Chromatin Loop Extrusion and Chromatin Unknotting [PDF]
Polymers, 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.
Andrzej Stasiak +2 more
exaly +8 more sources
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 +5 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 +2 more sources
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
Live-cell visualisation of chromatin for the study of radiation-induced chromosome aberrations [PDF]
, 2011 This thesis was submitted for the degree of Master of Philosophy and awarded by Brunel University.Chromosomes can be visualised during the metaphase stage of the cell cycle however, there are various limitations associated with the visualisation of ...
Malis, Georgios
core +7 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
Chromatin loops in gene regulation [PDF]
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2009 The control of gene expression involves regulatory elements that can be very far from the genes they control. Several recent technological advances have allowed the direct detection of chromatin loops that juxtapose distant genomic sites in the nucleus.
Stephan, Kadauke, Gerd A, Blobel
openaire +2 more sources
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
doaj +1 more source