Eric L. Garcia, PhD
Garcia Lab

RNA Mechanisms and Neuromuscular Biology

The overarching aim of my lab is to understand the fundamental roles that RNA plays in both health and disease. Using Drosophila as a model system, the specific focus of my lab is the contribution of RNA to neuromuscular health and disease, diseases like SMA (Spinal Muscular Atrophy) and ALS (Amyotorophic Lateral Sclerosis). The lab uses new high throughput sequencing technologies together with classic molecular biology and fly genetics to unravel complex biological questions.

Spatiotemporal appearance of RNA processing and gene expression changes in Survival Motorneuron (SMN) hypomorphs

When modeled in the fly, previous work has shown that SMA-causing point mutations found in patients recapitulate the full range of phenotypic severity seen in humans, SMN mutations that cause disease in humans also cause disease in flies. Transcriptomic comparison of SMN mutants with other snRNP biogenesis mutants revealed both mutant-specific and overlapping snRNP-dependent changes in gene expression and RNA processing. The relevance of these different changes to disease pathology is not known. Transcriptomic analysis of different developmental stages and tissues of SMA model flies will identify phenotypic and disease relevant RNA changes.

Students:

Christina R Savage, Grad Student (11/28/2018)

Software:

The bioinformatics analysis of the raw RNA-seq data uses publicly available software packages including:
Samtools, Bedtools, Tophat, Cufflinks, HISAT2, STAR, Bowtie2, MISO, DaPars and kallisto, among others. Some of these packages will require additional dependencies, including Python, numpy, scipy, pysam, matplotlib libraries and R.

The structure and function of non-coding RNA sequences in pre-mRNA.

The ability of RNA to fold into complex tertiary structures is a unique physical property that enables it to play an active and dynamic role in regulating gene expression. Although the structures of many small non-coding RNAs are well known, much less is known about the RNA folding patterns of mRNAs and how this folding impacts gene expression. Techniques for chemical probing followed by high throughput sequencing have been developed and are currently in use in the analysis of disease associated RNA structural changes. We will use this technology to understand the contribution of mRNA structure to pre-mRNA processing steps and the basic regulation of gene expression in Drosophila.

SHAPE-MaP

(selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling; pioneered by the Weeks lab) will be used to determine the secondary structure of Drosophila mRNAs. RNA mutational profiling includes high throughput sequencing and subsequent analysis with another publicly available software package, ShapeMapper/SuperFold, in addition to the bioinformatic tools noted above.

Personnel

Dr. Eric L. Garcia, PI, Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky Medical Center, Lexington, KY 40536

Publications

1. Garcia E.L., Wen Y., Matera A.G. (2016) Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant specific changes in pre-mRNA processing: implications for Spinal Muscular Atrophy. RNA 22:1215-1227
2. Garcia E.L., Lu Z., Meers M.P., Praveen K., Matera A.G. (2013) Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. RNA 19:1510-1516