Mapping chromatin loops in single cells [PDF]
Trends in Genetics, 2022 Recent advances in high-throughput chromatin conformation capture (Hi-C) technologies at the single-cell level enable the identification of cell type-specific chromatin loops directly from complex tissues. This may help to interpret noncoding variants identified by genome-wide association studies (GWAS) in disease-relevant cell types. We briefly review
Ming Hu, Miao Yu
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DNA loops after cell lysis resemble chromatin loops in an intact nucleus
The Ukrainian Biochemical Journal, 2018 The comet assay has proved itself to be not only a method of detection of DNA damages at the level of individual cells but also an approach for investigation of spatial organization of DNA loop domains in nucleoids.
K. S. Afanasieva +2 more
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Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize. [PDF]
PLoS Biology, 2020 In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear.
Yalin Liu +5 more
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Comprehensive Predictions of Mef2-Mediated Chromatin Loops, Which May Inhibit Ubx Binding by Blocking Low-Affinity Binding Sites [PDF]
Journal of Developmental BiologyGene regulation depends on the interaction between chromatin-associated factors, such as transcription factors (TFs), which promote chromatin loops to ensure tight contact between enhancer and promoter regions.
Katrin Domsch
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DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration [PDF]
BMC BioinformaticsBackground Chromatin loops are critical for the three-dimensional organization of the genome and gene regulation. Accurate identification of chromatin loops is essential for understanding the regulatory mechanisms in disease.
Junfeng Wang +4 more
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Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters [PDF]
Epigenetics & ChromatinChromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is ...
Stefan A. Koestler +4 more
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CD-Loop: a chromatin loop detection method based on the diffusion model
Frontiers in GeneticsMotivationIn recent years, there have been significant advances in various chromatin conformation capture techniques, and annotating the topological structure from Hi-C contact maps has become crucial for studying the three-dimensional structure of ...
Jiquan Shen, Yang Wang, Junwei Luo
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Extrusion of chromatin loops by a composite loop extrusion factor. [PDF]
Phys Rev E, 2021 12 pages, 7 ...
Yan H +5 more
europepmc +5 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
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SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data [PDF]
Nature Methods, 2021 Guoqiang Li +2 more
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