Biology subjects

MUCHARDT, C.

Publications and source records attributed to MUCHARDT, C..

4 recordsLinked to original sources

bioRxiv2025

Differential sensitivity to LINE 1-induced damage contributes to the expansion of Tet2-deficient HSCs upon chronic inflammatory stress

Chronic inflammation disrupts hematopoietic stem cell (HSC) function and drives the expansion of TET2-mutated clones, fostering clonal hematopoiesis of indeterminate potential (CHIP). However, the molecular mechanisms linking inflammation to these hematopoietic alterations remain poorly understood. Here, we uncover a pivotal role of transposable element (TE) derepression, specifically of the most recent LINE-1 (L1) elements, in mediating inflammation-induced HSC dysfunction. We show that chronic exposure to low-dose lipopolysaccharide (LPS) causes a loss of the heterochromatin mark H3K9me3 at L1s in wild-type (WT) HSCs, leading to L1 activation, DNA damage, and reduced clonogenic capacity. Remarkably, Tet2-/- HSCs are resistant to this LPS-induced L1 derepression and associated genomic instability. Furthermore, targeted degradation of L1 RNAs in WT HSCs diminishes the competitive advantage of Tet2-/- HSCs under chronic inflammatory conditions both in vitro and in vivo. These findings reveal epigenetic control of L1 elements as a previously unrecognized mechanism that links chronic inflammation to HSC impairment and clonal expansion of Tet2-mutant cells. This work highlights TE regulation as a critical determinant of hematopoietic fitness and clonal evolution under inflammatory stress.

cell biology↗

bioRxiv2025

Nuclear RNA exosome targeting onto chromatin loci in the degradation of unstable transcripts affects transcriptional programs in liver cells.

HP1, a hallmark of pericentromeric heterochromatin, is a chromatin-bound regulator of co-transcriptional processes including alternative splicing, but its role in RNA degradation remains unexplored. Here, we uncover a direct interaction between HP1 and the RNA exosome, a major RNA decay complex. In mouse embryonic liver cells, inactivation of all three HP1 isoforms led to accumulation of retrotransposon-derived RNAs and stabilization of enhancer RNAs. These changes coincided with increased activity at a subset of liver enhancers particularly sensitive to reduced exosome activity, many of which regulate genes encoding extracellular matrix components such as Col6a1 and Col6a2. Stratifying hepatocellular carcinoma samples by HP1 expression further revealed that tumors with low HP1 were marked by reduced RNA degradation, and increased expression of a similar subset of genes encoding extracellular matrix components and possibly contributing to tumor stiffness. These results suggest that HP1s impact on RNA turnover contributes to its function in cancer biology.

molecular biology↗

bioRxiv2022

Influenza A virus RNA Polymerase targets the chromatin of innate immune response genes

KEY POINTSO_LIFluPol is linked to RNAs in gene body and 3-downstream regions C_LIO_LIFluPol Chromatin-targets are involved in the cell defense C_LIO_LICap-snatching could occur everywhere during transcription elongation C_LI The influenza A virus (IAV) RNA polymerase (FluPol) primes the viral transcription by using capped 5-ends << snatched >> from host nascent RNAs. However, the exact localization of the FluPol on the genome or the timing of its snatching activity remains poorly characterized. Here, we have monitored IAV infection from the perspective of the FluPol interaction with the host chromatin template. Quantification of chromatin-bound RNAs shows a significant perturbation in host transcription that correlates with a relocalization of RNA polymerase II (RNAPII) from the gene bodies to downstream intergenic regions. This extended transcription leading to the production of RNA downstream of genes (DoGs) was previously linked to the NS1-mediated inhibition of the transcriptional termination. However, immunoprecipitation of FluPol-bound RNA in the chromatin fraction revealed that FluPol remains linked to nascent host transcripts during phases of transcriptional elongation and termination, thereby extending the window of opportunity in which cap-snatching may occur. In addition, chromatin-associated FluPol was enriched at transcription termination sites, suggesting that it may participate in the virus-induced termination defects. Finally, we observed that, rather than targeting just highly expressed genes, the FluPol was preferentially recruited to promoters activated by the viral infection and enhancers. Together, these observations suggest the FluPol uses the early immune response to target regulatory elements of defense-related genes at which it interferes with the fate of the transcripts, and possibly also limits RNAPII re-initiation by impairing the termination process. Author SummaryThe influenza A virus (IAV) exploits the transcriptional machinery of the infected cells to generate its own RNAs with the viral polymerase (FluPol) hijacking cap structures from host mRNAs. This "cap snatching" requires an interaction between FluPol and the cellular RNA polymerase (RNAPII) accumulating at transcription start sites (TSS) of genes. In parallel, another IAV factor interferes the termination of gene transcription, resulting in frequent transcription downstream of genes and reduced recycling of the RNAPII. Here, employing genome-wide ChIP assays, we show that FluPol selectively targets the TSS of infection-activated genes often associated with cellular defense mechanisms, and thereby contributing to their downregulation. In addition, we show that FluPol is not only recruited to promoters and enhancers, but also within genes, where it interacts with nascent RNAs during transcription and splicing. It is further detected beyond the 3 end of the genes, suggesting that FluPol exerts a broad influence on host transcription by affecting both transcription initiation through cap-snatching and transcription re-initiation via its involvement in the virus-induced transcription-termination defect at the end of genes.

molecular biology↗

bioRxiv2021

Alu repeats at the boundaries of regulatory elements shape the epigenetic environment of immune genes in T cells

Promoters and enhancers are sites of transcription initiation (TSSs) and carry active histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly characterized. Alu elements are good candidates for a boundary function, being highly abundant in gene-rich regions, while essentially excluded from regulatory elements. Here, we show that the interval from the TSS to the first upstream Alu accommodates all H3K4me3 and most H3K27ac marks, while excluding DNA methylation. Remarkably, the average length of this intervals greatly varies in-between tissues, being longer in stem-and shorter in immune-cells. The very shortest TSS-to-Alu intervals were observed at promoters active in T cells, particularly at immune genes, correlating with RNA polymerase II transcription through the first Alu and accumulation of H3K4me1 signal on this first Alu. Finally, DNA methylation at first-Alus was found to evolved with age, regressing from young to middle-aged, then recovering later in life. Thus, the first Alus upstream of TSSs appear as dynamic boundaries marking the transition from DNA methylation to active histone modifications at regulatory elements, while also participating in the recording of immune gene transcriptional events by positioning H3K4me1-modified nucleosomes.

molecular biology↗