Lin Lab of RNA Modifications and Transcriptome Engineering

The Lin Lab studies RNA modifications (“epitranscriptomics”) in human health and disease. Post-transcriptional RNA processing and modifications are key 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.


Transcriptome analysis using long-read nanopore sequencing

Long-read sequencing technologies, using third-generation DNA sequencers from Pacific Biosciences and Oxford Nanopore Technologies, are revolutionizing genomic research. These technologies have exciting transcriptomic applications, allowing direct resolution of transcript isoform structures and interrogation of repetitive RNA sequences. Using state-of-the-art nanopore long-read sequencing devices (MinION and GridION), we are developing new experimental methods to discover and quantify diverse RNA species in bulk tissues and single cells. By comparing the repertoire of full-length RNA transcripts between normal and diseased states (e.g. tumors), we hope to discover molecular markers or therapeutic targets of disease.

 

Functional consequences of A-to-I RNA editing events in UTRs

A critical, widespread mechanism for generating transcriptome diversity in eukaryotic cells, aberrations in RNA editing have been implicated in various diseases. Researchers have primarily studied the most abundant RNA editing type (A-to-I RNA editing) in protein-coding RNA regions, due to the potential for amino acid re-coding. However, based on an analysis of the RADAR database of A-to-I RNA editing events, nearly all such events (~96%) are located in untranslated regions (UTRs) of the mature mRNA. Moreover, their functions are largely unknown. By combining genomic, bioinformatic, and molecular approaches, such as Transcript Isoforms in Polysome sequencing (TrIP-seq), our lab studies the regulatory functions of A-to-I RNA editing events in 5’ and 3’ UTRs, as well as the roles of RNA editing in shaping complex traits and diseases.


Regulation of N6-methyladenosine by RNA binding proteins

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 wide array of clinical and biological samples. Additionally, our lab uses transcriptome engineering technologies to investigate the regulatory and functional consequences of m6A methylation. For instance, we use the CRISPRi system to systematically knockdown individual RNA binding proteins (RBPs) and investigate the relationship between the RNA m6A methylome and the RBP-RNA interactome.

Recent News

12/31/2021

Lin Lab Receives Award from CHOP Diagnostic Innovation Fund

The Lin Lab received an award from the CHOP Pathology Diagnostic Innovation Fund. This 1-year, $100,000 award was designed to accelerate development of new diagnostic tests, with the overall goal of encouraging translation of promising bench research to clinical tests. Dr. Lin will use the funding to develop an RNA-guided diagnostic technology for inborn errors of immunity (IEI), using the efficient and cost-effective TEQUILA-seq method for targeted long-read RNA sequencing of IEI genes.

4/19/2021

Dr. Lan Lin Awarded CGTC Seed Grant

The Lin lab was awarded a CHOP Cell & Gene Therapy Collaborative (CGCT) Seed Grant. CHOP Seed Grants are intended to promote early-stage development of new ideas, with the goal of achieving preclinical proof-of-concept by the end of the 2-year grant period. Dr. Lin will use the funding to further develop her lab’s microfluidic single-cell TCR screen, which is designed to develop novel therapies for pediatric AML.

12/7/2020

Dr. Lin Awarded Prestigious Grant from W.W. Smith Charitable Trust

Dr. Lan Lin was awarded a Medical Research Grant from the W.W. Smith Charitable Trust. The Grant provides 1 year of funding for basic research projects with high potential for direct impact in the fight against heart disease, cancer, and AIDS. Dr. Lin will use the funding to develop a novel microfluidic single-cell T-cell receptor (TCR) screen for pediatric acute myeloid leukemia (AML).

3/19/2020

Dr. Lan Lin Awarded Pilot Grant from the Frontiers in CDG Consortium

Dr. Lan Lin was awarded a Pilot and Feasibility Grant of $40,000 from the Frontiers in Congenital Disorders of Glycosylation (CDG) Consortium. The Grant provides 12 months of funding for “High Risk, High Reward” projects in CDG. Dr. Lin’s project will study the potential role of endogenously N-glycosylated RNA (glycoRNA) in samples from pediatric patients with CDG.

The Lin laboratory is grateful to our funding sources: