Closing the loops: chromatin loop dynamics after DNA damage [PDF]
NucleusChromatin is a dynamic polymer in constant motion. These motions are heterogeneous between cells and within individual cell nuclei and are profoundly altered in response to DNA damage.
Pierre-Alexandre Vidi +3 more
doaj +6 more sources
Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions [PDF]
Nature CommunicationsAlthough emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood.
Tianxin Liu +9 more
doaj +3 more sources
Chromatin Loop Extrusion and Chromatin Unknotting. [PDF]
Polymers (Basel), 2018 It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium.
Racko D +3 more
europepmc +8 more sources
A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture. [PDF]
PLoS ONE, 2015 Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli.
Teddy Jégu +13 more
doaj +3 more sources
Active loop extrusion modulates the mechanical response of chromatin under tension
Physical Review ResearchChromosomes are complex biopolymers folded into dynamic loops via a loop-extrusion process and may experience various mechanical forces in vivo. We develop a force-dependent model of chromatin loop extrusion and investigate its mechanical consequences on
Hossein Salari, Daniel Jost
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InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop. [PDF]
Brief Bioinform, 2023 Abstract Deciphering cell-type-specific 3D structures of chromatin is challenging. Here, we present InferLoop, a novel method for inferring the strength of chromatin interaction using single-cell chromatin accessibility data. The workflow of InferLoop is, first, to conduct signal enhancement by grouping nearby cells into bins, and then ...
Zhang F +9 more
europepmc +4 more sources
Extrusion of chromatin loops by a composite loop extrusion factor [PDF]
Physical Review E, 2021 12 pages, 7 ...
Hao Yan +5 more
openaire +3 more sources
Human tumor viruses: induction of three-dimensional alterations in the host genome structure
Frontiers in Microbiology, 2023 Certain viruses called tumor viruses or oncoviruses are capable to change the gene expression pattern of distinct human or animal cell types in tissue culture, resulting in uncontrolled proliferation as well as a change in the social behavior of the ...
Janos Minarovits
doaj +1 more source
ZNF143 in Chromatin Looping and Gene Regulation [PDF]
Frontiers in Genetics, 2020 ZNF143, a human homolog of the transcriptional activator Staf, is a C2H2-type protein consisting of seven zinc finger domains. As a transcription factor (TF), ZNF143 is sequence specifically binding to chromatin and activates the expression of protein-coding and non-coding genes on a genome scale.
Bingyu Ye +30 more
openaire +3 more sources
Prediction of CTCF loop anchor based on machine learning
Frontiers in Genetics, 2023 Introduction: Various activities in biological cells are affected by three-dimensional genome structure. The insulators play an important role in the organization of higher-order structure.
Xiao Zhang +7 more
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