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Research

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RNA biology & activities of RNA-protein machines

The Pyle Lab studies RNA structure and RNA recognition by proteins and small molecules. We use a combination of experimental biochemistry and cryo-electron microscopy to study the architectural features of large RNA molecules, such as self-splicing introns, noncoding RNAs and viral genomes. We also work on RNA-dependent ATPase enzymes that bind and remodel RNA structures, with an emphasis on proteins that are involved in viral replication and host innate immune response. The Pyle Lab has solved some of the largest RNA structures ever determined, such as group II introns and their protein partners. We have also solved many first-in-class protein structures, such as the RIG-I innate immune receptor and retroelement reverse transcriptases. These studies have been complemented by efforts to develop RNA and small molecule modulators of immune function and antiviral response. 

Photo by Ryuji Suzuki, 2023.

Research Projects

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S. Patel & A.M. Pyle et al. Nat Comm. 2023

Structure and Function of Large RNAs

Many cellular processes are catalyzed and regulated by large, highly structured RNA molecules. Our laboratory is interested in the tertiary structures of large RNA molecules that control eukaryotic gene expression and viral pathogenicity. We use a combination of biochemistry, cell biology and cryo-EM to monitor the architectural states of large RNAs and to understand the link between their molecular structure and function in biology. In addition to experimental techniques, we also develop and utilize computational methods to solve and analyze RNA structures.​

 

Relevant Publications
Structure and Function
Protein Machines
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Protein Machines on RNA Genes

Some of the most important motor proteins in our cells are nanomechanical enzymes that remodel RNA molecules or use RNA binding to initiate cell signaling. RNA helicases, polymerases, and surveillance proteins all play a vital role in the dynamic life of the cell. We study the molecular basis for their function using a combination of enzymology, cell biology and structural biology. Of particular interest to the Pyle Lab are the RIG-I-like innate immune receptor proteins and the diverse families of reverse transcriptase enzymes.

 

W. Wang & A.M. Pyle et al. Mol Cell. 2022

Relevant Publications
RNA and Viruses
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RNA and Viruses: The Machinery of Pathogenesis

Structured RNA genomes are essential for the function of many viruses, including Hepatitis C virus (HCV), flaviviruses (such as Dengue or Yellow Fever), and coronaviruses. We aim to elucidate the regulatory RNA motifs within the genomes of RNA viruses, to visualize their structures and to use the tools of molecular virology to understand their roles in the viral lifecycle. 

 

Modified from N. Huston & A.M. Pyle et al. Mol Cell. 2021

Relevant Publications
Drugging RNA
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Drugging RNA: Targeting RNA tertiary structures with small molecules

Pathogenic organisms ranging from fungi to viruses contain specific RNA tertiary structures that are essential for viability and infection.  These riboregulatory motifs have distinctive folded structures capable of specific drug binding, but since they are not found in humans, they represent ideal targets for the development of novel antimicrobial drugs that lack any human toxicity.        

 

O. Fedorova & A.M. Pyle et al. ACS Chem Biol. 2023

Relevant Publications

Software & Computational Tools

The Pyle Lab has developed a variety of programs to complement our experimental projects. These software and tools can be used for a variety of RNA sequence, structure, and modification predictions and analyses.

 

Please visit our GitHub page to download available programs

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Some of our tools also have web servers!

  • GitHub

MRTModSeq​

Author: Rafael de Cesaris Araujo Tavares, Gandhar Mahadeshwar, & Han Wan
Description: Rapid detection of RNA modifications with MarathonRT.
Reference: Araujo Tavares RC, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT. bioRxiv, 2023
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Arena

Author: Zion Perry & Chengxin Zhang

Description: Full atomic reconstruction of RNA structures from coarse-grained representations.

Reference: Perry ZR, Pyle AM, Zhang C. Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models. J Mol Biol, 2023

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RSCanner

Author: Gandhar Mahadeshwar, Rafael de Cesaris Araujo Tavares, Han Wan, & Zion Perry
Description: Rapid visualization of RNA secondary structure content across a transcript.
Reference: Mahadeshwar G, Araujo Tavares RC, Wan H, Perry ZR, Pyle AM. RSCanner: rapid assessment and visualization of RNA structure content. Bioinformatics, 2023
 

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rMSA

Author: Chengxin Zhang
Description: RNA sequence database search and multiple sequence alignment generation.
Reference: Zhang C, Zhang Y, Pyle AM. rMSA: a sequence search and alignment algorithm to improve RNA structure modeling. J Mol Biol, 2022
 

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US-align

Author: Chengxin Zhang
Description: Universal Structure Alignment of RNAs, DNAs, proteins and macromolecule complexes.
References: Zhang C, Shine M, Pyle AM, Zhang Y. US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes. Nat Methods, 2022 and Zhang C, Pyle AM. A unified approach to sequential and non-sequential structure alignment of proteins, RNAs and DNAs. iScience, 2022​

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CSSR

Author: Chengxin Zhang
Description: CSSR assigns RNA secondary structure to coarse-grained tertiary structure.
Reference: Zhang C and Pyle AM. CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures. Acta Cryst D, 2022.​​

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  • GitHub
  • GitHub
  • GitHub

Oligo-Synthesizers

MerMade 12 and H-8 SE

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SPR

PioneerFE

Fluorescence Microscope

Keyence BZ-X810

Lab Equipment

Plate Reader

Synergy Neo2

Biomolecular Imager

Amersham Typhoon

Tools & Therapeutics

MarathonRT was discovered by Chen Zhao and developed by Li-Tao Guo when they were members of the Pyle lab. It is an ultraprocessive reverse-transcriptase that moves rapidly through long, highly structured RNAs. It can be obtained from RNAConnect. Anna Pyle is a founder and advisor to RNAConnect.

Lab members Andrew Kohlway, Dahai Luo and Steve Ding demonstrated that short, triphosphorylated stem-loop RNAs are potent inducers of the RIG-I receptor, making them valuable tools for studying and treating viral infections. To develop SLRs, Anna Pyle teamed up with Akiko Iwasaki to found RIGImmune. Anna Pyle is a founder and advisor to the company.

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