Non-coding RNAs in disease: from mechanisms to therapeutics

K Nemeth, R Bayraktar, M Ferracin… - Nature Reviews Genetics, 2024‏ - nature.com
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are
not translated into proteins. Since their discovery, ncRNAs have emerged as important …

The dark proteome: translation from noncanonical open reading frames

BW Wright, Z Yi, JS Weissman, J Chen - Trends in cell biology, 2022‏ - cell.com
Omics-based technologies have revolutionized our understanding of the coding potential of
the genome. In particular, these studies revealed widespread unannotated open reading …

Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts

JW Guarnieri, JM Dybas, H Fazelinia, MS Kim… - Science translational …, 2023‏ - science.org
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host
mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating …

[HTML][HTML] A high-resolution map of human RNA translation

SP Chothani, E Adami, AA Widjaja, SR Langley… - Molecular cell, 2022‏ - cell.com
Translated small open reading frames (smORFs) can have important regulatory roles and
encode microproteins, yet their genome-wide identification has been challenging. We …

Cellular heterogeneity in TNF/TNFR1 signalling: live cell imaging of cell fate decisions in single cells

MK Preedy, MRH White, V Tergaonkar - Cell Death & Disease, 2024‏ - nature.com
Cellular responses to TNF are inherently heterogeneous within an isogenic cell population
and across different cell types. TNF promotes cell survival by activating pro-inflammatory NF …

Overlap** genes in natural and engineered genomes

BW Wright, MP Molloy, PR Jaschke - Nature Reviews Genetics, 2022‏ - nature.com
Modern genome-scale methods that identify new genes, such as proteogenomics and
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …

Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity

Y Takakura, M Machida, N Terada, Y Katsumi… - Nature …, 2024‏ - nature.com
Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial
damage. However, stress-independent autophagy is activated by unclear mechanisms in …

[HTML][HTML] Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins

TF Martinez, S Lyons-Abbott, AL Bookout… - Cell metabolism, 2023‏ - cell.com
Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators.
Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small …

ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs

S Miravet-Verde, R Mazzolini… - Nature …, 2024‏ - nature.com
Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a
technique designed to characterize proteomes by sequencing transposon insertions …

Inflammation causes remodeling of mitochondrial cytochrome c oxidase mediated by the bifunctional gene C15orf48

SA Clayton, KK Daley, L MacDonald… - Science …, 2021‏ - science.org
Dysregulated mitochondrial function is a hallmark of immune-mediated inflammatory
diseases. Cytochrome c oxidase (C c O), which mediates the rate-limiting step in …