Kevin M. Weeks

RNA Structure Coordinates Translation Across the Meiotic Program

In yeast meiosis, flexibly folded mRNAs are preferentially translated while cytoplasmic RNA helicase levels dip; raising Ded1p or breaking CCW22 UTR pairing mistimes translation and disrupts meiotic progression.

Large-scale structural analysis of pre-mRNA structure using RADIS

RADIS enables comprehensive pre-mRNA structural analysis across intronic and intergenic regions, revealing structural patterns and relationships with splice-site strength and variant effects.

Programmed Double-stranded RNA Formation Enables Meiotic Stage Transitions

The paper identifies dsRNA formation and NATs as a mechanism for selective mRNA clearance during meiosis, driven by transcription factors like Ndt80p.

fpocketR: A platform for identification and analysis of ligand-binding pockets in RNA

fpocketR identifies and analyzes ligand-binding pockets in RNA structures to discover potential drug targets.

A small cationic probe for accurate, punctate discovery of RNA tertiary structure

The paper introduces a small cationic probe, TMO, to detect RNA tertiary structures by identifying electronegative motifs that react selectively with TMO, revealing functional tertiary interaction sites.

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

The paper investigates the structural determinants of inverted Alu-mediated backsplicing in the HIPK3 gene using SHAPE-JuMP and finds that long-range Alu-mediated base pairs are required for circularization, but not full-length Alu elements.

A 36-base hairpin within lncRNA DRAIC, which is modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes

The paper identifies a 36-base hairpin in lncRNA DRAIC that interacts with IKKα's coiled-coil domain, inhibits NF-κB activity, and suppresses tumor phenotypes through alternative splicing regulation.

Ligand-binding pockets in RNA, and where to find them

This paper introduces fpocketR to detect RNA ligand-binding pockets and validates them with Frag-MaP, identifying new sites capable of binding drug-like ligands.

Scaffold-enabled high-resolution cryo-EM structure determination of RNA

This paper presents a scaffold strategy to improve cryo-EM resolution for small RNAs, demonstrating high-resolution structures of a TPP riboswitch and its ligand binding dynamics.

RNAvigate: Efficient exploration of RNA chemical probing datasets

RNAvigate provides a Python library for efficiently exploring RNA chemical probing datasets through automated parsing and visualization of diverse structural and functional data.

Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

This study shows that SARS-CoV-2 N-protein uses two distinct RNA motifs, both requiring dsRNA, to drive phase separation at specific temperatures, enabling multiple viral functions.

Quantitative prediction of variant effects on alternative splicing using endogenous pre-messenger RNA structure probing

The paper predicts variant effects on alternative splicing using structural probing data and a computational framework, achieving 90% accuracy for splice-altering variants.

Direct detection of RNA modifications and structure using single molecule nanopore sequencing

This paper demonstrates direct detection of RNA modifications and structure using single molecule nanopore sequencing, showing it can identify endogenous and exogenous modifications in rRNA from E. coli and S. cerevisiae.

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

The paper identifies distinct structural domains in the MUNC lncRNA that regulate different promyogenic genes through cis and trans mechanisms.

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

ShapeJumper processes SHAPE-JuMP sequencing data to identify RNA molecule proximal interactions with high resolution.