The chemical building blocks that make up RNA are central to its function. Pioneering studies in the 1970s were the first to show that cellular mRNAs contain chemically modified bases in addition to the standard A, G, C, and U residues. Recent technological advances have enabled the identification and investigation of these mRNA modifications on an unprecedented scale. As a result, our understanding of the "epitranscriptome" has rapidly accelerated in recent years, and we have gained new insights into this fundamental aspect of RNA biology.
One modified base which is particularly prevalent throughout the transcriptome is N6-methyladenosine, or m6A, which occurs when A residues become methylated. In 2012, Dr. Meyer's work led to the development of the first method for transcriptome-wide detection of m6A. This method, called MeRIP-Seq, revealed thousands of cellular mRNAs that contain m6A and sparked a renewed interest in the study of mRNA modifications (Meyer et al, Cell, 2012). Since then, laboratories around the world have sought to uncover the pathways that regulate m6A and the functional consequences of the m6A mark in regulating gene expression. Although remarkable progress has been made over the last several years, there are still many questions that remain unanswered.
A major goal of our laboratory is to understand how m6A contributes to fundamental aspects of gene expression control. We do this using biochemical methods, transcriptomics- and proteomics-based approaches, animal models, and other novel techniques developed in our laboratory. Although much of our focus is on RNA modifications, we also explore general mechanisms of RNA regulation in the cell.
Neurobiology Projects
Our previous studies were the first to reveal that m6A is highly abundant in the brain. However, our understanding of the role that m6A plays in regulating neurophysiological processes is still in its infancy. Currently, many projects in our laboratory are focused on understanding how m6A and other RNA modifications shape gene expression programs in the nervous system. We are particularly interested in exploring the role of mRNA modifications in regulating mRNA localization and local translation in neurons. These processes are central to the control of local gene expression that underlies synaptic plasticity. We are therefore also extending our molecular studies into mouse models to determine how m6A contributes to complex processes such as learning and memory and addiction.
In addition, several projects in our laboratory investigate the proteins that bind to methylated RNAs in the brain. We are currently exploring how these protein:RNA interactions contribute to both neurodevelopment and neurodegenerative disease. We have discovered previously unknown m6A binding proteins in the brain and elucidated their roles in both RNA regulation and neurodevelopment.
Technology Development
The Meyer lab works to develop novel technologies for probing the epitranscriptome. We recently developed DART-seq, a method for global m6A detection which overcomes many of the limitations of current antibody-based approaches for m6A profiling. DART-seq relies on targeted deamination of cytidine residues immediately adjacent to m6A sites, and it can profile m6A in cells from ultra-low amounts of total RNA. Recently, we demonstrated the ability of DART-seq to profile m6A in single cells (scDART-seq). This has enabled the discovery of previously unknown features of m6A within mRNAs and across individual cells of a population. Current projects in the lab are using scDART-seq to answer important biological questions about how the methylome is altered during distinct physiological states and to understand how m6A is distributed in complex tissues.
In addition to developing new tools for studying m6A, we have also developed novel methods for investigating RNA:protein interactions in cells. Recently, we developed TRIBE-STAMP, which enables the identification of single RNA molecules bound by two different RBPs in cells at the same time. To do this, TRIBE-STAMP takes advantage of the unique mutation signatures of the TRIBE/HyperTRIBE and STAMP methods, in which the ADAR and APOBEC1 deaminases are fused to distinct RBPs of interest. We applied TRIBE-STAMP to the YTHDF family of proteins and discovered that many mRNAs can be bound more than once by multiple YTHDF proteins throughout their lifetime. We expect TRIBE-STAMP will be of widespread utility for examining cooperation/competition between virtually any RBPs of interest in cells.