Biology subjects

Seiler, M.

Publications and source records attributed to Seiler, M..

8 recordsLinked to original sources

bioRxiv2026

Argonaute 1 associates with nucleolar snoRNP machinery and regulates pre-rRNA levels and cell growth

Argonaute proteins are best known as cytoplasmic effectors of small-RNA-mediated gene silencing, although their compartment-specific functions remain incompletely understood. Here, we identify a previously unrecognized nucleolar role for Drosophila Argonaute 1 (AGO1). We observed stress-induced redistribution of AGO1 into cytoplasmic and nuclear ribonucleoprotein assemblies, whereas a distinct AGO1 pool consistently localized to Fibrillarin-positive nucleoli. Co-immunoprecipitation further showed that AGO1 associates with Fibrillarin-containing complexes in vivo. Re-analysis of AGO1-associated small-RNA sequencing data revealed snoRNAs, particularly C/D box snoRNAs, among AGO1-bound RNA species and increased snoRNA representation following AGO1 overexpression. Structural modelling demonstrated that simultaneous molecular interaction of AGO1 and the Fibrillarin-containing snoRNP machinery with the same snoRNA is stereochemically feasible, providing a structural framework for their potential association within a nucleolar snoRNP assembly. Functionally, AGO1 depletion reduced pre-rRNA levels and decreased both nucleolar and cell size in the follicular epithelium. Depletion of Dicer-1 did not reproduce these growth defects, arguing against a general consequence of impaired miRNA biogenesis. Together, these findings identify AGO1 as a nucleolar regulator that associates with snoRNP machinery and links small-RNA biology to pre-rRNA homeostasis and cell growth.

cell biology↗

bioRxiv2025

Restoration of Higher-Order Cortical Processing in Rat V2 by Retinal Sheet Transplants in Degenerated Rats

Age-related macular degeneration (AMD) is a leading cause of central vision loss, and effective treatment options are limited once photoreceptors and the retinal pigment epithelium (RPE) are lost. In advanced stages, vision restoration requires strategies that replace or bypass degenerated retinal circuitry. Retinal sheet transplantation using fetal neural retinal tissue has emerged as a promising intervention, demonstrating long-term survival, integration with the host retina, and partial restoration of light-driven responses. We previously showed that such transplants can restore fundamental visual response properties in the primary visual cortex (V1) of rapidly degenerating rats. However, it remains unclear whether restored retinal input can support higher-order cortical computations that depend on the integration of classical and extra-classical receptive field mechanisms. In this study, we extend this investigation by evaluating whether fetal retinal sheet transplants can restore extra-classical surround modulation in neurons of higher visual areas (V2). Fetal retinal sheets (E18-E19) derived from donor rats were transplanted into one eye of Rho-S334ter line-3 rats at ages P41-P78, when rod degeneration is nearly complete and cones are largely nonfunctional. Animals were assessed 2.2-9.3 months post-surgery using in vivo extracellular single-unit recordings from V2, optokinetic testing, OCT imaging, and histology. Control groups included normal-vision rats, age-matched degenerated rats (AMC), and sham-operated line-3 rats. Transplants survived long term, developed laminated and rosetted photoreceptor structures, and integrated with the host retina. Optokinetic testing revealed significant improvement in spatial acuity in transplanted eyes compared with degenerated controls beginning at three months post-surgery. Transplanted rats exhibited a markedly higher proportion of visually responsive V2 neurons than degenerated animals (21.0% vs. 8.2%). They also showed significantly shorter response latencies and larger visually evoked response amplitudes, indicating improved transmission of retinal signals to the cortex. To quantify surround suppression, neurons were tested with sinusoidal gratings confined to the classical receptive field and gratings extended to full-field size. Transplanted rats displayed robust surround suppression properties similar to normal controls, including significantly reduced firing rates and narrower tuning under full-field conditions. A Support Vector Machine (SVM) classifier trained on net responses to CRF and FF stimulus sizes reliably distinguished control and transplanted neurons from degenerated ones but could not separate control from transplant, further indicating similar response properties in these two groups. These findings provide the first demonstration that retinal sheet transplants restore not only basic visual responses but also higher-order cortical mechanisms involving extra-classical surround suppression. This recovery of surround suppression in V2 suggests that transplanted retinal tissue can re-establish functionally meaningful circuits capable of supporting complex visual processing. The results underscore the therapeutic potential of retinal sheet transplantation for advanced retinal degenerative disease and provide the first evidence of surround suppression in the rat V2.

neuroscience↗

bioRxiv2025

Sedimentary ancient DNA metagenomic analysis provides new insights into farming in central Norway from the Bronze Age to late Medieval period

Sedimentary ancient DNA (sedaDNA) has been proposed as a key methodology for reconstructing paleoclimates and biodiversity over time. To a lesser extent, it has been explored as a complementary tool for reconstructing human-driven local environmental changes over time, such as those explored in open air archaeological sites. Our study employs a sedaDNA metagenomic approach to investigate land use and environmental change at the archaeological site of Torg[a]rdsletta in central Norway, spanning from the Bronze Age through the Medieval period. Stratigraphic sediment samples reveal temporal shifts in plant, animal and microbial communities, reflecting evolving human practices and climatic conditions. Progression through the layers indicate signs or land clearance, cultivation and animal husbandry in the region. Notably, a significant reduction in microbial and plant diversity during periods of climatic upheaval--such as the AD 536-540 volcanic event--correlates with landscape and societal adjustments. The findings demonstrate that sedaDNA complements traditional proxies, providing high-resolution insights into past land use, environmental interactions, and societal organization. The successful extraction of ancient genetic material underscores sedaDNAs potential to reconstruct dynamic prehistoric landscapes and anthropogenic impacts, offering further potential for understanding long-term human-environment relationships in Scandinavia.

