Biology subjects

Bujnowska, M.

Publications and source records attributed to Bujnowska, M..

3 recordsLinked to original sources

bioRxiv2025

Cell state plasticity emerging from co-regulated, competitive, and configurable interactions within the AP-1 network

AP-1 transcription factors have been implicated in cellular plasticity, differentiation-state heterogeneity, and phenotype switching in response to cancer therapies. Although AP-1 states, defined by combinatorial expression of AP-1 proteins, are heterogeneous within cell populations, only a subset of possible states is observed. How these states are constrained, why their distributions vary across cell populations, and what drives their phenotypically consequential transitions remain unclear. We develop a mechanistic ODE model of the AP-1 network, capturing dimerization-dependent, co-regulated, and competitive interactions. Calibrated to single-cell protein measurements across diverse melanoma populations and combined with statistical learning, the model reveals network features explaining population-specific AP-1 state distributions. These features correlate with MAPK signaling across tumor lines and individual cells. The model predicts and experiments validate adaptive AP-1 reconfiguration following MAPK inhibition, driving a dedifferentiated, therapy-resistant state that is attenuated through model-guided perturbations. These findings establish AP-1 as a configurable network and provide a quantitative framework for modulating AP-1 driven cell-state plasticity.

systems biology↗

bioRxiv2020

Kinetic model of small RNA-mediated regulation suggests that a small RNA can regulate co-transcriptionally

Small RNAs (sRNAs) are important regulators of gene expression in bacteria, particularly during stress responses. Many genetically and biochemically well characterized sRNAs regulate gene expression post-transcriptionally, by affecting translation and degradation of the target mRNA after they bind to their targets through base pairing. However, how regulation at each of these levels quantitatively contributes to the overall efficacy of sRNA-mediated regulation is not well understood. Here we present a general approach combining imaging and mathematical modeling to determine kinetic parameters at different levels of sRNA-mediated gene regulation. Unexpectedly, our data reveal that certain previously characterized sRNAs are able to regulate some targets co-transcriptionally, rather strictly post-transcriptionally, and suggest that sRNA-mediated regulation can occur early in the mRNAs lifetime, perhaps as soon as the sRNA binding site is transcribed. In addition, our data suggest several important kinetic steps that may determine the efficiency and differential regulation of multiple mRNA targets by an sRNA. Particularly, binding of sRNA to the target mRNA is likely the rate-limiting step and may dictate the regulation hierarchy observed within an sRNA regulon.

biophysics↗

bioRxiv2020

Deoxyribozyme-based Method for Site-specific Absolute Quantification of N6-methyladenosine Modification Fraction

N6-methyladenosine (m6A) is the most prevalent modified base in eukaryotic messenger RNA (mRNA) and long noncoding RNA (lncRNA). Although candidate sites for m6A modification are identified at the transcriptomic level, site-specific quantification methods for m6A modifications are still limited. Herein, we present a facile method implementing deoxyribozyme that preferentially cleaves the unmodified RNA. We leverage reverse transcription and real-time quantitative PCR along with key control experiments to quantify the absolute methylation fraction of specific m6A sites. We validate the accuracy of the method using synthetic RNA with controlled methylation fraction and apply our method on several endogenous sites that were previously identified in sequencing-based studies. This method provides a time and cost-effective approach for absolute quantification of the m6A fraction at specific loci, expanding the current toolkit for studying RNA modifications.

biochemistry↗