Neurogenesis in the neocortex follows a precise spatiotemporal sequence. The transcriptional and translational dynamics that control this process remain inadequately understood. Integrating kinetic analysis of gene expression (translation, transcription, and degradation rates) will enhance our ability to distinguish between diverse cell types, offering deeper insights into its developmental mechanisms.
Transposable elements (TEs) are a major constituent of human genes, occupying approximately half of the intronic space. During pre-messenger RNA synthesis, intronic TEs are transcribed along with their host genes but rarely contribute to the final mRNA product because they are spliced out together with the intron and rapidly degraded. Paradoxically, TEs are an abundant source of RNA-processing...
Transcription elongation by RNA polymerase II (Pol II) has emerged as a regulatory hub in gene expression, with TFIIS being one of the oldest and most highly conserved transcription elongation factors. Canonically, TFIIS helps release Pol II from backtracking and prolonged pauses to enable productive RNA synthesis. However, recent evidence points towards a broader role for TFIIS proteins. In...
How is time encoded in the products of gene expression in the brain? This critical question still needs to be answered despite the intense research on gene expression activity during neuronal development. We hypothesize that different transcription and translation kinetics guide the diversification and specification of neuronal lineages in the brain, within and between species: proteins being...
In the intricate realm of mammalian gene regulation, cis-regulatory elements play a crucial role in orchestrating precise gene expression during development. To exert their regulatory effect, they must come into physical contact with the promoters of their target genes, which is thought to be facilitated by loop extrusion. Here, ring-shaped cohesin complexes enhance the contacts within defined...
Predicting disease-specific gene sub-networks is a crucial step in network propagation, which operates on the principle that genes associated with a particular trait are likely to interact within molecular net-works. Many bioinformatics methods have been proposed in recent years to reduce the complexity of gene/protein networks. However, current module identification methods have limitations...
X-Chromosome Inactivation (XCI) is a process that has evolved in female mammals to compensate for the different doses of X-chromosomal genes between the sexes. While this process is known to be driven by the expression of the lncRNA Xist from one of the two X chromosomes, it remains to be elucidated what causes Xist expression to occur specifically in females but not in males in the first...
Mesenchymal stromal cells (MSC) are fibroblast-like non-hematopoietic cells with self-renewal and differentiation capacity, and thereby great potential in regeneration and wound healing. Currently, the cultured MSCs from different tissues and species are used in pre-clinical and clinical studies such as disease and developmental modelling in- and ex vitro, as well as (xeno)transplantation....
Biomolecular condensates play a critical role in regulating nearly every aspect of cellular functions. Despite the growing understanding of their biological roles, the precise molecular constituents responsible for these functions remain largely unidentified. Current techniques face significant challenges in accurately isolating target condensates from cells and specifically assaying their...
Epigenetic 'readers' are essential for genome regulation, recognizing DNA and histone modifications to influence chromatin organization and gene expression. Dysfunction in these proteins is associated with diseases such as cancer. PHF13, an H3K4me3 reader, modulates chromatin processes and is aberrantly expressed in various cancers. This study investigates how PHF13's expression, chromatin...
In mammals, the long non-coding RNA Xist, master regulator of X-chromosome inactivation (XCI), is expressed from one out of two X chromosomes in female cells. The fact that one Xist allele is stably silenced, while the other one is expressed, indicates epigenetic memory. We have shown previously that RE57, a promoter-proximal regulatory DNA element essential for Xist upregulation, gains the...
Cell states and their resistance to environmental stimuli are fundamentally governed by chromatin dynamics. Treatment of embryonic stem cells (ESCs) with mTOR inhibitors, such as INK128, induces a dormancy state marked by elevated expression of pluripotency markers alkaline phosphatase 1 and SSEA1, resulting in a more homogeneous pluripotent population as determined by flow-assisted cell...
The human bromo- and extra-terminal domain (BET) protein family consists of ubiquitously expressed BRD2, BRD3, BRD4, and the testis-specific BRDT. Although the BET proteins have similar structural features such as two bromodomains and an extra-terminal protein-protein interaction domain, the individual roles and potential shared functions have remained unclear. Research by our team recently...
Gene regulatory networks control the transcription of developmental genes. Each connection in the network is formed through intricate interactions between transcription factors (TF) and DNA binding sequences in cis-regulatory elements (RE). However, identifying several of these functional TF-RE interactions at once remains a challenge. Massively parallel reporter assays (MPRA) allow...
Morphogenesis is orchestrated by precise spatio-temporal gene expression controlled by regulatory landscapes. It is still unknown to what extent the organisation of enhancers within a locus dictates their overall activity. How does the layout of the regulatory landscape impact gene expression during development?
To address this question, we rearranged the mouse Bmp2 landscape by altering...
Developmental gene expression patterns result from the combined activities of multiple Cis-Regulatory Modules (CRMs) across regulatory landscapes. Different cooperation modes between CRMs have been reported, including additive, synergistic and repressive, mainly through reporter assays and combinatorial deletion experiments of few CRMs. However, to understand evolutionary traits and genetic...
X-chromosome inactivation (XCI) is the process by which female mammals inactivate one of their two X chromosomes to compensate the dosage imbalance of X-linked genes. The long non-coding RNA (lncRNA) Xist is the master regulator of XCI and it is upregulated from one of the two X chromosomes promoting the silencing of the whole chromosome in cis. Even though a wide range of Xist regulators...
Transposable elements (TEs) are mobile viral elements present in virtually all eukaryotic genomes. TE expansion poses a threat to genome integrity and different host defence mechanisms have been described, mainly focusing on prevention of TE insertion. However, until recently, it was unclear how pre-mRNA splicing is robustly accomplished while repressing exonisation of intronic TEs transcribed...
