Concurrent detection of chemically modified bases in yeast mitochondrial tRNAs by Nanopore direct RNA sequencing

biorxiv (pre-print), 2025

Reinsch, J. and Garcia, D.M.‡

Direct sequence of all 24 yeast mitochondrial tRNAs predicts modification landscape and newly described interdependencies.

A pseudouridine synthase shapes tRNA structural dynamics through both catalysis and remodeling

biorxiv (pre-print), 2025

Dennis, E.M.*, Conoan Nieves, N.E.*, Vaaler, A.L., Kadrmas, M., Barry, M.L., Garcia, D.M.‡, Widom, J.R.‡

Multi-pronged biophysical analysis of tRNA structural dynamics upon engagement with a ubiquitous tRNA modifying enzyme.

Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors

nucleic acids research, 2024

Shaw, E.A.*, Thomas, N.K.*, Jones, J.D., Abu-Shumays, R.L., Vaaler, A.L., Akeson, M., Koutmou, K.S., Jain, M.‡, Garcia, D.M.‡

Nanopore sequencing and mass spectrometry of all cytosolic tRNA isoacceptors from S. cerevisiae permitted detailed analysis of conserved modification in the T-loop and their interdependencies.

Biochemical principles in prion-based inheritance (review)

epigenomes, 2022

Dennis E.M. and Garcia, D.M.

a prion accelerates proliferation at the expense of lifespan

elifE, 2021

Garcia, D.M.*‡, Campbell, E.A.*, Jakobson, C.M., Tsuchiya, M., Shaw, E.A., DiNardo, A.L., Kaeberlein, M., Jarosz, D.F.‡

A highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation, increased cell size, and altered translation, at the cost of shortened lifespan.

• eLife Press Pack: How proteins help yeast adapt to changing conditions

prior training

adaptive variation in mutagenesis driven by protein self-assembly

SSRN (PRE-PRINT), 2025

Van Elgort, A., Jakobson, C.M., Byers, J.S.*, Futia, R.A.*, Chen, Y.R., Lozanoski, T.M., Harvey, Z.H., Xie, J.L., Garcia, D.M., Jarosz, D.F.‡

Protein self-assembly, common among DNA replication and repair factors, can materialize epigenetic memory that tunes rates of genome diversification to expand adaptive opportunities.

a non-amyloid prion particle that activates a heritable gene expression program

molecular cell, 2020

Chakravarty, A.K., Smejkal, T., Itakura, A., Garcia, D.M., Jarosz, D.F.

Discovered that phase separation of an evolutionary ancient RNA-binding protein allows it to act as a protein-based genetic element. 

A common bacterial metabolite elicits prion-based bypass of glucose repression

eLife, 2016

Garcia, D.M.*, Dietrich, D.*, Clardy, J.‡, Jarosz, D.F.‡

Activity-guided fractionation identified the first bacterial metabolite that potently induces a prion in nature. Demonstrated that chemically simple and ubiquitous small molecules can induce epigenetic states. Also finally explained a mysterious observation first made by Louis Pasteur over 140 years ago.

• eLife Insight: An acid tale of prion formation. Tuite, M.F., eLife 2016, 5:e22256

• Editor’s Choice: Bacteria stop fermentation with lactic acid. Science Signaling  9,457: ec288

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

Cell, 2016

Chakrabortee, S.*, Byers, J.S.*, Jones, S., Garcia, D.M., Bhullar, B., Chang, A., She, R., Lee, L., Fremin, B., Lindquist, S.‡, Jarosz, D.F.‡

Defined a new class of non-amyloid prions in yeast responsible for protein-based transgenerational inheritance that do not rely necessarily on stable protein aggregates like classic (amyloid) prions.

• Remembering the Past: A New Form of Protein-Based Inheritance. Tuite, M.F., Cell 167, 369–381

• Science Daily: Revising the meaning of ‘prion’. October 4, 2016

Rebels with a cause: molecular features and physiological consequences of yeast prions (Review)

FEMS Yeast Research, 2014

Garcia, D.M. and Jarosz, D.F.

Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs

Nature Structural and Molecular Biology, 2011

Garcia, D.M.*, Baek, D.*, Shin, C., Bell, G.W., Grimson, A., Bartel, D.P. 

Discovered new sequence features central to the microRNA pathway, an ancient and widespread mechanism of post-transcriptional gene control. Results were integrated into miRNA target prediction program TargetScan.org, used by tens of thousands of users per month.

science writing for the public

Extreme Tissue Regeneration

OZY magazine, 2014

Garcia, D.M.

Highlights research on planaria, nature's king of regeneration.

Note: OZY Media ceased operating in 2023 due to a fraud scandal uncovered years prior. Before their website disappeared, I hastily saved a copy of my piece using screen shots from my phone, linked below.

Great Adaptations: A versatile bacterium provides insight into multicellular microbial life and tackling deadly infections  

Natural History Magazine, 2012

Garcia, D.M.

Story of how evolution constructs beautifully fluid connections between ancient microbiology and human disease.

you'd prefer an argonaute 

wordpress, 2009–2015 

Garcia, D.M. (plus contributors from MIT Biology)

The original online journal club. A blog about RNA research and biomedical science. ~50,000 views.