Biology subjects

Schwaiger, M.

Publications and source records attributed to Schwaiger, M..

7 recordsLinked to original sources

bioRxiv2026

A new bioorthogonal PET reporter gene for cardiac regenerative medicine binding to DTPA-lanthanide complexes

The lack of non-invasive, quantitative methods to track the location and proliferation of transplanted cells hampers the clinical translation of cardiac regenerative therapies. Here, we establish a PET reporter for tracking human induced pluripotent stem cell (hiPSC)-derived cardiac cells across complementary two-dimensional (2D) and three-dimensional (3D) cardiac tissue models. Methods hiPSCs were genetically engineered using CRISPR-Cas9 to express a human-derived, anticalin-based, bioorthogonal PET reporter (DTPA-R) that specifically binds radiolabeled DTPA-metal complexes. The engineered hiPSCs were differentiated into ventricular progenitors (HVPs) and cardiomyocytes (CMs). Stability of reporter gene expression and its effects on cellular differentiation and function were evaluated. Uptake of [18F]F-DTPA*Tb by DTPA-R-positive and -negative HVPs was analyzed in vitro, and DTPA-R HVPs were evaluated in ex vivo cultured porcine myocardial slices with and without radiofrequency ablation (RFA) injury. Phantom studies were performed to evaluate PET detectability under clinically relevant large-animal and human imaging conditions and to assess how activity distribution affects signal detection in relation to DTPA-R cardiac cell-equivalent numbers. Results DTPA-R expression was maintained during the differentiation stages of hiPSC-derived cardiac cells and had no measurable impact on migration, differentiation, and functional integration. PET imaging enabled the specific detection of DTPA-R HVPs in intact and injured myocardial slices. At the initial phantom scan, the measured activity corresponded to cell-equivalent numbers of approximately 3.2 x 10^6 HVPs or 5.5 x 10^6 CMs. The compact 200 uL source remained clearly detectable at 6 h, whereas the more dispersed 1,000 uL source progressively approached background activity, indicating that PET detectability depended strongly on local activity concentration and distribution. Conclusion This study establishes a bioorthogonal PET reporter gene platform for quantitative imaging of hiPSC-derived cardiac cells, with no measurable adverse effects on the biological parameters examined, and provides a methodological foundation for future translational and in vivo imaging studies. The approach may also be applicable to other hiPSC-derived cell products beyond cardiac cell lineages.

bioengineering↗

bioRxiv2025

Remodeling Activity of ChAHP Restricts Transcription Factor Access to Chromatin

Transcription in eukaryotes is regulated by chromatin-based mechanisms that control nucleosome occupancy, chromatin modifications, and transcription factor binding. We have previously shown that the transcription factor ADNP forms the ChAHP complex with the chromatin remodeler CHD4 and HP1 proteins, acting as a site-specific regulator of transcription and antagonist of CTCF binding. However, the molecular basis of these functions remained unclear. Here, we demonstrate that the CHD4 subunit is essential to antagonize CTCF and silence transcription of transposons, while HP1 proteins are dispensable. Although the remodeling activity of CHD4 is not required for ChAHP chromatin association, it is critical for both transposon repression and CTCF antagonism. Our findings support a model wherein ADNP recruits chromatin remodeling activity in a sequence-specific manner, enabling transcriptional control and local modulation of chromatin architecture.

molecular biology↗

bioRxiv2025

ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment

Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements derived from RNA polymerase III (POL III)-transcribed short non-coding RNAs. SINEs retain sequence features recognized by the POL III machinery and constitute a substantial portion of vertebrate genomes. Despite their impact on genome stability and evolution, the mechanisms governing SINE transcription remain poorly understood. Although DNA methylation and heterochromatin formation have been implicated in their repression, we find these pathways play only a minor role in mouse embryonic stem cells. Instead, we identify the ChAHP complex as a key repressor of SINE B2 elements. ChAHP directly inhibits POL III transcription by blocking TFIIIB recruitment without affecting TFIIIC binding. This selective interference prevents transcription initiation and highlights a distinct regulatory mechanism. Our findings establish ChAHP as a non-canonical repressor of POL III-dependent SINE transcription, offering new insights into the control of this pervasive class of non-coding genomic elements.

molecular biology↗

bioRxiv2024

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin

Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyces pombe, one-third of TFs are solely homology-predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation-mass spectrometry and chromatin immunoprecipitation sequencing. Our study identified protein interactors for half the TFs, with over a quarter potentially forming stable complexes. We discovered DNA binding sites for most TFs across 2,027 unique genomic regions, revealing motifs for 38 TFs and uncovering a complex regulatory network of extensive TF cross- and autoregulation. Characterization of the largest TF family revealed conserved DNA sequence preferences but diverse binding patterns, and identified a repressive heterodimer, Ntu1/Ntu2, linked to perinuclear gene localization. Our TFexplorer webtool makes all data interactively accessible, offering new insights into TF interactions and regulatory mechanisms with broad biological relevance. HIGHLIGHTSO_LIComprehensive strain library of endogenously tagged S. pombe TFs C_LIO_LIExperimentally determined atlas of TF interactions with proteins and chromatin C_LIO_LITFexplorer web application for interactive exploration of TF interactomes C_LIO_LIIdentification of repressive Nattou complex linked to perinuclear gene localization C_LI

molecular biology↗

bioRxiv2024

ChAHP2 and ChAHP control diverse retrotransposons by complementary activities

Retrotransposon control in mammals is an intricate process that is effectuated by a broad network of chromatin regulatory pathways. We previously discovered ChAHP, a protein complex with repressive activity against SINE retrotransposons, composed of the transcription factor ADNP, chromatin remodeler CHD4, and HP1 proteins. Here we identify ChAHP2, a protein complex homologous to ChAHP, wherein ADNP is replaced by ADNP2. ChAHP2 is predominantly targeted to ERVs and LINEs, via HP1{beta}-mediated binding of H3K9 trimethylated histones. We further demonstrate that ChAHP also binds these elements in a mechanistically equivalent manner to ChAHP2, and distinct from DNA sequence-specific recruitment at SINEs. Genetic ablation of ADNP2 alleviates ERV and LINE1 repression, which is synthetically exacerbated by additional depletion of ADNP. Together, our results reveal that the ChAHP and ChAHP2 complexes function to control both non-autonomous and autonomous retrotransposons by complementary activities, further adding to the complexity of mammalian transposon control.

molecular biology↗

bioRxiv2023

Nitrogen signaling factor triggers a respiration-like gene expression program

Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin Nitrogen Signaling Factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program independently of the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.

microbiology↗

bioRxiv2022

Mouse Nuclear RNAi-defective 2 Promotes Splicing of Weak 5' Splice Sites

Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5 splice site (5SS). In mammals, many introns contain weak 5SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.

molecular biology↗