N6-methyladenosine-dependent regulation of gene expression by YTHDC1

Roundtree, Ian

Abstract

Reversible chemical modifications of DNA and proteins play fundamental roles in regulating eukaryotic gene expression, and are abhorrently perturbed in many forms of cancer. Recent work in our lab and others has identified analogous chemical modifications on messenger RNA (mRNA) and long noncoding RNA (lncRNA). FTO and ALKBH5, two ALKB family iron- and 2-ketoglutyrate-dependent dioxygenases, catalyze the demethylation of the most prevalent internal modification of mRNA, N6-methyladenosine (m6A). Characterization of the methyltransferase complex, combined with transcriptome-wide maps of m6A in mRNA, has generated an interest in RNA modification as a critical component of cellular physiology. Our research seeks to identify the biological roles of m6A by understanding the function of methyl-selective reader proteins of the YTH family. The role of m6A within the nucleus is unknown, but we have identified YTHDC1 as an m6A- selective RNA binding protein that binds mRNA within the cell nucleus. Preliminary results implicate YTHDC1 in the export of methylated RNA transcripts from the nucleus to the cytoplasm, where they can be actively translated. This represents a previously unknown function of m6A in mRNA, and contributes to a new paradigm of gene regulation as a function of RNA modification. This proposal aims to decipher the role of YTHDC1 as an effector of RNA methylation. We will use a combination of molecular biological, biochemical and genetic approaches to accomplish the following: (i) characterize protein-protein interactions of YTHDC1 by isolation of protein complexes and mass-spectrometry, as well as characterization of interacting proteins and m6A in mediating this mechanism of mRNA export; (ii) determine necessary protein and lncRNA components of novel nuclear granules defined by YTHDC1, termed YT bodies, with potential roles in cell cycle regulation. These experiments will further our understanding of the biological roles of m6A and provide molecular mechanisms by which this chemical modification affects fundamental biological processes. This work contributes to the fields of molecular biology, biochemistry, cell biology and genomics, and lays the groundwork for future studies concerning post-transcriptional gene regulatory mechanisms in human health and disease.

Public Health Relevance

Analogous to chemical modification of DNA and protein, modification of messenger RNA (mRNA) and long noncoding RNA (lncRNA) can have profound effects on gene regulation. We have found that YTH proteins, including the nuclear protein YTHDC1, selectively recognize RNA bearing methylation at the N6 position of adenosine. Understanding how such reader proteins mediate the effects of this common RNA modification will shed light on a highly conserved mode of gene expression regulation. Knowledge of such mechanisms will provide a basis for potential disease diagnosis, treatment and prevention.