Here we combine quantitative fluorescent in situ hybridisation experiments in human cells with polymer modelling to unravel mechanisms of chromatin folding. We show that chromatin becomes more compact after depletion of looping proteins. This is remarkable, since polymer models describing chromatin predict decompaction.
Results show that chromatin becomes more compact after reducing the concentration of these two looping proteins. The molecular basis for this counter-intuitive behaviour is explored by polymer modelling usingy the Dynamic Loop model (Bohn M, Heermann DW (2010) Diffusion-driven looping provides a consistent framework for chromatin organization.
Depletion of ATP, which captures Mg 2+ in the cell, increased the level of free Mg 2+ [37, 42] and led to stronger chromatin condensation and reduced chromatin motion [42].
RNA depletion by RNase A causes chromatin to precipitate out of solution, which falsely reduces the detection of PRC2 and may lead to the incorrect conclusion that PRC2 cannot bind chromatin ...
Most studies on how CTCF depletion or transcription inhibition impact chromatin architecture were carried out in asynchronously growing cells and thus do not distinguish requirements for ...
Recent technological developments allow the acute depletion of proteins on a minute-to-hour timescale in cells. 53,54 Combined with single-cell genomics, quantitative proteomics, and live-imaging technologies, these enable us to monitor immediate changes in chromatin organization, DNA replication, and cell-cycle progression, revealing the early ...
This study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation.
Further analysis revealed that CAF-1 depletion lowered histone mRNA levels, leading to histone imbalance and delayed chromatin maturation in S phase.
Here we combine quantitative fluorescent in situ hybridisation experiments in human cells with polymer modelling to unravel mechanisms of chromatin folding. We show that chromatin becomes more compact after depletion of looping proteins. This is remarkable, since polymer models describing chromatin predict decompaction.
Klein-Brill et al. track changes in nucleosome positioning at a detailed time course during rapid depletion and re-introduction of RSC, an essential ATP-dependent chromatin remodeler. Measuring changes in mRNA transcripts structure and levels they dissect how shifts in nucleosome positions affect choice of exact transcription start site.
We present a Monte Carlo model for genome folding at the 30-nm scale with focus on linker-histone and nucleosome depletion effects. We find that parameter distributions from experimental data do not lead to one specific chromatin fiber structure, but instead to a distribution of structures in the chromatin phase diagram. Depletion of linker histones and nucleosomes affects, massively, the ...
Transcription factors can undergo PS, incorporating chromatin regions containing enhancers and promoters within condensates to enhance long-range interactions for transcriptional activation. 18 ATAC-seq analysis showed that global chromatin accessibility decreased upon ZHX2 depletion under hypoxia (Figures 5 A and 5B), with 78% of the reduction ...
Comparison of diploid and polytene chromosomes in Drosophila melanogaster [35] Cell cycle dynamics and condensin-dependent chromatin reorganization in Schizosaccharomyces pombe [36] Comparison of G1 and M phase chromosomes in Saccharomyces cerevisiae and the distinct effects of cohesin and condensin depletion [37]
It also agrees with the recent finding that AHNAK depletion triggers an elevated p53 response due to enhanced 53BP1 chromatin binding and condensate formation 18 as does the loss of TIRR, a ...
The signal intensity of mitotic chromatin labeled by H2B-HaloTag-TMR also increased (Fig. 4C), suggesting a rise in depletion force and induced hypercondensation of mitotic chromosomes upon hypertonic treatment.
