Joseph A. Piccirilli

About

Joseph A. Piccirilli is a Professor of Biochemistry and Molecular Biology at the University of Chicago within the Department of Biochemistry & Molecular Biology. His research focuses on the structural and mechanistic understanding of RNA molecules, including their conformational dynamics, modifications, and interactions with small molecules. His work involves studying RNA's role in mitochondrial pathology, RNA structure prediction, and ligand recognition, contributing to the broader understanding of RNA biology and its implications in health and disease. Professor Piccirilli's research integrates structural biology, biochemistry, and molecular biology techniques to elucidate the fundamental principles governing RNA function and its potential therapeutic applications.

Research topics

• Chemistry
• Aerospace engineering
• Biochemistry
• Astrobiology
• Computational biology
• Genetics
• Biology
• Combinatorics
• Cell biology
• Mathematics

Selected publications

• The SARS-CoV-2 Programmed −1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography

  ACS Chemical Biology · 2021 · 80 citations

  Senior authorCorresponding

  The programmed -1 ribosomal frameshifting element (PFSE) of SARS-CoV-2 is a well conserved structured RNA found in all coronaviruses' genomes. By adopting a pseudoknot structure in the presence of the ribosome, the PFSE promotes a ribosomal frameshifting event near the stop codon of the first open reading frame Orf1a during translation of the polyprotein pp1a. Frameshifting results in continuation of pp1a via a new open reading frame, Orf1b, that produces the longer pp1ab polyprotein. Polyprotei…

  DOI

• Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

  Nature Chemistry · 2020 · 80 citations

  DOI

• RNA-Puzzles Round V: blind predictions of 23 RNA structures

  Nature Methods · 2024-12-02 · 60 citations

  articleOpen access

  RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between predicti…

  PublisherOA PDFDOI

• Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

  Nature Chemistry · 2020 · 55 citations

  DOI

• Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes

  Nature Communications · 2025-01-26 · 19 citations

  articleOpen access

  While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro-a new group-II intron-encoded RT-to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops with…

  PublisherOA PDFDOI

Recent grants

• The VS Ribozyme: Catalytic Mechanism, Transition State Structure, and Evolution

  NIH · $1.4M · 2019–2023

• Chaperone-Assisted RNA Crystallography

  NIH · $380k · 2013–2021

• NIH Grant R56AI081987

  NIH · $385k · 2010

Frequent coauthors

• Nan‐Sheng Li

  University of Chicago

  111 shared

• Michael E. Harris

  University of Florida

  88 shared

• Darrin M. York

  Quantitative BioSciences

  79 shared

• Qing Dai

  76 shared

• K. Y. Wong

  Prince of Wales Hospital

  53 shared

• Steven A. Benner

  Foundation for Applied Molecular Evolution

  43 shared

• Daniel Herschlag

  40 shared

• Hong Gu

  Peking University

  39 shared

Labs

• Joseph A. Piccirilli LabPI

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