ribosome can preferentially translate some mRNAs over others, and when mRNAs are selected for translation, ribosome stalling can reduce translation output and induce mRNA decay. Thus, the rRNA-tRNA-mRNA complex is a major determinant of gene expression in cells. However, the regulation of this complex is poorly understood. This is largely because the rRNA, tRNA, and mRNA communities are very distinct. No single lab has the expertise to study all three RNAs and their interactions. Additionally, our hypothesis is that the incredible diversity of nucleotide modifications in these RNAs may have a critical role in regulating the assembly of this complex. Our hypothesis is grounded by several emerging studies showing that rRNA, tRNA, and mRNA modifications are not constitutive—at certain nucleotide positions nucleotide modification stoichiometry is variable, depending on the tissue or disease context. Thus, this Center will bring together rRNA, tRNA, and mRNA researchers to work together to develop scalable technologies to map and quantify modifications in rRNA, tRNA, and mRNA, and to determine how these modifications control rRNA-tRNA; rRNA-mRNA, and tRNA-mRNA interactions to regulate gene expression.
Funded by:
Meet the Team
Samie Jaffrey
Principal Investigator
Greenberg-Starr Professor
Dept. of Pharmacology
Weill Cornell Medical College
Dr. Jaffrey is recognized as a founder of “epitranscriptomics” and coined this term in his seminal 2012 publication in Cell describing the first transcriptome-wide map of m6A. This paper was cited in Nature Methods’s Jan 2017 article naming epitranscriptomic mapping as its “Method of the Year.” Dr. Jaffrey is the recipient of the NIH Eureka Award and the NIH Director’s Transformative R01 award. He has received the Young Investigator Award from the American Society for Biochemistry and Molecular Biology, the Blavatnik Award for Young Scientists, the John J. Abel Award from the American Society for Pharmacology and Experimental Therapeutics, and is an elected member of the American Society of Clinical Investigation. Dr. Jaffrey is neuroscientist, chemical biologist, and molecular biologist and is a recognized pioneer in our understanding of post-transcriptional mechanisms of gene regulation, most recently epitranscriptomics. His work is highly interdisciplinary and operates at the interface of computation and genomic experiments.
Kate Meyer
Principal Investigator
Assistant Professor
Duke University School of Medicine
Dr. Meyer has been an Assistant Professor at Duke University since 2016. Prior to that, she conducted her postdoctoral studies at Weill Cornell Medical College where she worked with Dr. Jaffrey to develop the first method for transcriptome-wide m6A mapping and uncovered important roles for m6A in translation regulation. Her laboratory has pioneered novel methods for detecting and quantifying adenosine methylation in cells, including development of the first single-cell m6A mapping technology. Her studies have provided unprecedented insights into how m6A is regulated at the cellular level and have paved the way for future studies examining single-cell m6A dynamics.
Scott Blanchard
Co-Investigator
Endowed Chair in Molecular Imaging, Dept. of Structural Biology, St. Jude Children's Research Hospital
As a faculty member in the Department of Structural Biology at St. Jude Children’s research hospital since 2019 and at Weill Cornell Medicine since 2004, Dr. Blanchard has extensive research experience in single-molecule fluorescence imaging (~20 years), including approximately 80 publications on investigations of ribosomes, ribozymes, riboswitches and a diversity of integral membrane proteins (amino acid transporters, G protein Coupled Receptors, P-type ATPases and viral Envelope proteins). Dr. Blanchard pioneered the single-molecule methods to image the process of translation at the singlemolecule scale and has consistently demonstrated the capacity to innovate and contribute to this important problem area since becoming faculty in 2004.
https://www.scottcblanchardlab.com
Davide Ruggero
Co-Investigator
Professor, Dept. of Urology/Cellular/Molecular Pharmacology
University of California San Francisco
Dr. Ruggero has more than 20 years of experience in the fields of ribosome biogenesis and regulation of protein synthesis and has been a pioneer at the forefront of translational control and cancer. His lab has published seminal studies that have significantly advanced our understanding of how defects in translational control lead to cancer development. These include the genetic dissection of translation control downstream the oncogenic mTOR pathway in cancer and its therapeutic implications, which was the cover story of the March 2010 Cancer Cell (Hsieh et al, Cancer Cell 2010), the characterization of the translational landscape of mTOR signaling in steering prostate cancer initiation and metastasis (Hsieh et al, Nature 2012), and the identification of a novel sequencespecific cis-regulatory translation element controlled by mTOR, contained within the 5’UTRs of mRNAs encoding pro-tumorigenic factors (Hsieh et al, Nature 2012). His lab has defined the translational program of the mammalian cell cycle (Stumpf et al, Molecular Cell 2013) and the role of dysregulated eIF4E-dependent translational control in autism (Gkogkas et al, Nature 2013). His lab was the first to genetically prove that an increase in Myc protein synthesis is a key determinant of Myc oncogenic activity (Barna et al, Nature 2008). Dr. Ruggero’s recent groundbreaking work has opened an entirely new avenue of study, which has exploited Myc’s addiction to enhanced protein synthesis to elucidate an entire network of synthetic lethal interactions.
Shenglong Zhang
Co-Investigator
Associate Professor
Department of Chemistry; The RNA Institute, SUNY Albany
Shenglong Zhang received his doctorate in organic chemistry from Columbia University and his post-doctoral training in Harvard University. He was among the first pioneers in developing the next-generation sequencing (NGS) technologies and spearheaded the development of an LC-MS-based direct RNA sequencing. The new RNA sequencing technology is completely independent of base complementarity and provides a general solution towards de novo RNA sequencing and modification analysis. Its application in RNA biology helps to answer the longstanding questions of: 1) how aberrant modifications in cellular RNA correlate with human diseases such as cancers, diabetes, and neurodegenerative disorders; 2) how RNA modification patterns and levels change in response to cellular environments and environmental stress. His studies also provide new perspectives into RNA epigenetic regulations and facilitate the identification of new RNA biomarkers and targets for drug discovery and personalized medicine.
https://www.albany.edu/chemistry/shenglong-zhang-lab/
The Center is creating training opportunities to increase the exposure of biomedical researchers to genome-wide RNA biology experiments with an emphasis on epitranscriptomics. This includes both "wet experiments" and computational approaches required for analyzing epitranscriptomic datasets. The Center’s goal is to increase the number of investigators who can apply epitranscriptomic technologies in biomedical and translational research.
EPITRANSCRIPTOMICS METHODS WORKSHOPS
Each lab hosts workshops that will include laboratory exercises, such as RNA extraction, sample processing for different RNA modifications, and data analysis.
For inquiries to register, please email: aii2002@med.cornell.edu
OUTREACH
VISITING SCIENTIST PROGRAM
In order to provide comprehensive training in m6A mapping technologies developed by the Center, each lab provides training to visiting researchers so that they can teach others at their home institution. The visiting scientist program includes training in both experimental techniques as well as computational techniques.
For inquiries to register, please email: aii2002@med.cornell.edu
SUMMER INTERNSHIPS
This program is designed for individuals who aspire to work in Center Co-I laboratories and are eager to gain in-depth knowledge and practical skills through training in epitranscriptomics-focused research environments. Participants will have the opportunity to engage directly with ongoing research projects, receiving comprehensive, hands-on exposure to cutting-edge methodologies, technologies, and analytical approaches in the field. In addition to providing rigorous scientific training, the program also seeks to broaden participation and enhance representation within the fields of genomics and epitranscriptomics. By fostering an inclusive environment that supports diverse perspectives, the program contributes to advancing both scientific discovery and equity in biomedical research.
For inquiries to register, please email: aii2002@med.cornell.edu
