Biology subjects

Tessarz, P.

Publications and source records attributed to Tessarz, P..

12 recordsLinked to original sources

bioRxiv2025

Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells

Pluripotent stem cells (SCs) rely on metabolic rewiring to regulate self-renewal and differentiation. The hexosamine biosynthetic pathway (HBP) integrates multiple metabolic inputs to produce uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), a central substrate for protein and lipid glycoconjugates. While UDP-GlcNAc levels influence pluripotency, the broader metabolic roles of the HBP in stem cell maintenance and differentiation remain largely unexplored. Using proteomic and metabolomic analyses, we uncovered extensive enzymatic remodelling of the HBP during early mouse embryonic stem cell (mESC) differentiation, including a significant decrease in N-acetylglucosamine-6-phosphate (GlcNAc6P) levels, despite stable UDP-GlcNAc levels. Isotope labelling experiments revealed that pluripotent stem cells maintain UDP-GlcNAc biosynthesis through a combination of glucose-driven de novo synthesis and the N-Acetylglucosamine (GlcNAc) salvage pathway, both of which are downregulated during differentiation. Functionally, we identified GlcNAc6P--a point of convergence of the de novo synthesis and the salvage pathways--as a pivotal metabolite of stem cell fate. Preventing GlcNAc6Ps deacetylation by deleting or depleting AMDHD2 impaired mESC differentiation. Mechanistically, we demonstrated that GlcNAc6P catabolism is essential for sustaining cytosolic acetate and in turn acetyl-CoA levels, which are critical for lipid synthesis and histone modifications required for pluripotency exit. These findings establish AMDHD2 as a key supplier of cellular acetate and reveal an essential metabolic link between HBP activity and acetyl-CoA homeostasis. By expanding the role of the HBP beyond UDP-GlcNAc production, this study reveals an unrecognised metabolic vulnerability that can be exploited to manipulate stem cell identity.

molecular biology↗

bioRxiv2023

Dimension Reduction by Spatial Components Analysis Improves Pattern Detection in Multivariate Spatial Data

We introduce a multivariate statistical approach for pattern recognition in spatial transcriptomics data. Our algorithm (SPACO) constructs a low-dimensional projection of the data maximising Morans I, which mitigates non-spatial variation and outperforms PCA for pre-processing. Our method also provides a calibrated, powerful test of spatial gene expression that excels in robustness and specificity.

bioinformatics↗

bioRxiv2022

Hypoxia promotes osteogenesis via regulation of the mito-nuclear communication

Bone marrow mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. Several studies have highlighted the critical role of hypoxia (low oxygen concentration) in the regulation of stem cell function, reporting differentiation defects following a switch to normoxia (high oxygen concentration). However, the molecular events triggering changes in stem cell fate decisions in response to high oxygen remain elusive. Here, we study the impact of normoxia in the mito-nuclear communication, with regards to stem cell differentiation. We show that normoxia-cultured MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces rewiring of metabolism, resulting in high acetyl-CoA levels, histone hypo-acetylation occurs due to trapping of acetyl-CoA inside mitochondria, likely due to lower CiC activity. Strikingly, restoring the cytosolic acetyl-CoA pool via acetate supplementation remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is heavily perturbed in response to high oxygen and identify CiC as a novel, oxygen-sensitive regulator of MSC function.

cell biology↗

bioRxiv2022

Reduced polymerase pausing compensates for increased chromatin accessibility in the aging liver

Regulation of gene expression is tightly linked to the organization of the mammalian genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation with age. Here, we used a multi-omic approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility and transcriptional regulation in a whole tissue. We observe that aging in murine liver is accompanied by an increase in chromatin accessibility at promoter regions of protein-coding genes. Yet, although promoter accessibility is a requirement for transcription, the increased accessibility does not result in enhanced transcriptional output. Instead, aging is accompanied by a decrease of promoter-proximal pausing of RNA polymerase II (Pol II). We propose that these changes in transcriptional regulation are due to a reduced stability of the pausing complex and may represent a mechanism to compensate for the age-related increase in chromatin accessibility in order to prevent aberrant transcription.

