Biology subjects

Seraphin, B.

Publications and source records attributed to Seraphin, B..

6 recordsLinked to original sources

bioRxiv2026

Pho92 direct interaction with Not1 recruits the CCR4-NOT complex to m6A containing mRNAs to modulate meiosis in S. cerevisiae

N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic mRNAs. In S. cerevisiae, m6A is exclusively deposited during meiosis, where it plays an essential role in meiotic progression. In this context, the absence of Pho92, the sole known m6A-binding protein in budding yeast, leads to the abnormal persistence of m6A-containing mRNAs, ultimately resulting in delayed meiosis. Here, we investigate how m6A recognition by Pho92 regulates gene expression. Using complementary in vivo and in vitro approaches, we identify direct interactions between Pho92 and Not1, the scaffold subunit of the CCR4-NOT deadenylase complex. Structural analyses reveal that a short evolutionarily conserved motif in Pho92 adopts an -helical conformation that docks onto specific regions of Not1. Functionally, these interactions are required for efficient meiotic progression. Altogether, our findings demonstrate that Pho92 couples m6A recognition to the main deadenylase to shape the meiotic transcriptome. More broadly, our work provides mechanistic insights into how epitranscriptomic signals interface with the core mRNA decay machinery to regulate gene expression during cellular differentiation.

molecular biology↗

bioRxiv2026

Pat1 globally activates deadenylation-dependent decapping to clear inefficiently translated oligo(A)-tailed transcripts

In eukaryotes, mRNA turnover occurs mainly through the 5'- 3' mRNA decay pathway and involves deadenylation, decapping, and exonucleolytic mRNA body digestion. While the conserved protein Pat1 has initially been described as an activator of decapping for some deadenylated mRNAs, the role of deadenylation-dependent decapping has recently been questioned. Hence, Pat1 has alternatively been suggested to regulate specific mRNA decay pathways, given its modest impact on overall transcriptome composition. Here, we combine multi-omic and genetic approaches to characterize a PAT1 deletion mutant in Saccharomyces cerevisiae. Although transcriptome and proteome analyses confirm that only a limited subset of genes is affected by Pat1 inactivation, poly(A)-tail sizing demonstrates that Pat1 loss leads to transcriptome-wide accumulation of capped oligo(A)-tailed mRNAs. Together with the observation that oligo(A)-tailed mRNAs are bound by Pat1 in vivo in wild-type cells, this indicates that Pat1 is a general activator of deadenylation-dependent decapping. We further show that oligo-adenylated mRNAs are translated in {Delta}pat1 cells, albeit inefficiently. Altogether, our data indicate that Pat1 mediates the clearance of oligo(A)-tailed mRNAs protecting cells from the ensuing inefficient translation, without inducing major changes in overall transcript distribution.

molecular biology↗

bioRxiv2026

TBPL2-dependent transcription controls RNA stability and cellular organization in growing oocytes

During oocyte growth, the marked increase in cell size is accompanied by robust RNA polymerase II (Pol II) transcription, generating transcripts that are either translated into proteins or stored as part of the maternal transcriptome. While the RNA decay machinery is known to critically regulate the maternal transcriptome during oocyte maturation, its contribution during the growth phase remains poorly understood. We previously identified an oocyte-specific transcription machinery dependent on the TATA-binding protein paralog TBPL2, which is required for oocyte growth. To investigate how the absence of TBPL2-mediated transcription affects the cellular state of the oocyte, we characterized the phenotypic consequences of the Tbpl2-/- mutation in growing oocytes. Our data reveal that both nuclear and cytoplasmic organizations are profoundly disrupted in the absence of TBPL2-mediated transcription. Given that cytoplasmic organization is closely linked to RNA storage capacity, we examined the expression and localization of proteins involved in mRNA regulation, stability and storage. We observed a marked impairment in the redistribution of these key factors in Tbpl2-/- oocytes. To assess the impact of TBPL2 on RNA storage, we analyzed poly(A) tail length and found a global increase in polyadenylation in mutant oocytes. Gene-specific poly(A) tail analyses revealed differential mRNA changes, with shortened tails for a downregulated transcript and elongated tails for an upregulated one, suggesting stabilization of the latter. Collectively, our findings indicate that TBPL2-mediated transcription is essential for maintaining proper cellular organization in growing oocytes, at least in part by ensuring the functional integrity of the RNA decay machinery.

developmental biology↗

bioRxiv2023

Multiple Myeloma associated DIS3 mutations drive AID-dependent IgH Translocations

Role of dominant DIS3 mutations in multiple myeloma (MM) remains elusive. These mutations decrease the exoribonucleolytic activity of DIS3, a key nuclear RNA-degrading enzyme. Utilizing knock-in mice with clinical Dis3 G766R variant, we demonstrate an increased frequency of aberrant chromosomal translocations in B-cells, leading to plasmacytoma, an early-stage MM model. DIS3-dependent translocations display characteristics of aberrant activation-induced deaminase (AID) activity. In clinical MM samples with DIS3 mutations, driver genes also show AID-dependent lesions. Mechanistically, mutated DIS3 accumulates on chromatin-associated RNA substrates, including aberrant AID action sites, fostering oncogenic chromosomal rearrangements. Translocations occur during immunoglobulin class switch recombination, a process otherwise unaffected in MM patients or mice with mutated DIS3. Dis3 G766R mutation does not alter chromatin architecture in activated B-cells but hijacks it to bring together enhancers with proto-oncogenes permanently. In conclusion, gain-of-function DIS3 mutations increase nuclear exosome and AID affinity to chromatin, facilitating IGH translocations and driving MM transformation.

molecular biology↗

bioRxiv2023

HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon

Proteins containing a RNB domain, originally identified in E. coli RNase II, are widely present throughout the tree of life. Many RNB proteins are endowed with 3-5 exoribonucleolytic activity but some have lost catalytic function during evolution. Database searches identified a new RNB domain containing protein in human: HELZ2. Analysis of genomic and expression data with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 harbors also two RNA helicase domains and several zinc-fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3-5 ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.

molecular biology↗

bioRxiv2022

The S. cerevisiae m6A-reader Pho92 impacts meiotic recombination by controlling key methylated transcripts

N6-methyladenosine (m6A), the most abundant internal modification of eukaryotic mRNAs, participates in the post-transcriptional control of gene expression. In Saccharomyces cerevisiae, m6A is only found during meiosis. Although the deletion of the m6A- methyltransferase Ime4 impairs this process, the molecular impact of m6A on gene expression remains ill defined. Here we investigated the function of the budding yeast m6A reader Pho92. We found that Pho92 is specifically expressed during meiosis and impacts meiotic progression. We used high-throughput RNA sequencing and mapping of Pho92-binding sites following UV-crosslinking to show that Pho92 is recruited to specific mRNAs in an m6A-dependent manner during the meiotic prophase, preceding their down-regulation. Strikingly, point mutations altering m6A sites in mRNAs targeted by Pho92 are sufficient to delay their down-regulation and, in one case, to impact meiotic progression. Altogether, our results indicate that Pho92 facilitate the meiotic progression by accelerating the down-regulation of timely-regulated mRNAs during meiotic recombination.

molecular biology↗