Siyu Chen

The adaptive architecture of tRNA dependencies across physiological tumor environments

The paper maps tRNA dependencies in cancer cells across different environments, finding that tRNA dependencies are environmentally sensitive while some dependencies are shared across cell lines.

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4

Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis

The paper identifies ZZEF1 as a tRNA-specific transcription factor that suppresses breast cancer metastasis by regulating tRNA-LysUUU expression and affecting codon-specific translation.

A Suite of Foundation Models Captures the Contextual Interplay Between Codons

The paper introduces cdsFM, a suite of codon-resolution large language models that predict the functional consequences of synonymous codon choices and identify pathogenic variants.

Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, No-Go-Decay and autophagy

The paper identifies a mechanism called Mito-ENCay that limits MMF1 mRNA expression by targeting it to mitochondria and triggering quality control processes.

Disome-seq reveals widespread ribosome collisions that recruit co-translational chaperones

The paper uses disome-seq to detect ribosome collisions during translation, revealing their role in recruiting co-translational chaperones for protein folding.

Overdosage of balanced protein complexes reduces proliferation rate in aneuploid cells

The paper shows that overdosage of balanced protein complexes reduces proliferation in aneuploid yeast and human cancer cells.