The Lin Laboratory of RNA Modification and
Transcriptome Engineering

The Lin laboratory studies RNA modifications (a.k.a “epitranscriptomics”) in human health and diseases. Post-transcriptional RNA processing and modifications are important mechanisms for gene regulation and functional diversity in eukaryotic cells. We develop and apply high-throughput sequencing strategies and transcriptome engineering technologies to study the regulation and function of RNA modifications including alternative splicing, A-to-I RNA editing, and m6A RNA methylation.

 

    1. Transcriptome Analysis Using Long-read Nanopore Sequencing Technologies
      Long-read sequencing technologies, using 
      third-generation DNA sequencers from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies, are revolutionizing genomic research. These technologies have exciting transcriptomic applications, allowing the direct resolution of transcript isoform structures and the interrogation of repetitive RNA sequences. Our lab recently acquired state-of-the-art long-read sequencing devices (Oxford Nanopore MinION and GridION). We are developing new experimental methods to discover and quantify diverse RNA species in bulk tissues and single cells, based on Nanopore long-read sequencing. By comparing the repertoire of full-length RNA transcripts between normal and diseased states (e.g. between normal and tumor cells), we hope to discover molecular markers or therapeutic targets of disease.
    2. Functional consequences of A-to-I RNA editing events in untranslated regions (UTRs).
      RNA editing is an important and widespread mechanism for generating transcriptome diversity in eukaryotic cells. Aberrant RNA editing has been implicated in a variety of diseases including neurological diseases and cancer. The most abundant type of RNA editing is the A-to-I RNA editing (the deamination of adenosine to inosine) mediated by the ADAR family of RNA editing enzymes. The most studied A-to-I RNA editing events are located in protein coding regions of an RNA transcripts due to the potential to recode an amino acid.

      Using TrIP-seq to measure and contrast RNA editing levels (ϕ) in RNA fractions associated with different numbers of ribosomes.


      However, the vast majority of A-to-I RNA editing events are located in the untranslated regions and their functions are largely unknown. We will combine genomic, bioinformatic, and molecular approaches to study the regulatory functions of A-to-I RNA editing events in the 5’ and 3’ UTRs, as well as the roles of RNA editing in shaping complex traits and diseases.

    3. Regulation of N6-methyladenosine (m6A) by RNA binding proteins (RBPs). N6-methyladenosine (m6A) is an abundant and dynamically regulated class of RNA base modification in mRNAs and non-coding RNAs. It affects multiple aspects of RNA metabolism and controls developmental transitions by regulating mRNA decay and translation. We are developing sensitive sequencing methods to detect RNA m6A methylation in a wider array of clinical and biological samples and using transcriptome engineering technologies to investigate the regulatory and functional consequences of m6A methylation. Specifically, we will utilize CRISPRi system to systematically knockdown individual RNA binding proteins (RBPs) and investigate the relationship between the RNA m6A methylome and the RBP-RNA interactome.

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The Lin laboratory is grateful to our funding sources: