eIF3d controls the persistent integrated stress response

S Mukhopadhyay, ME Amodeo, ASY Lee - Molecular cell, 2023 - cell.com
Cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and
activating gene programs necessary for survival. Here, we show that the integrated stress …

The evolution of RNA structural probing methods: from gels to next‐generation sequencing

E Mailler, JC Paillart, R Marquet… - Wiley …, 2019 - Wiley Online Library
RNA molecules are important players in all domains of life and the study of the relationship
between their multiple flexible states and the associated biological roles has increased in …

A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress

AM Lamper, RH Fleming, KM Ladd, ASY Lee - Science, 2020 - science.org
Shutoff of global protein synthesis is a conserved response to cellular stresses. This general
phenomenon is accompanied by the induction of distinct gene programs tailored to each …

Selective packaging of HIV-1 RNA genome is guided by the stability of 5′ untranslated region polyA stem

OA Nikolaitchik, S Liu, JP Kitzrow… - Proceedings of the …, 2021 - National Acad Sciences
To generate infectious virus, HIV-1 must package two copies of its full-length RNA into
particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA …

Chemical and enzymatic probing of viral RNAs: From infancy to maturity and beyond

O Gilmer, E Quignon, AC Jousset, JC Paillart… - Viruses, 2021 - mdpi.com
RNA molecules are key players in a variety of biological events, and this is particularly true
for viral RNAs. To better understand the replication of those pathogens and try to block them …

Validating the EMCV IRES Secondary Structure with Structure–Function Analysis

A Maloney, S Joseph - Biochemistry, 2023 - ACS Publications
The encephalomyocarditis virus internal ribosome entry site (EMCV IRES) is a structured
RNA sequence found in the 5′ UTR of the genomic RNA of the encephalomyocarditis virus …

High resolution biosensor to test the cap** level and integrity of mRNAs

I Moya-Ramírez, C Bouton, C Kontoravdi… - Nucleic Acids …, 2020 - academic.oup.com
Abstract 5′ Cap structures are ubiquitous on eukaryotic mRNAs, essential for post-
transcriptional processing, translation initiation and stability. Here we describe a biosensor …

RNA Chemical Labeling with Site‐Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin‐Sensing Riboswitch Aptamer Domain

M Palasser, K Breuker - ChemPlusChem, 2022 - Wiley Online Library
High‐resolution mass spectrometry was used for the label‐free, direct localization and
relative quantification of CMC+‐modifications of a neomycin‐sensing riboswitch aptamer …

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA

DM Dayeh, WA Cantara, JP Kitzrow… - Nucleic acids …, 2018 - academic.oup.com
The recent identification and development of RNA-guided enzymes for programmable
cleavage of target nucleic acids offers exciting possibilities for both therapeutic and …

RNAthor–fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis

J Gumna, T Zok, K Figurski, K Pachulska-Wieczorek… - PloS One, 2020 - journals.plos.org
RNAs adopt specific structures to perform their functions, which are critical to fundamental
cellular processes. For decades, these structures have been determined and modeled with …