Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo #Drosophila
Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo #Drosophila
PubMed link
pubmed.ncbi.nlm.nih.gov
New lab preprint lead by Ziqing, Siran and Ayse! doi.org/10.64898/202... In it they show that: 1) oskar mRNA clustering is driven by the synergistic action of osk concentration, the Staufen RBP and osk RNA palindrome.
doi.org
Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo https://www.biorxiv.org/content/10.64898/2026.04.30.721893v1
Our first graduate student, Siran Tian, is graduating. For her thesis, she characterized intermolecular base pairing (PMCID: PMC12398620) and the role of the conserved DEAD-box RNA helicase Vasa in regulating protein–protein and protein–RNA interactions (PMCID: PMC12724462) in fly germ granules.
Also check out the News and Views by Ayse Ecer and Tatjana Trcek! nature.com/articles/s41...
RNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell Biology
Geisterfer, Jalihal et al. show spatially distinct effects of Whi3 condensates on target translation in Ashbya syncytia. In vitro, translation is enriched at condensate–solute interfaces but repressed...
nature.com
New preprint from the Trcek lab, with Siran Tian as the lead author - congratulations Siran! doi.org/10.64898/202...
Conserved RNA helicase Vasa regulates ribonucleoprotein condensates through protein interaction and mRNA recruitment
Germlines contain ribonucleoprotein condensates known as germ granules, which concentrate proteins and mRNAs essential for animal development. Vasa, a conserved DEAD-box RNA helicase, is a core and hi...
doi.org
New preprint from the Trcek lab, with Siran Tian as the lead author - congratulations Siran! doi.org/10.64898/202...
Conserved RNA helicase Vasa regulates ribonucleoprotein condensates through protein interaction and mRNA recruitment
Germlines contain ribonucleoprotein condensates known as germ granules, which concentrate proteins and mRNAs essential for animal development. Vasa, a conserved DEAD-box RNA helicase, is a core and hi...
doi.org
New paper from the Trcek lab, with Siran Tian as the lead author - congratulations Siran!: www.nature.com/articles/s41...
Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development - Nature Communications
Tian et al. show that RNA folding limits extensive base pairing among mRNAs in Drosophila germ granules. Instead, mRNAs interact via scattered bases exposed on the surface of folded RNAs, which may pr...
nature.com
New preprint from the Trcek lab - Jeffrey Liao as the lead author! We studied intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress doi.org/10.1101/2025...
Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress
Cellular stress induces global translational repression, leading to exposure of RNA sequences that could engage in intermolecular base pairing. However, characterization of these interactions in stres...
doi.org
Our new paper is out in PNAS! We show that competition for binding to the Hfq matchmaker disfavors mismatched sRNA-mRNA combinations while allowing matched sRNA-mRNAs to form stable pairs. Kudos to Jorjethe Roca and Yi-Lan Chen for their fantastic work on this problem! doi.org/10.1073/pnas...
Competition for Hfq drives kinetic selection of mRNA targets by Escherichia coli small noncoding RNAs | PNAS
Small noncoding RNAs (sRNAs) regulate gene expression in Escherichia coli bacteria in response to diverse stimuli in the environment and the host. ...
doi.org
Congrats, Jorjethe and Yi-Lan! 👏👏
Woodson Lab@woodsonlab.bsky.social · last yr.Our new paper is out in PNAS! We show that competition for binding to the Hfq matchmaker disfavors mismatched sRNA-mRNA combinations while allowing matched sRNA-mRNAs to form stable pairs. Kudos to Jorjethe Roca and Yi-Lan Chen for their fantastic work on this problem! doi.org/10.1073/pnas...
New method drop: HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning. www.biorxiv.org/content/10.1...
Excited to share our lab's preprint! We found that flexible RNAs have much broadened ion atmospheres than structured RNAs. This leads us to speculate the implications on molecular recognition and phase behavior. Please check full text for other interesting details www.biorxiv.org/content/10.1...
RNA structural complexity dictates its ion atmosphere
Electrostatic interactions mediated by the surrounding ions govern virtually every facet of RNA behavior. Most studies have focused on rigid, well-folded motifs, leaving the structurally heteregeneous...
biorxiv.org
Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress https://www.biorxiv.org/content/10.1101/2025.05.21.655305v1
Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress https://www.biorxiv.org/content/10.1101/2025.05.21.655305v1
New preprint from the Trcek lab - Jeffrey Liao as the lead author! We studied intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress doi.org/10.1101/2025...
Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress
Cellular stress induces global translational repression, leading to exposure of RNA sequences that could engage in intermolecular base pairing. However, characterization of these interactions in stres...
doi.org