Lucas Ferguson

OTTR-CLASH: improved biochemical and bioinformatic identification of Argonaute 2-mediated microRNA-target RNA interactions

The paper introduces OTTR-CLASH, a method that improves the detection of miRNA-target interactions by using a modified RT and enhanced bioinformatics pipeline.

Translational Downregulation of 5' TOP mRNAs During T Cell Exhaustion

The paper identifies translational repression of 5' TOP mRNAs in exhausted human CD8+ T cells despite elevated mTOR activity.

Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies

The paper identifies nuclear small regulatory RNAs in multivesicular bodies and shows their trafficking requires ESCRT machinery but not LC3 lipidation.

miRNA-Mediated Regulation of Gene Expression During Early Activation in Jurkat Cells

The paper analyzes miRNA-mediated gene regulation during early T cell activation using multi-omics data, revealing distinct regulatory patterns based on translation efficiency and miRNA binding site density.

Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR

This study benchmarks the OTTR protocol for characterizing tRNAs and tRNA fragments in yeast and mouse, showing its accuracy and revealing new insights into sperm small RNA content.

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.

Context-dependent translation inhibition as a novel oncology therapeutic modality

This paper develops interdictors that selectively inhibit translation elongation in the human ribosome, showing their efficacy in tumor growth inhibition in a breast cancer model.

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.

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.

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.

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.

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.

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.