Before technically defining chromatin, let’s understand what it is. Let’s look at the following diagram to understand chromatins:Figure 1: Chromatin fiber. Credit: Genome.gov. Biology definition: Chromatin is a substance made up of DNA or RNA and proteins, such as histones. It condenses ...
As discussed previously, the full-stack model has a number of advantages, such as being able to differentiate constitutive from cell type-specific annotations and simplifying the overall genome annotation across cell types, in that there is a single genome annotation per position [21]. However, th...
Salt-dependent aggregation of chromatin, which now is thought to be a phase separation process, has been studied since the 1950s, although for most of this time the phenomenon was considered to be irreversible precipitation of the chromatin from solution. We start this section by summarizing the ...
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...
Previous work has shown that there are three types of canonical sequences that strongly regulate nucleosome positioning and thus chromatin accessibility: putative nucleosome-positioning elements, putative nucleosome-repelling sequences, and homopolymeric runs of A/T. It is postulated that these elements ...
polymer chain with each bead representing chromatin of length in the range ~1 kb to 1Mb12,13,14,15,16,17,20,21,22,23,24. However, physical dimensions and elastic properties of chromatin are not well understood. What is the diameter of a 1 kb, 10 kb, or 100 kb chromatin ...
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 ...
Birds exhibit a unique asymmetry in terms of gonad development. The female left gonad generates a functional ovary, whereas the right gonad regresses. In males, both left and right gonads would develop into testes. How is this left/right asymmetry established only in females but not in males ...
The BIND&MODIFY method is based on the indirect labeling of DNA regions bound to the protein of interest using an engineered recombinant fusion protein, protein A-M.EcoGII (pA-M.EcoGII), whose methyltransferase activity can be locally controlled (Fig.1a). The recently characterized adenosine met...
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 ...