molecular biology↗

bioRxiv2021

Single-cell resolution unravels spatial alterations in metabolism, transcriptome and epigenome of ageing liver

Epigenetic ageing clocks have revealed that tissues within an organism can age with different velocity. However, it has not been explored whether cells of one type experience different ageing trajectories within a tissue depending on their location. Here, we employed lipidomics, spatial transcriptomics and single-cell ATAC-seq in conjunction with available single-cell RNA-seq data to address how cells in the murine liver are affected by age-related changes of the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. Particularly periportal hepatocytes were characterized by decreased mitochondrial function and strong alterations in the epigenetic landscape, while pericentral hepatocytes - despite accumulation of large lipid droplets - did not show apparent functional differences. In general, chromatin alterations did not correlate well with transcriptional changes, hinting at post-transcriptional processes that shape gene expression during ageing. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.

cell biology↗

bioRxiv2021

Single organoid RNA-sequencing reveals high organoid-to-organoid variability

Over the last decades, organoids have been established from the majority of tissue resident stem and iPS cells. They hold great promise for our understanding of mammalian organ development, but also for the study of disease or even personalized medicine. In recent years, several reports hinted at intraculture organoid variability, but a systematic analysis of such a heterogeneity has not been performed before. Here, we used RNA-seq of individual organoids to address this question. Importantly, we find that batch-to-batch variation is very low, even when prepared by different researchers. On the other hand, there is organoid-to-organoid variability within a culture. Using differential gene expression, we did not identify specific pathways that drive this variability, pointing towards possible effects of the microenvironment within the culture condition. Taken together, our study provides a framework for organoid researchers to properly consider experimental design.

cell biology↗

bioRxiv2021

Methylation of Q105 on histone H2A is part of a dynamic regulatory mechanism integrating metabolism with ribosome biogenesis through recruitment of Nhp2

Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signaling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105, is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signaling pathway as well as acetylation of histone H3 at position K56, thus integrating signals from cell cycle, metabolic and proliferative states. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes the methylation on H2AQ105. Based on functional and proteomic data we suggest that Nhp2 functions as an adapter to bridge the rDNA chromatin with components of the small subunit processome and might help to efficiently coordinate transcription of rRNA with its post-transcriptional processing.

molecular biology↗

bioRxiv2020

The RNA-binding protein Puf5 buffers mRNA levels against chromatin-mediated changes in nascent transcription

Gene expression is a dynamic process regulated at all stages, starting with opening of chromatin, transcription, and continuing with mRNA export, translation and, finally, degradation. While there are feedback mechanisms within the system, it is not clear whether these extend to crosstalk between chromatin architecture and mRNA decay. Here, we show that changes in nascent transcription, mediated by mutating H3K56 to alanine, are post-transcriptionally buffered by the Pumilio protein Puf5, which stabilizes transcripts in a context-dependent manner. Depleting Puf5 in an H3K56A background leads to synthetic lethality. This genetic interaction can be explained by a decrease in translation due to downregulation of its direct mRNA targets, largely consisting of ribosomal protein genes. Importantly, we show that this post-transcriptional buffering is not only linked to H3K56A, but may be a more widespread phenomenon that also buffers against an increase in nascent RNA transcription in order to maintain physiological mRNA levels and cellular homeostasis.

molecular biology↗

bioRxiv2020

Polyamine-controlled proliferation and protein biosynthesis are independent determinants of hair follicle stem cell fate

