Print Email Facebook Twitter Predicting cell population-specific gene expression from genomic sequence Title Predicting cell population-specific gene expression from genomic sequence Author Michielsen, L.C.M. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center) Reinders, M.J.T. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center) Mahfouz, A.M.E.T.A. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center) Date 2024 Abstract Most regulatory elements, especially enhancer sequences, are cell population-specific. One could even argue that a distinct set of regulatory elements is what defines a cell population. However, discovering which non-coding regions of the DNA are essential in which context, and as a result, which genes are expressed, is a difficult task. Some computational models tackle this problem by predicting gene expression directly from the genomic sequence. These models are currently limited to predicting bulk measurements and mainly make tissue-specific predictions. Here, we present a model that leverages single-cell RNA-sequencing data to predict gene expression. We show that cell population-specific models outperform tissue-specific models, especially when the expression profile of a cell population and the corresponding tissue are dissimilar. Further, we show that our model can prioritize GWAS variants and learn motifs of transcription factor binding sites. We envision that our model can be useful for delineating cell population-specific regulatory elements. Subject sequence to prediction modelssingle-cell RNA-sequencinggene expression predictiontranscriptional regulationcell populations To reference this document use: http://resolver.tudelft.nl/uuid:75f56794-1226-4ead-bd79-ffb9d591b56d DOI https://doi.org/10.3389/fbinf.2024.1347276 ISSN 2673-7647 Source Frontiers in Bioinformatics, 4 Part of collection Institutional Repository Document type journal article Rights © 2024 L.C.M. Michielsen, M.J.T. Reinders, A.M.E.T.A. Mahfouz Files PDF fbinf-04-1347276.pdf 2.54 MB Close viewer /islandora/object/uuid:75f56794-1226-4ead-bd79-ffb9d591b56d/datastream/OBJ/view