Biology subjects

Kolter, C.

Publications and source records attributed to Kolter, C..

3 recordsLinked to original sources

bioRxiv2025

Specificity and exon target space of splicing modifying compounds

Modulation of splicing has become an established therapeutic strategy, with proven clinical applications and continued potential to target specific exons to influence gene expression. Recent advancements led to the identification of small molecule splicing modifiers such as Risdiplam and Branaplam. These compounds induce the inclusion of exons that are typically skipped due to their weak 5' splice site. While Risdiplam has a preference to induce exons with a N-3G-2A-1 sequence at the 3' exon end, Branaplam has a proclivity towards introducing A-3G-2A-1 -ending exons. However, the variables that determine the selectivity and specificity of splicing modulators are still not completely understood, as evidenced by the hundreds of unaffected N-3G-2A-1 -ending exons present in the human genome. In this study, we delve into the molecular mechanisms governing the specificity of splicing-modifying compounds, focusing on their interactions with RNA structures at splice sites. Using biochemical assays, whole transcriptome analyses, and genetic perturbation approaches, our findings reveal contributions of primary sequence codependencies that help determine the required secondary structural conformation, thus governing responsiveness to splicing modulator induction. Based on these learnings, we were able to reprogram the specificity of splicing modulators by genetic manipulation of the U1 snRNA component of the spliceosome. Our findings further the understanding of splicing modulators and might help to identify new targets and compounds.

molecular biology↗

bioRxiv2024

Benchmarking tools for transcription factor prioritization

Spatiotemporal regulation of gene expression is controlled by transcription factor (TF) binding to regulatory elements, resulting in a plethora of cell types and cell states from the same genetic information. Due to the importance of regulatory elements, various sequencing methods have been developed to localise them in genomes, for example using ChIP-seq profiling of the histone mark H3K27ac that marks active regulatory regions. Moreover, multiple tools have been developed to predict TF binding to these regulatory elements based on DNA sequence. As altered gene expression is a hallmark of disease phenotypes, identifying TFs driving such gene expression programs is critical for the identification of novel drug targets. In this study, we curated 84 chromatin profiling experiments (H3K27ac ChIP-seq) where TFs were perturbed through e.g., genetic knockout or overexpression. We ran nine published tools to prioritize TFs using these real-world data sets and evaluated the performance of the methods in identifying the perturbed TFs. This allowed the nomination of three frontrunner tools, namely RcisTarget, MEIRLOP and monaLisa. Our analyses revealed opportunities and commonalities of tools that will help to guide further improvements and developments in the field.

bioinformatics↗

bioRxiv2024

The transcription factor ZNF469 regulates collagen production in liver fibrosis

Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the worlds population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.

molecular biology↗