Biology subjects

Malzl, D.

Publications and source records attributed to Malzl, D..

11 recordsLinked to original sources

bioRxiv2026

Depletion of lamin-associated polypeptide 2alpha leads to chromatin reorganization and binding of A-type lamins to open genomic regions

BackgroundLamins are major regulators of the spatial and functional organization of chromatin. Lamins at the nuclear periphery form the lamina that anchors heterochromatin to the nuclear envelope. A subpool of A-type lamins localizes in the nuclear interior, where they also bind to euchromatic genomic regions. A-type lamin properties and chromatin association are regulated by lamin-associated polypeptide 2alpha (LAP2). Here we systematically analyze, how LAP2 depletion affects chromatin organization, accessibility and gene expression on a genome-wide level. ResultsLAP2 depletion in mouse dermal fibroblasts positively and negatively affects chromatin accessibility and gene expression throughout the genome, which correlates with changes in chromatin association of A-type lamins and the nucleosomal remodeler proteins BRG1 and CHD4. In particular, A-type lamins bind to open chromatin regions close to BRG1 and CHD4 binding sites and deregulated genes, but do not directly accumulate on genes and BRG1 and CHD4-enriched sites. Unsupervised clustering of the datasets on LAP2-bound genomic regions confirms spreading of A-type lamins to active chromatin regions containing deregulated genes and an enrichment of chromatin remodelers on a subset of these genomic regions. ConclusionsLAP2 depletion in fibroblasts leads to a gross rearrangement of chromatin. Genome-wide chromatin reorganization is linked to spreading of A-type lamins to active chromatin regions and accompanied by a restriction of chromatin remodelers to a subset of active genomic regions. These changes correlate with changes in chromatin accessibility and gene expression throughout the genome, particularly in regions where lamin binding is gained in LAP2 knockout versus wildtype cells.

genomics↗

bioRxiv2026

reComBat-seq: Regularized negative binomial regression for batch-effect correction in underdetermined transcriptomics datasets

MotivationBatch effect correction is essential for the integration of large-scale transcriptomics datasets such as single-cell RNA-seq or multi-study bulk RNA-seq datasets for reducing technical noise that may mask biological signal. Existing correction methods, either do not produce count data output which is crucial for state-of-the-art downstream analyses such as differential expression analysis or fail to converge in underdetermined study designs. ResultsWe present reComBat-seq, a method that extends the Negative Binomial regression framework of ComBat-seq by incorporating Elastic Net regularization. This approach resolves problems with rank-deficient design matrices while also preserving the integer nature of count data. Benchmarking on simulated and real datasets such as single-cell RNA-seq data demonstrates that reComBat-seq successfully removes batch effects in complex study designs while maintaining compatibility with downstream differential expression tools. Availability and ImplementationreComBat-seq source code can be found at https://github.com/menchelab/reComBat-seq. All code to reproduce the presented analyses can be found at https://github.com/menchelab/reComBatseq_Studies. Data produced in this study is available at https://doi.org/10.5281/zenodo.19736515. Used single-cell RNA-seq data can be found at https://doi.org/10.5281/zenodo.14234956. Supplementary InformationProofs and volcano plots of differential expression analysis

bioinformatics↗

bioRxiv2025

tRNA thiolation defects disrupt cellular proteostasis and tissue homeostasis in mammals

Sulfur modification of tRNA wobble uridines is an evolutionarily conserved mechanism that ensures efficient protein synthesis. In humans, loss of this anticodon modification due to mutations in CTU2 (cytosolic thiouridylase 2) causes DREAM-PL syndrome, a severe congenital disorder often leading to early postnatal death. However, the mechanisms by which loss of tRNA thiolation drives pathology remain unclear. Here, we show that loss of CTU2 triggers significant cellular proteostasis defects in patient cells and model cell lines. Structural and biochemical analyses reveal that the pathogenic CTU2L63P mutation destabilizes the CTU1/CTU2 complex and abolishes tRNA binding and thiolation. Acute loss of CTU2 caused codon-specific ribosome pausing at A-ending codons decoded by thiolated tRNAs, and decreased ribosome occupancy of A-rich transcripts in a dosage-dependent manner. Codon-biased mRNAs transcribed from genes critical for ciliogenesis are predicted to be most affected, linking their reduced translation to DREAM-PL etiology in humans. Surprisingly, Ctu2L63P mice display severe thiolation defects, but develop normally, are viable and fertile. Our findings highlight the importance of functional tRNA thiolation for organismal health in humans and identify species-specific vulnerabilities during embryonic development in mammals.

cell biology↗

bioRxiv2024

Specific origin selection and excess functional MCM2-7 loading in ORC-deficient cells.

The six subunit Origin Recognition Complex (ORC) loads excess MCM2-7 on chromosomes to promote initiation of DNA replication and is believed to be important for origin specification. Mapping of origins in cancer cell lines engineered to delete three of the subunits, ORC1, ORC2 or ORC5 shows that specific origins are still used and are mostly at the same sites in the genome as in wild type cells. The few thousand origins that were up-regulated in the absence of ORC suggest that GC/TA skewness and simple repeat sequences facilitate, but are not essential for, origin selection in the absence of the six-subunit ORC. Despite the lack of ORC, excess MCM2-7 is still loaded at comparable rates in G1 phase to license dormant origins and is also repeatedly loaded in the same S phase to permit re-replication. Thus, origin specification and excess MCM2-7 loading on origins do not require the six-subunit ORC in human cancer cell lines.

molecular biology↗

bioRxiv2024

Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats

Single-cell RNA-seq characterizes biological samples at unprecedented scale and detail, but data interpretation remains challenging. Here we introduce CellWhisperer, a multimodal machine learning model and software that connects transcriptomes and text for interactive single-cell RNA-seq data analysis. CellWhisperer enables the chat-based interrogation of transcriptome data in English language. To train our model, we created an AI-curated dataset with over a million pairs of RNA-seq profiles and matched textual annotations across a broad range of human biology, and we established a multimodal embedding of matched transcriptomes and text using contrastive learning. Our model enables free-text search and annotation of transcriptome datasets by cell types, states, and other properties in a zero-shot manner and without the need for reference datasets. Moreover, Cell-Whisperer answers questions about cells and genes in natural-language chats, using a biologically fluent large language model that we fine-tuned to analyze bulk and single-cell transcriptome data across various biological applications. We integrated CellWhisperer with the widely used CELLxGENE browser, allowing users to in-teractively explore RNA-seq data through an integrated graphical and chat interface. Our method demonstrates a new way of working with transcriptome data, leveraging the power of natural language for single-cell data analysis and establishing an important building block for future AI-based bioinformatics research assistants.

bioinformatics↗

bioRxiv2024

Core Tri-fucosylation of Nematode N-glycans Requires Golgi α-mannosidase III Activity that Impacts Animal Growth and Behaviours

Many nematodes possess N-glycans with complex core chitobiose modifications, which is a feature observed in various free-living and parasitic nematodes but is absent in mammals. Using Caenorhabditis elegans as a model to study N-glycan biosynthesis, we demonstrated that the core N-acetylglucosamine (GlcNAc) residues can be modified by three fucosyltransferases in the Golgi, namely FUT-1, FUT-6 and FUT-8. While the asparagine-linked GlcNAc is modified with a 1,3- and 1,6-linked fucose by FUT-1 and FUT-8 respectively, the distal GlcNAc residue is 1,3-fucosylated solely by FUT-6. Interestingly, FUT-6 can only fucosylate N-glycan structures lacking the 1,6-mannose upper arm, indicating that a specific -mannosidase is required to generate substrates for subsequent FUT-6 activity. By analysing the N-glycomes of aman-3 mutants (tm5400 and a CRISPR/Cas9 knockout, hex-2;hex-3;aman-3) using offline HPLC-MALDI-TOF MS/MS, we observed that the absence of the aman-3 gene abolishes 1,3-fucosylation of the distal GlcNAc of N-glycans, which suggests that AMAN-3 is the relevant mannosidase on whose action FUT-6 depends. To further investigate it, we recombinantly expressed AMAN-3 in insect cells and characterised its enzymatic activity in vitro. In contrast to the classical Golgi -mannosidase II (AMAN-2), AMAN-3 displayed a cobalt-dependent 1,6-mannosidase activity towards N-glycans. Using AMAN-3 and other recombinant C. elegans glycoenzymes, we remodelled a fluorescein conjugated-Man5GlcNAc2 structure; we were able to mimic N-glycan biosynthesis in the Golgi and generate a tri-fucosylated glycan in vitro. We performed confocal microscopy studies using a knock-in strain (aman-3::eGFP) and could show the Golgi localisation of AMAN-3. In addition, using a high-content computer-assisted C. elegans analysis platform, we observed that AMAN-3 deficient worms display significant developmental delays, morphological and behavioural alterations in comparison to the wild type. Therefore, our data suggested that AMAN-3 participates in nematode N-glycan biosynthesis in the Golgi and generates substrates for FUT-6; thereby, this enzyme is essential for the formation of the unusual tri-fucosylated chitobiose cores of nematode N-glycans, which may play important roles in nematode development and behaviour. BackgroundTri-fucosylation of N-glycan core is a conserved feature seen in the N-glycomes of several nematode species. However, beyond the three core fucosyltransferases, we know very little about the biosynthesis and biological function of these core modifications. ResultsComparative glycomics data revealed that aman-3 mutants possess underfucosylated N-glycomes. Biochemical characterisation of AMAN-3 clarified its optimal reaction conditions and substrate specificity and, we demonstrated a Golgi localisation. Thereafter in vitro reconstruction of biosynthesis of a core tri-fucosylated N-glycan was achieved using 8 recombinant C. elegans glycoenzymes. Notably, aman-3 deficient worms exhibited significant developmental and behavioural changes. ConclusionAMAN-3 is a Golgi -mannosidase required for core fucosylation of the distal N-acetylglucosamine of N-glycoproteins. SignificanceThis study elucidates the key role of a novel Golgi -mannosidase in the biosynthesis of the unusual N-glycans of C. elegans and related nematodes, thereby setting the stage for new approaches to study the roles of glycan in the biology and immunology of nematode glycoproteins.

