A viral ORFeome library for systems-level genetic dissection of host-pathogen interactions

A scalable library of ∼13,000 barcoded viral open reading frames from >500 viral species enables functional genomic screens across the virome. Applying this platform identified viral regulators of cellular proliferation, antigen presentation, and interferon signaling. This platform enables systematic exploration of viral protein function.

dlvr.it

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all ve...

biorxiv.org

Ubiquitin selective ribosome profiling reveals systematic principles of co-translational quality control

Protein biogenesis is a stress- and error-sensitive process that can lead to nascent protein misfolding and aggregation, challenging cellular proteostasis. Co-translational ubiquitination (CTU) is a c...

biorxiv.org

αKG-mediated carnitine synthesis drives DNA repair via histone acetylation - Nature

The metabolite αKG promotes carnitine synthesis and increases site-specific histone acetylation, thereby promoting homologous recombination-mediated DNA repair, which has potential implications f...

nature.com

RNA imbalance as a hallmark of cellular ageing

Nature Cell Biology - This Perspective highlights the failures of an ageing cell in properly maintaining mRNA health at the various steps of the mRNA life cycle that result in vulnerability to...

rdcu.be

biorxiv.org

Bacteria Have Millions of Secret Weapons Against Viruses

Millions of new proteins with predicted roles in defence against viruses have been identified in bacteria. It was thought that around 0.5% of the average bacterial genome had some involvement in immun...

pasteur.fr

RNA-triggered cell killing with CRISPR–Cas12a2 - Nature

Cas12a2 enables RNA-triggered, sequence-specific killing of eukaryotic cells via widespread DNA shredding, allowing selective elimination of cells on the basis of gene expression, including virus-infe...

nature.com

Expanding the human proteome with microproteins and peptideins - Nature

A large-scale proteomics analysis of the dark proteome by the TransCODE Consortium reveals many translated non-canonical open reading frames to encode microproteins and peptideins.

nature.com

Expanding the human proteome with microproteins and peptideins - Nature

A large-scale proteomics analysis of the dark proteome by the TransCODE Consortium reveals many translated non-canonical open reading frames to encode microproteins and peptideins.

nature.com

An expanded reference catalog of translated open reading frames for biomedical research

Abstract. Non-canonical (i.e. unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidenc

academic.oup.com

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology

Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...

nature.com

China turns the tables in biotech

For at least a century, major scientific research initiatives have reliably occurred in the United States, usually in response to geopolitical competition. This helped establish the country’s status a...

science.org

biorxiv.org

biorxiv.org

Hallmarks of cancer—Then and now, and beyond

Hanahan revisits the evolving framework of cancer hallmarks, synthesizing 25 years of conceptual refinement into a multidimensional view of tumor biology. This review highlights how aberrant capabilit...

cell.com

Systematic Analysis of C-Termini of Small Open Reading Frame-Encoded Peptides in Human Cancer Cell Lines

The C-termini often regulate protein biological functions through specific structures or modifications. Small open reading frame-encoded peptides (SEPs) make up a novel class of gene expression products that participate in various biological activities. Their C-termini have also been found to affect their function, but the polymorphism of SEPs’ C-termini has not yet been systematically elucidated. Using C-terminal proteomics, we identified 3636 C-terminal peptides from 2168 proteins in three human cancer cell lines, including 3364 peptides from 1901 classical proteins and 272 peptides from 267 SEPs. Approximately 20% of all of the identified C-terminal peptides had been reported in previous studies, originating from mRNA alternative splicing or protease cleavage, while more than 85% of the C-terminal peptides from SEPs were novel. Bioinformatics analysis revealed that most new SEP C-termini are likely produced by protease cleavage by the KLK, MMP, and CAT protease families. Others without accurately predicted hydrolysis sites may originate from alternative splicing or protein trimming. The intact and hydrolysis products of some SEPs were verified by immunoblotting. Some cleavage occurs in the predicted domain, which might affect SEPs’ function. This study enriches the SEP sequence information, provides experimental evidence for SEP in vivo processing, and supports the subsequent functional analysis of SEP.

pubs.acs.org