The molecular basis of translation initiation and its regulation in eukaryotes

J Brito Querido, I Díaz-López… - Nature Reviews Molecular …, 2024 - nature.com
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional
regulation of gene expression has been studied for several decades, it has been clear over …

A critical review of bottom-up proteomics: the good, the bad, and the future of this field

EJ Dupree, M Jayathirtha, H Yorkey, M Mihasan… - Proteomes, 2020 - mdpi.com
Proteomics is the field of study that includes the analysis of proteins, from either a basic
science prospective or a clinical one. Proteins can be investigated for their abundance …

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

F Meier, AD Brunner, M Frank, A Ha, I Bludau… - Nature …, 2020 - nature.com
Data-independent acquisition modes isolate and concurrently fragment populations of
different precursors by cycling through segments of a predefined precursor m/z range …

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

AD Brunner, M Thielert, C Vasilopoulou… - Molecular systems …, 2022 - embopress.org
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging
and deep sequencing. However, proteins are the main drivers of cellular function and in …

Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

A Stukalov, V Girault, V Grass, O Karayel, V Bergant… - Nature, 2021 - nature.com
The emergence and global spread of SARS-CoV-2 has resulted in the urgent need for an in-
depth understanding of molecular functions of viral proteins and their interactions with the …

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

ST Gebreyesus, AA Siyal, RB Kitata, ESW Chen… - Nature …, 2022 - nature.com
Single-cell proteomics can reveal cellular phenotypic heterogeneity and cell-specific
functional networks underlying biological processes. Here, we present a streamlined …

Pervasive functional translation of noncanonical human open reading frames

J Chen, AD Brunner, JZ Cogan, JK Nuñez, AP Fields… - Science, 2020 - science.org
Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of
canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based …

Dietary restriction of cysteine and methionine sensitizes gliomas to ferroptosis and induces alterations in energetic metabolism

PS Upadhyayula, DM Higgins, A Mela, M Banu… - Nature …, 2023 - nature.com
Ferroptosis is mediated by lipid peroxidation of phospholipids containing polyunsaturated
fatty acyl moieties. Glutathione, the key cellular antioxidant capable of inhibiting lipid …

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

CS Hughes, S Moggridge, T Müller, PH Sorensen… - Nature protocols, 2019 - nature.com
A critical step in proteomics analysis is the optimal extraction and processing of protein
material to ensure the highest sensitivity in downstream detection. Achieving this requires a …

Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes

Y Hori, C Engel, T Kobayashi - Nature reviews Molecular cell biology, 2023 - nature.com
One of the first biological machineries to be created seems to have been the ribosome.
Since then, organisms have dedicated great efforts to optimize this apparatus. The …