Biology subjects

Weirich, S.

Publications and source records attributed to Weirich, S..

4 recordsLinked to original sources

bioRxiv2025

A Population Model Reveals Surprising Role of Stochastic Cell Division in Epigenetic Memory Systems

Epigenetic memory systems can store transient environmental signals in bacteria in form of DNA methylation patterns. A synthetic zinc finger protein (ZnF4) binds to the DNA in a methylation-dependent manner and represses the expression of the DNA methyltransferase CcrM. The ON-state of these systems is characterized by high CcrM expression, high methylation levels, and low ZnF4 binding, but the mechanisms ensuring long-term ON-state stability remain unclear. Measurements showed a gradual shift of cell populations from ON to OFF starting after about four days of cultivation. We use a hybrid modeling approach integrating flow-cytometry data and bulk methylation measurements to test the hypothesis that stochastic cell division is a key factor in this transition. Interestingly, model parameters cluster into two groups with opposite effects of cell division rates on ON-state stability. Experiments under varying growth conditions show that faster cell division increases memory stability -- an initially unexpected result. Model simulations provide a potential explanation for this observation and deepen our understanding about the mechanisms and timing of the ON/OFF switch in individual cells.

systems biology↗

bioRxiv2024

SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain

SETDB1 is a major H3K9 methyltransferase involved in heterochromatin formation and silencing of repeat elements. It contains a unique Triple Tudor Domain (3TD) which specifically binds the dual modification of H3K14ac in the presence of H3K9me1/2/3. Here, we explored the role of the 3TD H3-tail interaction for the H3K9 methylation activity of SETDB1. We generated a binding reduced 3TD mutant and demonstrate in biochemical methylation assays on peptides and recombinant nucleosomes containing H3K14ac analogs, that H3K14 acetylation is crucial for the 3TD mediated recruitment of SETDB1. We also observe this effect in cells where SETDB1 binding and activity is globally correlated with H3K14ac, and KO of the H3K14 acetyltransferase HBO1 causes a drastic reduction in H3K9me3 levels at SETDB1 dependent sites. Further analyses revealed that 3TD particularly important at specific target regions like L1M repeat elements, where SETDB1 KO cannot be efficiently reconstituted by the 3TD mutant of SETDB1. In summary, our data demonstrate that the H3K9me3 and H3K14ac are not antagonistic marks but rather the presence of H3K14ac is required for SETDB1 recruitment via 3TD binding to H3K9me1/2/3-K14ac and establishment of H3K9me3.

biochemistry↗

bioRxiv2023

E2F1 methylation by SETD6 regulates SETD6 expression via positive feedback mechanism

The protein lysine methyltransferase SETD6 has been shown to influence different cellular activities and are critically involved in the regulation of diverse developmental and pathological processes. However, the upstream signal which regulates the mRNA expression of SETD6 is not known. Bioinformatics analysis revealed that SETD6 promoter has a binding site for the transcription factor E2F1. Using various experimental systems, we confirmed that E2F1 binds to the SETD6 promoter and regulates SETD6 mRNA expression. Our further observation that this phenomenon is SETD6 dependent, suggested that SETD6 and E2F1 are linked. We next demonstrate that SETD6 mono-methylates E2F1 specifically at K117 in-vitro and in cells. Finally, we show that E2F1 methylation at K117 positively regulates the expression level of SETD6 mRNA. Depletion of SETD6 or overexpression of E2F1 K117R mutant which canot be methylated by SETD6, reverses the effect. Taken together, our data provide evidence for a positive feedback mechanism which regulates the expression of SETD6 by E2F1 in a SETD6 methylation dependent manner and highlight the importance of protein lysine methyltransferases and lysine methylation signaling in the regulation of gene transcription.

molecular biology↗

bioRxiv2023

The T1150A cancer mutant of the protein lysine dimethyltransferase NSD2 can introduce H3K36 trimethylation

Somatic mutations in protein lysine methyltransferases are frequently observed in cancer cells. We show here that the NSD1 mutations Y1971C, R2017Q and R2017L observed mostly in solid cancers are catalytically inactive suggesting that NSD1 acts as tumor suppressor gene in these tumors. In contrast, the frequent T1150A in NSD2 and its T2029A counterpart in NSD1, both observed in leukemia, are hyperactive and introduce up to H3K36me3 in biochemical and cellular assays, while wildtype NSD2 and NSD1 only generate up to H3K36me2. MD simulations with NSD2 revealed that H3K36me3 formation is possible due to an enlarged active site pocket of T1150A and loss of direct contacts of T1150 to critical residues which regulate the product specificity of NSD2. Bioinformatic analyses of published data suggest that the NSD2 T1150A mutation in lymphocytic leukemia could alter gene regulation by antagonizing H3K27me3 finally leading to the upregulation of oncogenes.

molecular biology↗