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Trcek Lab

@trceklab.bsky.social
44 followers 58 following 23 posts
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Reposted by Trcek Lab
fly paper broadcast @fly-broadcast.bsky.social · 18/05/2026
Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo #Drosophila
pubmed.ncbi.nlm.nih.gov
Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo #Drosophila
PubMed link
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Trcek Lab @trceklab.bsky.social · 06/05/2026
Therefore, mRNA clustering driven by palindrome-mediated intermolecular base pairing may be more widespread than previously appreciated and may represent an important mechanism for controlling mRNA spatial organization during early Drosophila development.
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Trcek Lab @trceklab.bsky.social · 06/05/2026
4) Computational analyses identified a subset of early embryonic mRNAs in Drosophila predicted to harbor RNA palindromes similar to those found in osk.
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Trcek Lab @trceklab.bsky.social · 06/05/2026
2) They demonstrate that oskar mRNA dimerization occurs at lower concentration thresholds in the presence of Staufen and the palindrome element. 3) They further show that the palindrome is essential for heterotypic association between oskar mRNA and a reporter mRNA.
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Trcek Lab @trceklab.bsky.social · 06/05/2026
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
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Reposted by Trcek Lab
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 05/05/2026
Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo www.biorxiv.org/content/10.64898/20…
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Trcek Lab @trceklab.bsky.social · 19/03/2026
We are incredibly proud of her achievements and will miss her as she moves on to pursue her postdoctoral research.
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Trcek Lab @trceklab.bsky.social · 19/03/2026
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.
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Reposted by Trcek Lab
Gladfelter Lab @gladfelterlab.bsky.social · 08/03/2026
Also check out the News and Views by Ayse Ecer and Tatjana Trcek! nature.com/articles/s41...
nature.com
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...
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Reposted by Trcek Lab
Trcek Lab @trceklab.bsky.social · 26/12/2025
New preprint from the Trcek lab, with Siran Tian as the lead author - congratulations Siran! doi.org/10.64898/202...
doi.org
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...
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Trcek Lab @trceklab.bsky.social · 26/12/2025
4) nanos mRNA localization counteracts Vasa-mediated enhancement of Oskar mobility. While germ granule mRNA localization requires Vasa, this process opposes Vasa’s effect on Oskar condensates, providing an RNA-mediated negative feedback mechanism that regulates condensate properties.
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Trcek Lab @trceklab.bsky.social · 26/12/2025
3) mRNA localization to Oskar condensates requires Vasa and its interaction with Oskar. Although germ granules contain diverse proteins, Vasa and Oskar are necessary and sufficient for robust germ granule mRNA localization to the granules.
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Trcek Lab @trceklab.bsky.social · 26/12/2025
2) Vasa’s modulation of condensate properties requires direct protein-protein interaction. This activity requires specific binding interfaces between Vasa and Oskar, but is less dependent on Vasa helicase activity.
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Trcek Lab @trceklab.bsky.social · 26/12/2025
1) Vasa modulates the material properties of ribonucleoprotein condensates in fly oocytes and human cells. Recruitment of Vasa increases the mobility of the germ-granule nucleator Oskar, thereby preventing aggregation of granules.
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Trcek Lab @trceklab.bsky.social · 26/12/2025
This new function in regulating protein condensation extends beyond its established function as an RNA helicase. Specifically, Siran shows that:
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Trcek Lab @trceklab.bsky.social · 26/12/2025
She investigated the role of a conserved DEAD-box RNA helicase Vasa in condensation of germ granules in Drosophila. Her work reveals a previously unrecognized function of Vasa in regulating the material properties of Oskar ribonucleoprotein condensates through its direct interaction with Oskar.
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Trcek Lab @trceklab.bsky.social · 26/12/2025
New preprint from the Trcek lab, with Siran Tian as the lead author - congratulations Siran! doi.org/10.64898/202...
doi.org
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...
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Trcek Lab @trceklab.bsky.social · 31/08/2025
4) Germ granule mRNAs are replete with GC-rich complementary sequences predicted to be competent of engaging in persistent intermolecular base pairing however in vivo these interactions are unrealized and restricted by RNA folding.
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Trcek Lab @trceklab.bsky.social · 31/08/2025
3) Engineered germ granule mRNAs with exposed GC-rich complementary sequences (CSs) within stem loops induce sustained base pairing in vitro and enhanced intermolecular interactions in vivo. But, the presence of these structures disrupts development, and GC-rich CSs exacerbate this phenotype.
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Trcek Lab @trceklab.bsky.social · 31/08/2025
We find that: 1) mRNAs remain structured within germ granules 2) mRNAs base pair intermolecularly without high sequence complementarity or significant melting of secondary structure. Base pairing is driven by scattered and discontinuous stretches of bases appearing on the surface of structured RNAs
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Trcek Lab @trceklab.bsky.social · 31/08/2025
New paper from the Trcek lab, with Siran Tian as the lead author - congratulations Siran!: www.nature.com/articles/s41...
nature.com
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...
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Reposted by Trcek Lab
Trcek Lab @trceklab.bsky.social · 28/05/2025
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...
doi.org
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...
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Reposted by Trcek Lab
Woodson Lab @woodsonlab.bsky.social · 19/07/2025
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...
doi.org
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. ...
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Reposted by Trcek Lab
Elise White @elisew00.bsky.social · 19/07/2025
Congrats, Jorjethe and Yi-Lan! 👏👏
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Reposted by Trcek Lab
Miha Modic @paraspeckle.bsky.social · 02/06/2025
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...
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Reposted by Trcek Lab
Hung Nguyen @tienhungf91.bsky.social · 28/05/2025
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...
biorxiv.org
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...
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Trcek Lab @trceklab.bsky.social · 28/05/2025
Jeffery is presenting his work at the annual RNA society meeting in San Diego - visit his poster! #RNA25; #RNA2025
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Trcek Lab @trceklab.bsky.social · 28/05/2025
Jeffery is presenting his work at the annual RNA society meeting in San Diego - visit his poster! #RNA25; #RNA2025
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Reposted by Trcek Lab
bioRxivpreprint @biorxivpreprint.bsky.social · 27/05/2025
Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress www.biorxiv.org/content/10.1101/202…
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Reposted by Trcek Lab
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 27/05/2025
Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress www.biorxiv.org/content/10.1101/202…
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Trcek Lab @trceklab.bsky.social · 28/05/2025
We propose that the combined suppression of intermolecular base pairing and the increased RNA structural diversity may serve as a mechanism to preserve normal RNA function during stress, while also facilitating the reversible assembly of stress granules
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Trcek Lab @trceklab.bsky.social · 28/05/2025
c) However, these RNAs increase in structural diversity in a manner dependent on oxidative stress and the stress granule nucleating proteins G3BP1 and G3BP2. d) In the absence of the main stress granule nucleating proteins G3BP1 and G3BP2, mRNAs remain dispersed in cells during oxidative stress
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Trcek Lab @trceklab.bsky.social · 28/05/2025
We show that: a) Oxidative stress downregulates intermolecular base pairing of reporter mRNAs engineered to enhance detection of such interactions. b) RNA regions within transcripts that enrich in stress granules remain structured during stress.
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Trcek Lab @trceklab.bsky.social · 28/05/2025
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...
doi.org
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...
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