Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show that fasting induces an intestine-specific, reversible and large-scale spatial ...
Footprint-free prediction of TF binding and chromatin information One alternative to determine f-VICEs for TFs without ChIP-seq data is to rely on binding predictions using chromatin accessibility data. This motivated us to first evaluate the performance of current TF binding prediction algorithms. Mo...
the density of nucleosomes, rather than the structure of the 30-nm fiber, is what seems to distinguish different chromatin regions (e.g., nucleosome density is higher in
Conclusions At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD ...
A large fraction ofhistonesynthesis insomatic cells(unlikeXenopusoocytes and egg) is coupled toDNA replicationduring the S-phase of the cell cycle. As theDNA contentof the chromosome is doubled, so must the protein component be duplicated to reconstruct two daughter chromosomes. A normalstoichiometr...
of every eukaryotic cell. In order for the cell to express certain genes, the chromatin must be made accessible to transcription factors. Chromatin can be modified by epigenetic mechanisms likehistone modificationsduring transcription in order to inhibit or express certain genes. This process is ...
Chromatin in eukaryotic cells is a negatively charged long polymer consisting of DNA, histones, and various associated proteins. With its highly charged and heterogeneous nature, chromatin structure varies greatly depending on various factors (e.g. chemical modifications and protein enrichment) and the ...
What we think is significant, is the fact that the component structure of chromatin interaction networks is sufficiently well manifested to be taken into consideration when analysing these networks. Here we propose a method that can be used for efficient automatic discovery of such components, which...
roX2 is a unique outlier both in having the highest FC and the highest FDR (Fig. 2f), suggestive of a direct interaction with MSL2, while the weakly enriched or low FDR transcripts found throughout the X chromosome are likely proximity interactions....
Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-ce