Biology subjects

Dubiez, E.

Publications and source records attributed to Dubiez, E..

5 recordsLinked to original sources

bioRxiv2026

ULTRAPETALA1 remodels PRC2 recruitment to nucleosomes

Polycomb Repressive Complex 2 (PRC2) establishes transcriptional repression through trimethylation of histone H3 lysine 27 (H3K27me3), a modification essential for developmental patterning. Here, we describe a novel plant-specific PRC2 variant (PRC2.3) that employs a distinct nucleosome-targeting mechanism mediated by accessory factor ULTRAPETALA1 (ULT1), which promotes H3K27me3 deposition at over 1,300 developmental genes. The cryo-EM structure of the PRC2SWN-ULT1-nucleosome complex reveals that ULT1 antagonizes the canonical PRC2 binding mode and instead bridges PRC2 to the nucleosome using its own interaction surfaces. ULT1 binds consecutive purines in the nucleosomal DNA and the histone H2A/H2B acidic patch, while enabling PRC2 to accommodate H3K36 modifications. We further show that in planta ULT1 enhances H3K27me3 at purine-rich loci and at genes associated with H3K36 marks, and identify the ULT1-H2A/H2B interface as required for reproductive transition and flower organogenesis. Our findings demonstrate that PRC2 can deploy mechanistically distinct recruitment strategies to control key developmental switches.

Molecular Biology↗

bioRxiv2026

Lysine acetylation facilitates competitive recruitment of translation termination factor eRF3a by PABPC1 C-terminal domain

In eukaryotic cells, almost all mRNA transcripts are polyadenylated in the nucleus, with the poly(A)-tail being critical for their export, translation and stability. PABPC1 is a multifunctional RNA-binding protein (RBP) that binds poly(A)-tails and is a key driver of mRNA post-transcriptional regulation. It achieves this in part by interacting with a broad range of PAM2-motif containing proteins that bind the same common site within PABPC1s PABC domain but result in diverse regulatory outcomes. Regulation of this intricate network of interactions remains poorly understood but our previous studies revealed the regulatory potential of mutually-exclusive acetylation or dimethylation of a key lysine sidechain (K606). To address this, we undertook a systematic study of PAM2-motifs, identifying translation termination factor eRF3a and translation repressor PAIP2 as having a >ten-fold higher affinity for PABPC1 relative to eleven other PAM2-motif partner proteins. Acetylation of PABPC1 at K606 specifically enhances its affinity for eRF3a in vitro, and we present the crystal structure of the specifically K606 acetylated C-terminal domain of PABPC1 in complex with the PAM2 motif of eRF3a, providing structural and functional insights into how acetylation facilitates competitive eRF3a recruitment to PABPC1 and mRNA. We further demonstrate that K606 acetylation promotes PABPC1-eRF3a interaction in cells, thereby antagonising other PAM2-dependent RNA effectors. Taken together, our results show that acetylation of lysine 606 in the PABC domain can specifically modulate PABPC1 partner selectivity, providing crucial insight into how PABPC1 multifunctionality can be regulated to coordinate mRNA usage and fate in the cytoplasm.

molecular biology↗

bioRxiv2026

KDM7B-mediated demethylation of RNF113A regulates small cell lung cancer sensitivity to alkylation damage

Chemoresistance remains a major obstacle to effective cancer treatment, often driven by enhanced DNA repair mechanisms that enable tumor cells to withstand genotoxic therapies. One such pathway involves the atypical DNA damage repair complex ALKBH3-ASCC, activated by the E3 ligase RNF113A in response to alkylation damage. We previously showed that SMYD3-dependent methylation of RNF113A stimulates this pathway, enhancing DNA repair and promoting resistance. Here, we identify KDM7B/PHF8 as the bona fide RNF113A demethylase, establishing one of the first functional examples of a dynamic, reversible non-histone methylation event regulating genome integrity. KDM7B antagonizes SMYD3 activity by maintaining low levels of methylated RNF113A, thereby limiting ASCC activation and sensitizing cancer cells to alkylating agents. To dissect this regulation in depth, we focused on small cell lung cancer (SCLC), a particularly aggressive malignancy characterized by limited therapeutic options and rapid acquisition of resistance. In SCLC, high KDM7B levels correlate with improved patient prognosis, whereas xenografts with reduced expression exhibit diminished responses to alkylating treatment. Moreover, CRISPR-based on/off modulation of KDM7B in genetically engineered SCLC mouse models demonstrates its central role in determining tumor response to chemotherapy. Our findings position the RNF113A-ASCC axis as a central modulator of chemoresistance, regulated through a post-translational methylation switch representing an innovative therapeutic vulnerability that could be exploited to enhance the efficacy of alkylating agents. Targeting this pathway may provide new opportunities to overcome chemoresistance, with KDM7B levels serving as a predictive biomarker to guide treatment in SCLC.

cell biology↗

bioRxiv2024

Structural basis for the synergistic assembly of the snRNA export complex

The nuclear cap-binding complex (CBC) and its partner ARS2 play crucial roles in regulating Pol II transcript fate through mutually exclusive interactions with RNA effectors. One such effector, PHAX, mediates the nuclear export of U-rich small nuclear RNAs (snRNAs). Here we present the cryo-EM structure of the snRNA export complex comprising phosphorylated PHAX, CBC, CRM1, Ran-GTP and capped RNA. The central region of PHAX bridges the CBC-bound capped RNA to the CRM1-RanGTP, while also significantly reinforcing cap dinucleotide binding. Additionally, PHAX interacts with a distant region of CRM1 facilitating contacts of an essential phosphorylated region with the prominent basic surface of RanGTP. The importance of these interactions is confirmed by in vitro and in cell mutagenesis experiments. CBC engagement within the snRNA export complex is incompatible with its interactions with other RNA effectors such as ALYREF or NCBP3. Taken together, we demonstrate that snRNA export complex formation requires synergistic binding of all its components, which in turn displaces ARS2 from the CBC, and commits the complex for export.

molecular biology↗

bioRxiv2023

Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex

The nuclear cap-binding complex (CBC) co-ordinates co-transcriptional maturation, transport, or degradation of nascent Pol II transcripts. CBC with its partner ARS2 form mutually exclusive complexes with diverse effectors that promote either productive or destructive outcomes. Combining Alphafold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18 and other effectors compete for binding to ARS2. In ternary CBCA complexes with either PHAX, NCBP3 or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.

biochemistry↗