The aim of our study is to provide a comprehensive and comparative snapshot of the proto-epigenomic landscape in the three major subtypes of Renal Cell Carcinoma (RCC). Here we perform epigenomic and proteomic analyses on 40 patients spanning clear cell (ccRCC), papillary (pRCC) and chromophobe (chRCC) renal cell carcinoma. Our simultaneous profiling of the DNA methylation and...
Noncoding RNAs (ncRNAs) are a large family of RNAs that are not coding for known proteins. About 17 categories of non-coding RNA molecules have been identified so far. Among them, long ncRNAs (lncRNAs) and microRNAs (miRNAs) are the most studied classes of ncRNAs potentially involved in pathological conditions (Ratti et al. 2020).
While most of the efforts in the area have been focused on...
You may think that mass spectrometry, flow cytometry and genomics generate loads of data. But have you ever thought about the pixel? A modern microscope typically records 4 to 12 million individual data points per image, the pixels, and this up to 50 times per second resolved in space and time. An average confocal microscope is capable to count the photons within 120x120 nm. In image analysis...
Long-read transcriptome sequencing (LRTS) offers a direct method for capturing full-length transcripts within a cellular system. Unlike next-generation sequencing (NGS), LRTS circumvents the issue of ambiguous alignment by eliminating the need for fragmentation during library preparation. This makes it particularly adept at accurately detecting isoforms, alleles, and transcripts from gene...
Identifying differentially methylated regions (DMRs) among samples or multiple groups in an unsupervised manner remains challenging due to the computational complexity. Here, we present metilene3, a fast and sensitive approach to call DMRs without prior information needed and to construct differentially methylated trees (DMTrees) for sample clustering and linkage discovery. Metilene3 detects...
Paediatric leukaemia remains the most prevalent cancer among children and teens, with acute lymphocytic leukaemia (ALL) accounting for approximately 80% of cases and exhibiting a higher prevalence in males. Among B-ALL subtypes, the TCF3(E2A)-PBX1 fusion t(1;19) is the third most common, present in about 3-5% of B-ALL cases. This translocation results in aberrant protein products with...
Xist, the master regulator of X-chromosome inactivation (XCI) in mammals, is upregulated in the epiblast during the formative phase of pluripotency, specifically in females. In the past, its regulation has been tightly linked to repression during naive pluripotency. However the identity of activators at the onset of XCI remains unknown. To fill this gap, we perform a comprehensive CRISPR...
It is now generally accepted that, different classes of regulatory elements generate specific chromatin profiles: Nucleosomes adjacent to promoters are marked by histone modification H3K27ac and H3K4me3, and the promoters themselves are located in accessible regions. Active enhancers also lie in accessible regions but the neighbouring nucleosomes are marked by H3K27ac and H3K4me1. However,...
Throughout embryogenesis, Polycomb repressive complex 2 (PRC2) silences transcription via its histone-modifying activity to establish and maintain distinct gene expression that drives cellular plasticity and identity. However, the spatial and temporal dynamics of PRC2 during development and its molecular mechanisms that control proper embryogenesis remain largely unknown. This is especially...
During tumorigenesis, normal cells undergo dramatic changes at multiple levels, from morphological to genetic and epigenetic ones. Often, multiple genetic alterations accumulate that can be classified based on their impact on tumor fitness into driver and passenger events. Patterns of somatic mutations are characteristic for different cancer types, e.g. the ratio of point mutations to...
Whether you simply ask if your gene of interest is expressed in a cell, where the cell is located in 3D, and how to proof hypothesis indicated by sequencing and omics-data: Mic-Service can help you to visualize biological events across scales in space and time. As a central microscopy facility, we offer comprehensive support for a broad range of imaging techniques ranging from wide-field...
The development of the micropeptide ‘killswitch’ as a tool to study the intrinsic function of biomolecular condensates on a physiological level has made great progress so far. It makes use of the killswitch solidifying biomolecular condensates, and can be used in a targeted manner. However, the molecular mechanism on how the killswitch acts is not fully understood. The killswitch is composed...
The maturation of lineage-committed embryonic hepatocytes requires timed activation of gene regulatory networks (GRNs) while silencing embryonic programs to achieve adult hepatic metabolic functions. Our knowledge of the key transcription regulators governing GRN rewiring during late development remains incomplete, hindering the derivation of functional hepatocytes in vitro. To address this,...
Transcriptional regulation, governed by interactions between transcription factors (TFs) and DNA, is crucial for cellular function. We have previously shown that TF activity is sub-maximal and that we can enhance TFs transactivation by changing a sequence feature related to phase separation dynamics at the expense of binding specificity, thus indicating that TF encode a trade-off between...
The COVID-19 pandemic provided critical insights into basic immunology, validating longstanding concepts with large-scale observations. Thereby, the rapid development and deployment of effective vaccines, achieved through the synergy of basic and applied research, significantly reduced global morbidity and mortality. However, there was a notable disillusionment as an anticipated sterilizing...
Splicing and transcription complexes seem to directly communicate to coordinate their outputs, even though the mechanisms underlying this cross-talk remain unclear.
Two models for the recognition of the splicing unit were proposed: intron- and exon-definition. In the first, the spliceosome recognizes the intron as the splicing unit and places the basal splicing machinery across it. This is...
The presence of hair is one of the characterising traits of the mammalian clade, but this structure has also widely diversified across species: the development of spines in hedgehogs serves as an iconic example. Hairs and spines undergo comparable developmental steps, starting with the formation of placodes on the skin surface, which will in time invaginate into the dermis and create the root...
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide...
