In JOSS, Feb 24, 2021
A multitude of proteins bind to DNA at regulatory regions to control the expression of neighbouring genes. Their binding can be revealed by chromatin accessibility assays such as DNase-seq, MNase-seq or ATAC-seq. The size of the sequencing fragments generated by these assays, as well as their …
In F1000Research, Feb 3, 2021
Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify...
In Genome Res., Oct 22, 2020
Despite increasingly detailed knowledge of gene expression patterns, the regulatory architectures that drive them are not well understood. To address this, we compared transcriptional and regulatory element activities across five adult tissues of C. elegans, covering ∼90% of cells, and defined …
In Nature, Sep 9, 2020
Nuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation are not well understood. Studying how the lncRNA Xist establishes the inactive-X-chromosome (Xi)-compartment, we found that the Xist RNA-binding-proteins …
In J. Cell Biol., Sep 7, 2020
Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes or tumor suppressors. However, most of the altered regions are devoid of known cancer drivers. Here, we identify lncRNAs frequently lost or amplified in cancer. Among them, we found amplified lncRNA …
In eLife, Oct 26, 2018
An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 …
In Curr. Opin. Cell Biol., Jun 1, 2018
Since the discovery of chromosome territories, it has been clear that DNA within the nucleus is spatially organized. During the last decade, a tremendous body of work has described architectural features of chromatin at different spatial scales, such as A/B compartments...