biochemistry↗

bioRxiv2024

Spermidine/spermine N1-acetyltransferase controls tissue-specific regulatory T cell function in chronic inflammation

Regulatory T cells (Tregs) are a critical immune component guarding against excessive inflammatory responses. During chronic inflammation, Tregs fail to control effector T cell responses. The causes of Treg dysfunction in these diseases are poorly characterized and therapies are aimed at blocking aberrant effector responses rather than rescuing Treg function. Here we utilized single-cell RNA sequencing data from patients suffering from chronic skin and colon inflammation to uncover SAT1, the gene encoding spermidine/spermine N1-acetyltransferase (SSAT), as a novel marker and driver of skin-specific Treg dysfunction during TH17-mediated inflammation. Tregs expressing SAT1 exhibit a tissue-specific inflammation signature and show a proinflammatory effector-like profile. In CRISPRa on healthy human skin-derived Tregs increased expression of SAT1 leads to a loss of suppressive function and a switch to a TH17-like phenotype. This phenotype is induced by co-receptor expression on keratinocytes exposed to a TH17 microenvironment. Finally, the potential therapeutic impact of targeting SSAT was demonstrated in a mouse model of skin inflammation by inhibiting SSAT pharmacologically, which rescued Treg number and function in the skin and systemically. Together, these data show that SAT1 expression has severe functional consequences on Tregs and provides a novel target to treat chronic inflammatory skin disease.

immunology↗

bioRxiv2023

RIF1 regulates replication origin activity and early replication timing in B cells

The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin, regulates early origin firing and promotes early replication. RIF1 has a minor role in gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal new layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.

molecular biology↗

bioRxiv2022

Large neutral amino acid levels tune perinatal neuronal excitability and survival

Surprisingly little is known about the critical metabolic changes that neural cells have to undergo during development and how even mild, temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically-relevant large neutral amino acids, lead to a form of autism spectrum disorder, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different stages of life. We found that the cerebral cortex undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes. But what are the consequences of interfering with this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of large neutral amino acids and lipids in the cerebral cortex are highly interconnected. Deletion of Slc7a5 in neurons perturbs specifically the postnatal metabolic state leading to a shift in lipid metabolism and a stage- and cell-type-specific alteration in neuronal activity patterns, resulting in a long-term cortical circuit dysfunction.

neuroscience↗

bioRxiv2022

A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination

Conflicts between transcription and cohesin-mediated loop extrusion can majorly influence 3D chromatin architecture but whether these structural changes affect biological function is unknown. Here, we show that a critical step in antibody class switch recombination (CSR) in activated B cells, namely, the juxtaposition (synapsis) of donor and acceptor switch (S) recombination sequences at the immunoglobulin heavy chain locus (Igh), occurs at the interface of a de novo topologically associating domain (TAD) boundary formed via transcriptional activity at acceptor S regions. Using Tri-C to capture higher-order multiway chromatin conformations, we find that synapsis occurs predominantly in the proximity of distal 3 CTCF-binding sites and that this multiway conformation is abolished upon downregulation of transcription and loss of the TAD boundary at the acceptor S region. Thus, an insulating de novo TAD boundary created by the conflict between transcription and loop extrusion plays a direct role in the mechanism of CSR.

molecular biology↗

bioRxiv2021

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations

Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. Yet, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT), mediated by replication origin activity, directly regulates the genesis of lymphomagenic Myc translocations during antibody maturation in B cells. Reduced levels of the replicative helicase, the minichromosome-maintenance (MCM) complex, decreases translocations and globally abrogates the RT program. Ablating a single replication origin at Myc causes an early-to-late RT switch with major loss of translocations, a phenotype that is reversed by restoring early RT. Finally, this novel RT-regulated mechanism occurs after DSB formation and independently of DSB frequency. Thus, RT constitutes a distinct regulatory event in translocation biogenesis linking DSB formation to DSB ligation.

molecular biology↗