genomics↗

bioRxiv2024

A consensus motif in ASH1 and further transcripts unifies several RNA motifs required for interaction with the She2p/She3p transport machinery and mRNA localization in yeast

Asymmetric localization of the ASH1 transcript is a central step in the regulation of mating type switching in Saccharomyces cerevisae and a paradigm for localized mRNAs specifically recognized by the She2p/3p transport machinery. Four RNA elements in ASH1 are known to mediate bud localization, but it remained unclear what a consensus motif of all four She2p/3p recognition sites (SRS) might look like. In this study, we derive the SRS consensus motif, which is characterized by an L-shaped, double-stranded RNA conformation with two cytosine-containing sequence motifs at conserved positions and a central asymmetric bulge. It is noteworthy that the spatial arrangement of these features can be retained, despite their altered order within the nucleotide sequence. We termed these variations "configurations" and confirmed in biochemical studies that SRS function in ASH1 elements is preserved when changing configurations. We tested other known and predicted SRS elements in target transcripts of She2p/3p by biochemical and biophysical studies and confirmed the conserved SRS function even in switched configuration. Consistently, we present the SRS instance collection, which includes further predictions of SRS instances of transcript targets of the She2p/3p translocation pathway.

cell biology↗

bioRxiv2022

Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS/AML

Splicing modulation is a promising treatment strategy pursued to date only in splicing-factor mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer, including myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. Here, we show that cohesin mutations are biomarkers of sensitivity to drugs targeting the splicing-factor SF3B1 (H3B-8800 and E-7107). We identify drug-induced alterations in splicing and corresponding reduced gene expression of a large number of DNA repair genes, including BRCA1 and BRCA2, as the mechanism underlying this sensitivity in cell line models, primary patient samples and patient-derived xenograft (PDX) models of AML. We find that DNA damage repair genes are particularly sensitive to exon skipping induced by SF3B1 modulators given their long length and large number of exons per transcript. Furthermore, we demonstrate that treatment of cohesin-mutant cells with SF3B1 modulators not only results in impaired DNA damage response and accumulation of DNA damage, but it significantly sensitizes cells to subsequent killing by PARP inhibitors and chemotherapy, and leads to improved overall survival of PDX models of cohesin-mutant AML in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS and AML, and we propose this as a broader strategy for therapeutic targeting of other DNA damage-repair deficient cancers. One Sentence SummaryWe identify an unexpected effect of SF3B1 splicing inhibitors on regulation of DNA damage repair genes and show efficacy of combination treatment in cohesin-mutant MDS and AML.

cancer biology↗

bioRxiv2022

Cyclin CLB2 mRNA localization determines efficient protein synthesis to orchestrate bud growth and cell cycle progression

Clb2 is a conserved B-type cyclin essential for mitotic progression in Saccharomyces cerevisiae, with expression tightly regulated at transcriptional and proteolytic levels. However, it remains unclear whether Clb2 protein synthesis is regulated and responsive to cell growth. Here, we show that CLB2 mRNA localizes to the bud via the She2/She3 complex, while Clb2 protein accumulates in the mother nucleus. This mRNA localization enhances translation without affecting protein localization. A structured RNA element, a ZIP-code, is located within the coding sequence and is required, but not sufficient, for both mRNA transport and protein expression. Mutation of this ZIP code disrupts mRNA localization, reduces Clb2 synthesis, increases budded phase duration and daughter cell size. In wild-type cells, Clb2 protein levels scale with bud growth, a coupling lost in ZIP code mutants. These findings reveal a mechanism by which mRNA localization and translation are coordinated to link cell growth with cell cycle progression.

cell biology↗

bioRxiv2020

Operation of a TCA cycle subnetwork in the mammalian nucleus

Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these required metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in the cell. Here we show that a substantial part of the mitochondrial tricarboxylic acid (TCA) cycle, the biosynthetic hub of epigenetic modification factors, is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins, supporting their nuclear location. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization and gene expression regulation.

systems biology↗

bioRxiv2020

Sex-biased ZRSR2 mutations in myeloid malignancies impair plasmacytoid dendritic cell activation and apoptosis

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive leukemia of plasmacytoid dendritic cells (pDCs). BPDCN occurs at least three times more frequently in men than women, but the reasons for this sex bias are unknown. Here, studying genomics of primary BPDCN and modeling disease-associated mutations, we link acquired alterations in RNA splicing to abnormal pDC development and inflammatory response through Toll-like receptors. Loss-of-function mutations in ZRSR2, an X chromosome gene encoding a splicing factor, are enriched in BPDCN and nearly all mutations occur in males. ZRSR2 mutation impairs pDC activation and apoptosis after inflammatory stimuli, associated with intron retention and inability to upregulate the transcription factor IRF7. In vivo, BPDCN-associated mutations promote pDC expansion and signatures of decreased activation. These data support a model in which male-biased mutations in hematopoietic progenitors alter pDC function and confer protection from apoptosis, which may impair immunity and predispose to leukemic transformation. STATEMENT OF SIGNIFICANCESex bias in cancer is well recognized but the underlying mechanisms are incompletely defined. We connect X chromosome mutations in ZRSR2 to an extremely male-predominant leukemia. Aberrant RNA splicing induced by ZRSR2 mutation impairs dendritic cell inflammatory signaling, interferon production, and apoptosis, revealing a sex- and lineage-related tumor suppressor pathway.

cancer biology↗