Publications by authors named "Dries Rombaut"
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View Article and Find Full Text PDFSingle cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3' end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings.
View Article and Find Full Text PDFArticle Synopsis
- Long intergenic non-coding RNAs (lincRNAs) are important in cancer, especially neuroblastoma, where they help control gene activity.
- Researchers studied RNA from neuroblastoma tumors and cells to find many lincRNAs that are linked to bad outcomes for patients and are connected to key cancer genes like MYCN, ALK, and PHOX2B.
- The study also found that certain lincRNAs might help regulate these key genes, showing how they could be important for understanding and treating neuroblastoma better.
Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with features of a cell identity transcription factor, driving proliferation through activation of p21-DREAM repressed FOXM1 target genes.
View Article and Find Full Text PDFBackground: Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA (lncRNA) annotation are mainly based on evolutionary constraints, which may result in false negatives due to the overall limited conservation of lncRNAs.
Results: To tackle this problem we have developed the Zipper plot, a novel visualization and analysis method that enables users to simultaneously interrogate thousands of human putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity.