Biology subjects

Wernig-Zorc, S.

Publications and source records attributed to Wernig-Zorc, S..

4 recordsLinked to original sources

bioRxiv2023

The long non-coding RNA MALAT1 modulates NR4A1 expression through a downstream regulatory element in specific cancer-cell-types

Chromatin-associated long non-coding RNAs (lncRNAs) have been shown to define chromatin density, regulate gene expression, and are involved in the initiation and progression of various cancer types. Despite the wealth of studies describing transcriptome changes upon lncRNA modulation, little data is showing the direct effects of lncRNA on regulatory elements (REs) that drive gene expression. Here we explored the molecular mechanism of the chromatin-interacting lncRNA, MALAT1, through RNA- and ATAC-seq, using HeLa cells as a model system. Time-resolved MALAT1 knock-down assays revealed its direct regulation of a limited number of protein-coding genes. Loss of MALAT1 resulted in a substantial loss of chromatin accessibility downstream of the NR4A1 gene, associated with its down-regulation. CRISPR-i assays revealed that this region corresponds to a new downstream RE. Next, using TCGA data, we identified a direct correlation between the expression of NR4A1 and the accessibility of the downstream RE in breast cancer. The molecular mechanism was validated on estrogen receptor (ER) positive breast cancer cells (MCF7) and Pancreatic Duct Epithelioid Carcinoma (PANC1) cells, not showing this effect according to TCGA data. Indeed, MALAT1 regulates the expression of NR4A1 in a cell type-specific manner by changing the accessibility of the downstream RE. MALAT1 exhibits a molecular mechanism that fine-tunes the expression of cancer drivers, like NR4A1, in ER-positive breast cancer cells, but not in other cell types.

cell biology↗

bioRxiv2022

Optimized MNase-seq pipeline reveals a novel gene regulation via differential nucleosome stability

Micrococcal nuclease sequencing (MNase-seq) is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease, and the requirement for high sequencing depth. Here, we present the newly developed nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. nucMACC represents the first systematic, and genome-wide approach for detecting unstable ("fragile") nucleosomes. We characterized the regulatory nucleosomal landscape in D. melanogaster and S. cerevisiae. Two functionally distinct sets of promoters were identified, one associated with an unstable nucleosome and the other being nucleosome depleted. Chromatin structure analysis shows that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies. TeaserThe nucMACC pipeline quantifies the local and global functional alterations of chromatin structure.

bioinformatics↗

bioRxiv2020

Macrovesicular steatosis in nonalcoholic fatty liver disease is a consequence of purine nucleotide cycle driven fumarate accumulation

SummaryNonalcoholic fatty liver disease (NAFLD) affects ~88% of obese individuals and is characterised by hepatic lipid accumulation. Mitochondrial metabolic dysfunction is a feature of NAFLD. We used a human pluripotent stem cell-based system to determine how mitochondrial dysfunction is linked to hepatic lipid accumulation. We induced lipid accumulation in hepatocyte-like cells (HLCs) using lactate, pyruvate and octanoate (LPO). Transcriptomic analysis revealed perturbation of mitochondrial respiratory pathways in LPO exposed cells. Using 13C isotopic tracing, we identified truncation of the TCA cycle in steatotic HLCs. We show that increased purine nucleotide cycle (PNC) activity fuels fumarate accumulation and drives lipid accumulation in steatotic cells. These findings provide new insights into the pathogenesis of hepatic steatosis and may lead to an improved understanding of the metabolic and transcriptional rewiring associated with NAFLD.Competing Interest StatementProfessor David Hay is a founder, shareholder and director in Stemnovate Limited.View Full Text

biochemistry↗

bioRxiv2020

Altered hypothalamic DNA methylation and stress-induced hyperactivity in a novel model of early life stress

Early life stress during childhood is associated with a number of psychiatric disorders that manifest across the life course. Preterm birth is a profound stressor, and an important cause of cognitive impairment, as well as neurodevelopmental and psychiatric disorders. However, the mechanisms that link events during the early neonatal period with later functional problems are poorly understood. We developed a novel mouse model of early life stress (modified maternal separation; MMS) with specific relevance to preterm birth (PTB) and hypothesised it would affect the hypothalamic transcriptome and DNA methylome and impact on behaviour in adulthood. MMS consisted of repeatedly stimulating pups for 1.5 hours/day, whilst separated from their mother, from postnatal day (P)4-6. 3 RNA sequencing and DNA methylation immunoprecipitation (meDIP) sequencing was performed on the hypothalamus at P6. Behaviour was assessed with the elevated plus and open field mazes, and in-cage monitoring at 3-4 months of age. Although MMS was only associated with subtle changes in gene expression there were widespread alterations in DNA methylation. Notably, differentially methylated regions were enriched for synapse-associated loci. MMS also resulted in hyperactivity in the elevated plus and open field mazes, but in-cage monitoring revealed that this was not representative of habitual hyperactivity. In conclusion we describe a novel model of early life stress with relevance to PTB, with marked effects on DNA methylation in the hypothalamus and with stress-specific hyperactivity in young adulthood. We suggest that these results have implications for the understanding of early life stress mediated effects on brain development.

developmental biology↗