Research Interests of the Yi Laboratory
We probe the pathways and mechanisms of DNA/RNA modification and de-modification.
In order to do so, we integrate multiple disciplines including chemical biology, epigenetics, nucleic acid chemistry, cell biology, biochemistry, genomics, and structural biology.
An ultimate goal is to uncover new functions and regulatory mechanisms of the epigenetic DNA/RNA modifications.
1. RNA Modifications and Epitranscriptomics
More than 100 distinct post-transcriptional modifications have been characterized so far; they were considered to be static and unalterable after covalent installation. Recent discoveries of reversible RNA methylation in the form of N6-methyladenosine (m6A) have demonstrated RNA modification-mediated regulation of gene expression, leading to the emerging field of “epitranscriptomics”.
In addition to m6A, there are other epitranscriptomic marks. My laboratory recently discovered that pseudouridine (Ψ) and N1-methyladenosine (m1A), two post-transcriptional modifications in non-coding RNAs, are also present in mammalian mRNAs. My laboratory showed that these epitranscriptomic marks are prevalent in mRNA, dynamically-regulated by various stimuli and reversible by potential “eraser” proteins in the case of m1A. However, the biological consequences of mRNA pseudouridylation and m1A methylation are unknown. Utilizing epitranscriptome sequencing tools we have developed, we hope to elucidate the functional consequences and regulatory mechanisms of these RNA modifications, hence leading to new territories in the nascent field of epitranscriptomics.
2. TET- and TDG-dependent Active DNA Demethylation
The ten-eleven translocation (TET)-dependent generation and removal of oxidized derivatives of 5-methylcytosine (5mC), namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), uncovered a new paradigm of active DNA demethylation in mammalian genomes. Besides acting as demethylation intermediates, these oxidized variants of 5mC may also play functional roles. Emerging evidence has suggested 5hmC as a stable epigenetic modification implicated in many biological processes and various diseases. 5fC and 5caC, further oxidation products of 5hmC, accumulate at distal regulatory elements as active DNA demethylation intermediates and can be removed through base excision repair by mammalian thymine DNA glycosylase (TDG). My laboratory recently developed “fC-CET”, a bisulfite-free, base-resolution method for the genome-wide identification of 5fC sites. We will continue to develop robust and sensitive sequencing technologies, including those applicable to single-cell studies and clinical investigations, to dissect the functional roles of these epigenetic DNA modifications.
3. DNA Repair and Protein-DNA Interactions
Aberrant modification to DNA can lead to cytotoxic or mutagenic consequences. Once damaged, cellular DNA must be promptly repaired. Organisms have evolved a variety of mechanisms to repair these cytotoxic or mutagenic damages; in the Yi Group, we are interested in the base-excision repair and direct repair pathways. One component of our research is to utilize a novel chemical cross-linking technique to stabilize protein-DNA interactions in these systems. For instance, my group recently revealed an unprecedented mechanism of DNA repair glycosylase hNEIL1: it promotes tautomerization of thymine glycol—a preferred substrate—for efficient substrate recognition and excision. An integrative approach uniting chemical synthesis, structural biology and biochemical/biophysical characterization is used to study these interactions in DNA/RNA base repair and modification proteins.
4. Genome Editing
Genome editing tools, especially those based on the CRISPR/Cas system, show alluring prospect in therapeutic applications. Effective correction of point mutations by base editors (BE), which directly converse one type of DNA base to another at targeted locus, offers an attractive tool to cure various genetic diseases. However, precise evaluation of genome-wide off-target editing events remains challenging. Integrating our expertise in chemical biology and genomics, we aim to develop unbiased tools for the genome-wide evaluation of the accuracy of these editors. The ultimate goal is to not only improve the specificity of existing tools, but also to develop new technologies that are eventually suitable for clinical applications.