Stem cell differentiation is accompanied by an increase in mRNA translation. The rate of protein biosynthesis is influenced by the polyamines putrescine, spermidine, and spermine that are essential for cell growth and stem cell maintenance. However, the role of polyamines as endogenous effectors of stem cell fate and whether they act through translational control remains obscure. Here, we investigated the function of polyamines in stem cell fate decisions using hair follicle stem cell (HFSC) organoids. HFSCs showed lower translation rates than progenitor cells, and a forced suppression of translation by direct targeting of the ribosome or through specific depletion of natural polyamines elevated stemness. In addition, we identified N1-acetylspermidine as a novel parallel regulator of cell fate decisions, increasing proliferation without reducing translation. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions. Key PointsO_LILow mRNA translation rates characterize hair follicle stem cell (HFSC) state C_LIO_LIDepletion of natural polyamines enriches HFSCs via reduced translation C_LIO_LIN1-acetylspermidine promotes HFSC state without reducing translation C_LIO_LIN1-acetylspermidine expands the stem cell pool through elevated proliferation C_LI

cell biology↗

bioRxiv2020

Deregulated mito-nuclear communication alters chromatin plasticity and differentiation potential of mesenchymal stem cells upon ageing

Ageing is accompanied by a general decline in the function of many cellular pathways, with metabolic alterations, epigenetic modifications, and stem cell exhaustion representing three important hallmarks of the ageing process. However, whether these pathways are causally or functionally related at a molecular level remains poorly understood. Here, we use bone marrow-derived mesenchymal stem cells (MSCs) isolated from young and old mice to address how age-dependent changes in metabolism and epigenetics are linked and how they impact on the ageing transcriptome and differentiation potential. Given that MSCs maintain specific age-associated properties even under prolonged culture conditions, such as the age-dependent decrease in osteogenic differentiation, they are an excellent model to investigate in vitro the connection of ageing hallmarks on a mechanistic level. In this study, we demonstrate that upon ageing, osteogenic potential of MSCs declines as a consequence of deregulated mito-nuclear communication, mediated by decreased levels of the citrate carrier (CiC). Age-dependent down-regulation of CiC results in acetyl-CoA trapping within mitochondria, hypo-acetylation of histones and chromatin compaction. Together, these changes lead to an altered transcriptional output and are responsible for the reduced differentiation capacity into osteoblasts. Strikingly, short-term supplementation of aged cells with acetate, an exogenous source for cytosolic acetyl-CoA production, rescues not only the age-associated reduction of histone acetylation, but also the osteogenesis defect, representing a potential target for in vitro MSC rejuvenation.

cell biology↗

bioRxiv2018

The repressive and alleviating nature of FACT shapes the transcriptional landscape in ES cells

The conserved and essential histone chaperone FACT (Facilitates Chromatin Transcription) reorganizes nucleosomes during DNA transcription, replication and repair and ensures both, efficient elongation of RNA Pol II and nucleosome integrity. In mammalian cells, FACT is a heterodimer, consisting of SSRP1 and SUPT16. Here, we show that in contrast to yeast, FACT accumulates at the transcription start site of genes reminiscent of RNA Polymerase II profile. Depletion of FACT in mouse embryonic stem cells leads to up-regulation of pro-proliferative genes and key pluripotency factors concomitant with hyper-proliferation of mES cells. Using MNase-, ATAC-, and Nascent Elongating Transcript Sequencing (NET-seq) we show that up-regulation of genes coincides with loss of nucleosomes upstream of the TSS and concomitant increase in antisense transcription, indicating that FACT impacts the promoter architecture to regulate expression of these genes. Finally, we demonstrate a role for FACT in cell fate determination and show that FACT depletion primes ES cells for the neuronal lineage.

molecular biology↗

bioRxiv2018

NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. To better map transcription genome-wide at base pair resolution and with transcription/elongation factor dependency we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). NET-prism introduces an immunoprecipitation to capture RNA Pol II - associated proteins, which reveals the interaction of these proteins with active RNA Pol II. Application of NET-prism on different Pol II subunits (Pol II S2ph, Pol II S5ph), elongation factors (Spt6, Ssrp1), and components of the pre-initiation complex (PIC) (TFIID, TBP, and Mediator) reveals diverse Pol II signals, at a single nucleotide resolution, with regards to directionality and intensity over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity.

genomics↗