Biology subjects

Steinbrecht, D.

Publications and source records attributed to Steinbrecht, D..

3 recordsLinked to original sources

bioRxiv2025

Perturb-seq identifies TCF7 as a central nexus linking MAPK- and Wnt-driven gene expression

The MAPK pathway is a central signaling cascade whose dysregulation contributes to numerous diseases. While its upstream regulation is well studied, the mechanisms by which MAPK activation leads to diverse transcriptional outcomes remain incompletely understood. To address this shortcoming, we mapped the target gene sets controlled by 22 RAF-inducible transcription factors using targeted Perturb-seq and integrated these data with time-resolved transcriptional profiling. Network reconstruction revealed a topology dominated by two central hubs, EGR1 and FOS, which co-regulate partially overlapping target gene sets. In addition, we uncovered a positive feedback loop between EGR1, a canonical RAF-MAPK effector, and TCF7, a transcription factor typically linked to Wnt signaling. Through this interaction, TCF7 emerges as a nexus that integrates MAPK and Wnt pathway inputs. Together, these findings define the architecture of RAF-MAPK-driven transcriptional regulation and demonstrate how cross-talk between oncogenic signaling pathways can be encoded in transcriptional networks. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/694273v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@53d6d5org.highwire.dtl.DTLVardef@3d6b5borg.highwire.dtl.DTLVardef@5333e6org.highwire.dtl.DTLVardef@74519e_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting

Eukaryotic mRNAs are transcribed, processed, translated, and degraded in different subcellular compartments. Here, we measured mRNA flow rates between subcellular compartments in mouse embryonic stem cells. By combining metabolic RNA labeling, biochemical fractionation, mRNA sequencing, and mathematical modeling, we determined the half-lives of nuclear pre-, nuclear mature, cytosolic, and membrane-associated mRNAs from over 9000 genes. In addition, we estimated transcript elongation rates. Many matured mRNAs have long nuclear half-lives, indicating nuclear retention as the rate-limiting step in the flow of mRNAs. In contrast, mRNA transcripts coding for transcription factors show fast kinetic rates, and in particular short nuclear half-lives. Differentially localized mRNAs have distinct rate constant combinations, implying modular regulation. Membrane stability is high for membrane-localized mRNA and cytosolic stability is high for cytosol-localized mRNA. mRNAs encoding target signals for membranes have low cytosolic and high membrane half-lives with minor differences between signals. Transcripts of nuclear-encoded mitochondrial proteins have long nuclear retention and cytoplasmic kinetics that do not reflect co-translational targeting. Our data and analyses provide a useful resource to study spatiotemporal gene expression regulation.

systems biology↗

bioRxiv2024

Targeted Perturb-seq Reveals EGR1 and FOS as Key Regulators of the Transcriptional RAF-MAPK Response

The MAPK pathway is an important cellular signaling cascade whose dysregulation causes a variety of diseases. While the upstream regulators of this cascade have been extensively characterized, the understanding of how its activation translates into different transcriptional responses remains poorly understood. This study attempts to fill this knowledge gap by using targeted Perturb-seq against 22 transcription factors in an inducible model system for RAF-MAPK signaling. A topology-based modeling approach is applied to the obtained data to construct a directional interaction network. By removing coherent feed-forward loops and integrating the expression kinetics of transcription factors, a parsimonious network structure is derived that distinguishes direct from indirect interactions between the investigated transcription factors and their targets. In particular, EGR1 and FOS are found to act as orthogonal upstream regulators of the RAF-MAPK response. The results presented here provide valuable insights into the organization of the transcriptional network downstream of RAF-MAPK signaling and thus provide a basis for a better understanding of this complex process.

systems biology↗