Biology subjects

Jäschke, A.

Publications and source records attributed to Jäschke, A..

6 recordsLinked to original sources

bioRxiv2026

RiboGRAM learns multi-scale non-coding RNA grammar for structural and regulatory inference

Protein-coding sequences are read through the triplet genetic code, whereas the organization of molecular information within non-coding RNA sequences remains elusive. Here, we identify a non-coding RNA grammar defined by multi-scale motif usage and 5'-to-3' positional gradients, and develop RiboGRAM to learn this organization. Across nine organisms, non-coding RNAs showed scale-dependent divergence from coding sequences, with directional U-rich and AU-rich gradients. Integrating multi-scale sequence encoding with contextual modeling, RiboGRAM organized RNA families, revealing motif-associated and pair-like patterns across layers. Without structural supervision, non-coding RNA pretraining improved base-pair recovery over coding or messenger RNA pretraining, with representations supporting alignment-free diffusion-based 3D modeling of short RNAs. In human RNA-protein binding profiles, RiboGRAM identified position-resolved motif organization across protein targets and cell types, with sequence-preference shifts associated with reduced cross-cell transferability. Together, these results establish a learnable grammar of non-coding RNA sequence organization for structural and regulatory inference.

bioinformatics↗

bioRxiv2022

Identification of NAD-RNAs and ADPR-RNA decapping in the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii

NAD is a coenzyme central to metabolism that was also found to serve as a 5-terminal cap of bacterial and eukaryotic RNA species. The presence and functionality of NAD-capped RNAs (NAD-RNAs) in the archaeal domain remain to be characterized in detail. Here, by combining LC-MS and NAD captureSeq methodology, we quantified the total levels of NAD-RNAs and determined the identity of NAD-RNAs in the two model archaea, Sulfolobus acidocaldarius and Haloferax volcanii. A complementary differential RNA-Seq (dRNA-Seq) analysis revealed that NAD transcription start sites (NAD-TSS) correlate with well-defined promoter regions and often overlap with primary transcription start sites (pTSS). The population of NAD-RNAs in the two archaeal organisms shows clear differences, with S. acidocaldarius possessing more capped small non-coding RNAs (sncRNAs) and leader sequences. The NAD-cap did not prevent 5[->]3 exonucleolytic activity by the RNase Saci-aCPSF2. To investigate enzymes that facilitate the removal of the NAD-cap, four Nudix proteins of S. acidocaldarius were screened. None of the recombinant proteins showed NAD decapping activity. Instead, the Nudix protein Saci_NudT5 showed activity after incubating NAD-RNAs at elevated temperatures. Hyperthermophilic environments promote the thermal degradation of NAD into the toxic product ADPR. Incorporating NAD into RNAs and the regulation of ADPR-RNA decapping by Saci_NudT5 is proposed to provide additional layers of maintaining stable NAD levels in archaeal cells. ImportanceThis study reports the first characterization of 5-terminally modified RNA molecules in Archaea and establishes that NAD-RNA modifications, previously only identified in the other two domains of life, are also prevalent in the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii. We screened for NUDIX hydrolases that could remove the NAD-RNA cap and showed that none of these enzymes removed NAD modifications, but we discovered an enzyme that hydrolyzes ADPR-RNA. We propose that these activities influence the stabilization of NAD and its thermal degradation to potentially toxic ADPR products at elevated growth temperatures.

molecular biology↗

bioRxiv2022

Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging

Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here we report the development of RhoBAST:SpyRho, a fluorescent light-up aptamer (FLAP) system ideally suited for visualizing RNAs in live or fixed cells with various advanced fluorescence microscopy modalities. Overcoming problems associated with low cell permeability, brightness, fluorogenicity, and signal-to-background ratio of previous fluorophores, we designed a novel probe, SpyRho (Spirocyclic Rhodamine), which tightly binds to the RhoBAST aptamer. High brightness and fluorogenicity is achieved by shifting the equilibrium between spirolactam and quinoid. With its high affinity and fast ligand exchange, RhoBAST:SpyRho is a superb system for both super-resolution SMLM and STED imaging. Its excellent performance in SMLM and the first reported super-resolved STED images of specifically labeled RNA in live mammalian cells represent significant advances over other FLAPs. The versatility of RhoBAST:SpyRho is further demonstrated by imaging endogenous chromosomal loci and proteins.

biophysics↗

bioRxiv2020

Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. In BriefIn budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/065920v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@19b86f4org.highwire.dtl.DTLVardef@1b923f3org.highwire.dtl.DTLVardef@1e74f69org.highwire.dtl.DTLVardef@10e787f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIYeast cells have thousands of short NAD-RNAs related to the 5-ends of mRNAs C_LIO_LIRNA polymerase II prefers a YAAG promoter motif for NAD incorporation into RNA C_LIO_LINAD-RNA is strongly guarded against by Rai1, Dxo1, and Npy1 decapping enzymes at different subcellular sites C_LIO_LIIn vitro, NAD-mRNAs are rejected from translation C_LI

cell biology↗

bioRxiv2020

RhoBAST - A Rhodamine-Binding Aptamer for Super-Resolution RNA Imaging

RhoBAST is a novel fluorescence light-up RNA aptamer (FLAP) that transiently binds a fluorogenic rhodamine dye. Fast dye association and dissociation result in intermittent fluorescence emission, facilitating single-molecule localization microscopy (SMLM) with an image resolution not limited by photobleaching. We demonstrate RhoBAST's excellent properties as a RNA marker by resolving subcellular and subnuclear structures of RNA in live and fixed cells by SMLM and structured illumination microscopy (SIM).

cell biology↗

bioRxiv2019

The 5’-NAD cap of RNAIII modulates toxin production in Staphylococcus aureus isolates

1Nicotinamide adenosine dinucleotide (NAD) has been found to be covalently attached to the 5-ends of specific RNAs in many different organisms, but the physiological consequences of this modification are largely unknown. Here we report the occurrence of several NAD-RNAs in the opportunistic human pathogen Staphylococcus aureus. Most prominently, RNAIII, a central quorum-sensing regulator of this bacteriums physiology, was found to be 5-NAD-capped to a significant extent. NAD incorporation efficiency into RNAIII was found to depend in vivo on the -1 position of the P3 promoter. Reduction of RNAIIIs NAD content led to a decreased expression of alpha- and delta-toxins, resulting in reduced cytotoxicity of the modified strains. These effects to not seem to be due to changes in RNAIIIs secondary structure upon NAD attachment, as indicated by largely unaltered patterns in in vitro chemical probing experiments. Our study represents a large step towards establishing a biological function of the 5-NAD cap, which for RNAIII in S. aureus is to modulate the expression of virulence factors.\n\n2 ImportanceNumerous organisms, including bacteria, are endowed with a 5-NAD cap in specific RNAs. While the presence of the 5-NAD cap modulates the stability of the modified RNA species, a significant biological function and phenotype have not been assigned so far. Here, we show the presence of a 5-NAD cap in RNAIII from S. aureus, a dual-function regulatory RNA involved in quorum-sensing processes and regulation of virulence factor expression. We also demonstrate that altering the natural NAD modification ratio of RNAIII leads to a decrease in exotoxin production, thereby modulating bacteriums virulence. Our work unveils a new layer of regulation of RNAIII and the agr system that might be linked to the redox state of the NAD molecule in the cell.

microbiology↗