Nicholas T. Ingolia

Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs

The paper shows that under metabolic stress, many mRNAs lack cap methylation, yet they are still functional, suggesting cap methylation is a stress-responsive regulatory layer.

Calcium-dependent synaptic proteomics reveals EGFR signaling at active synapses

The paper develops a method to profile synaptic proteomes under physiological conditions and identifies EGFR signaling as a key activity-dependent process at synapses.

A Neuronal Gene Expression Program Underlying Sustained Network Activity

The paper identifies a gene expression program in active neurons that supports sustained network activity, distinct from immediate early gene responses and enriched for excitability regulators.

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

Translation elongation as a rate limiting step of protein production

The paper shows that slow translation elongation reduces protein output per mRNA, independent of mRNA stability, and demonstrates a dynamic balance between initiation and elongation rates.

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems

The paper introduces CiBER-seq, a CRISPRi platform that improves the sensitivity and scope of genome-wide screens by normalizing expression reporters against control promoters, and validates its ability to capture post-transcriptional and post-translational regulation.

Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling

The paper identifies regulatory sequences in disordered regions of RNA binding proteins and shows how they modulate mRNA decay through interactions with core machinery.

eIF3 engages with 3'-UTR termini of highly translated mRNAs

The paper shows eIF3 binds to 3'-UTR termini of highly translated mRNAs, suggesting a general role in translation regulation and mRNA circularization.

Mapping the Genetic Architecture of the Adaptive Integrated Stress Response in S. cerevisiae

The paper uses CiBER-seq to analyze how genetic perturbations affect ISR dynamics in yeast, finding that translation-related perturbations increase ISR activation while ribosome biogenesis impairments reduce it.

Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing

The paper improves the OTTR method for RNA sequencing by reducing bias and increasing precision in capturing RNA sequences from degraded or processed RNAs.

CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

The paper introduces CiBER-seq, a method combining CRISPRi and barcoded expression reporters to measure transcriptional responses in human cells, revealing regulatory networks and cell-type-specific factors in NF-κB signaling.

Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response

This study shows Dbp1 is a less effective paralog of Ded1 in yeast, supporting impaired translation and lacking heat stress response, used in nutrient-deficient conditions.

Streamlined and sensitive mono- and diribosome profiling in yeast and human cells

The paper introduces a streamlined ribosome profiling method using P1 nuclease and Ordered Two-Template Relay, improving sensitivity and reducing bias in yeast and human cells.

Surveying the global landscape of post-transcriptional regulators

The paper identifies post-transcriptional regulators in budding yeast by analyzing protein fragments and their effects on mRNA, revealing modular domains and interactions involved in mRNA regulation.

Dysregulation of amino acid metabolism upon rapid depletion of cap-binding protein eIF4E

This study investigates how eIF4E depletion affects amino acid metabolism and reveals novel translational control mechanisms involving GCN4 and PCL5.

Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα

This study identifies PELOTA's role in modulating C/EBPα isoform selection through ribosome rescue and mTOR-mediated effects during myeloid cell development.

A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

The paper identifies a fungal mutation that allows survival on plants producing toxic rocaglates by altering eIF4A, a target of these compounds.

Molecular recording of calcium signaling via calcium-dependent protein proximity labeling

This paper introduces Cal-ID, a tool that records calcium signaling and neuronal activity by biotinylating nearby proteins, enabling high-resolution molecular mapping.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

Robust T cell activation requires an eIF3-driven burst in T cell receptor translation

This study identifies eIF3's role in regulating TCR translation via 3-UTR binding, enhancing CAR-T cell efficacy in vitro.

The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression

This study identifies key residues in SARS-CoV-2 nsp1 that regulate host and viral mRNA translation, revealing functional differences between these mRNA types.

A specific eIF4A paralog facilitates LARP1-mediated translation repression during mTORC1 inhibition

The paper shows that eIF4A1, not eIF4A2, facilitates LARP1-mediated translation repression during mTORC1 inhibition by preferentially binding TOP mRNAs.

A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast

The paper develops a genome-scale CRISPRi guide library for yeast, validates its coverage through fitness defects, and improves guide measurement accuracy with barcoding and in vitro transcription.

CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes

CiBER-seq quantifies genetic perturbation effects on gene expression in yeast by linking CRISPRi guides to phenotypes via barcoded sequencing.

Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome

This study shows that eS7A ubiquitination during ER stress in yeast regulates mRNA translation and affects stress outcomes.

A burst in T cell receptor translation mediated by eIF3 interactions with T cell receptor mRNAs

The paper identifies eIF3's role in enhancing TCR translation during T cell activation through interactions with 3-UTRs of TCR mRNAs.

Repression of ferritin light chain translation by human eIF3

The paper identifies eIF3 as a repressor of FTL mRNA translation and shows that SNPs causing hyperferritinemia disrupt this repression.

Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

The paper introduces APEX-Seq, a proximity labeling technique to map RNA localization and interactions, revealing insights into translation initiation complexes and stress granule composition.

An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries

This paper describes a continuous-culture turbidostat system for analyzing complex genetic libraries in yeast and bacteria, demonstrating its use in growth rate analysis, protein fusion selection, and mutational studies.

Double Stranded DNA Damage and Genome Editing Trigger Ribosome Remodeling and Translational Shutdown

This study shows that DNA double-strand breaks cause ribosome remodeling and translational shutdown, independent of p53 and preceding transcriptional changes.