CD-Loop: a chromatin loop detection method based on the diffusion model [PDF]
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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Multi-scale phase separation by explosive percolation with single-chromatin loop resolution [PDF]
Computational and Structural Biotechnology Journal, 2022 The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber.
Kaustav Sengupta +8 more
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Cohesin residency determines chromatin loop patterns [PDF]
eLife, 2020 The organization of chromatin into higher order structures is essential for chromosome segregation, the repair of DNA-damage, and the regulation of gene expression.
Lorenzo Costantino +4 more
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TM-Loop: Transformer multi-omics hierarchical detection of chromatin loop [PDF]
Scientific ReportsChromatin loops form the hierarchical 3D genome architecture and act as critical regulatory hubs, bringing distant cis-elements together to precisely control target gene transcription.
Haixia Zhai +4 more
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Chromatin looping-based CRISPR screen identifies TLK2 as chromatin loop formation regulator in cancer stemness plasticity [PDF]
Nature CommunicationsTargeting cancer cell plasticity through chromatin organization is an emerging research area, yet the molecular mechanisms that govern chromatin loop formation remain unclear.
Zifeng Wang +17 more
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Chromatin loop anchors contain core structural components of the gene expression machinery in maize [PDF]
BMC Genomics, 2021 Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher ...
Stéphane Deschamps +7 more
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NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction [PDF]
Advanced ScienceChromatin loops play a crucial role in gene regulation and cellular function, providing key insights into understanding the 3D structure of the genome and its impact on cellular homeostasis.
Wenjie Huang +5 more
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CNNKSCEC: a deep learning-based framework for chromatin loop prediction with multi-source feature integration [PDF]
Frontiers in GeneticsMotivationChromatin in the cell nucleus adopts a complex three-dimensional (3D) structure shaped by folding and interactions, with chromatin loops serving as fundamental organizational units.
Junfeng Wang +5 more
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An extrinsic motor directs chromatin loop formation by cohesin [PDF]
The EMBO JournalThe ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve ...
Thomas M Guérin +4 more
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CTCF-anchored chromatin loop dynamics during human meiosis [PDF]
BMC BiologyBackground During meiosis, the mammalian genome is organised within chromatin loops, which facilitate synapsis, crossing over and chromosome segregation, setting the stage for recombination events and the generation of genetic diversity.
Vera B. Kaiser, Colin A. Semple
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