Cells whose accessibility landscape has been profiled with scATAC-seq cannot readily be annotated to a particular cell type. In fact, annotating cell-types in scATAC-seq data is a challenging task since, unlike in scRNA-seq data, we lack knowledge of "marker regions" which could be used for cell-type annotation. Current annotation methods typically translate accessibility to expression space...
Liver disease is the only major disease where mortality is rising every year. The Covid-19 pandemic also had a major impact with a 21% death increase from liver disease in 2021 compared to 2019 in the UK. Thus, liver diseases are global health care challenge. The main reason of this situation lies in the absence of curative option for end stage liver disease with the only treatment being organ...
Stem cell-based embryo models provide a means to study the inconspicuous processes of embryonic development at cellular and molecular levels. Various models of early mouse development have been developed over the last years, such as gastruloids and trunk like structures (TLS), that recapitulate symmetry breaking, axial elongation, along with transcriptional and structural features of the...
CRISPR knock-out (KO) screens measure the dependency of a cell line to the inactivation of specific genes in a high-throughput manner [1]. In addition, repeating KO screen with drugs highlights potential drug resistance and sensitivity mechanisms. Repeated over multiple cell lines with recurrent alterations, this allows the extraction of biomarkers driving drug dependencies. Those biomarkers...
Cis-regulatory elements such as promoters and enhancers coordinate the cell-type specific transcription of their target genes. Promoters sit directly upstream of the transcription start site, while often many partially redundant enhancers are distributed in extended regulatory domains surrounding their target gene. Despite their significance, the mechanisms by which enhancers cooperate and...
Extraembryonic cells share a characteristic DNA methylation landscape that is globally distinct from the somatic methylome found in virtually all embryonic and adult cell types. This non-canonical methylome is characterised by intermediate methylation globally and at hundreds of CpG islands. Why these cells, which form supporting structures for the embryo, utilize an alternate regulatory...
Most mammalian genes are interrupted with introns that need to be spliced out to produce a functional mRNA following transcription. Splicing is a multi-step, ATP-dependent process conserved in all Eukaryotes, and under defined conditions can be carried out in cell-free lysates. In mammalian nuclei, large, irregularly shaped multi-component membraneless organelles, known as Nuclear Speckles...
