SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data [PDF]
Nature Communications, 2023 Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells.
Lindsay Lee +14 more
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Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops [PDF]
Nature Communications, 2022 The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to ...
Keji Zhao, Yaqiang Cao, Kairong Cui
exaly +3 more sources
cPRC1.2 and CTCF-mediated transition from poised to active chromatin loops at bivalent genes [PDF]
EMBO ReportsPolycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Although the role of CTCF in chromatin organization is well-known, the involvement
Aflah Hanafiah +9 more
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CapsNetYY1: identifying YY1-mediated chromatin loops based on a capsule network architecture [PDF]
BMC Genomics, 2023 Background Previous studies have identified that chromosome structure plays a very important role in gene control. The transcription factor Yin Yang 1 (YY1), a multifunctional DNA binding protein, could form a dimer to mediate chromatin loops and active ...
Zhimin Zhang +3 more
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DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes. [PDF]
PLoS Computational Biology, 2022 In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions.
Siguo Wang +6 more
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CellLoop: Identifying single-cell 3D genome chromatin loops [PDF]
Nature CommunicationsSingle-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a computational
Yusen Ye +8 more
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A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops [version 1; peer review: 2 approved] [PDF]
F1000ResearchBackground Chromatin loops play a critical role in gene regulation by connecting regulatory loci and gene promoters. The identification of changes in chromatin looping between cell types or biological conditions is an important task for understanding ...
Eric Davis +4 more
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CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model [PDF]
Genome BiologyEmerging DNA language models provide powerful tools to address the challenge of accurately predicting chromatin loops, fundamental structures governing 3D genome organization and gene regulation.
Zhijie He +7 more
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The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy. [PDF]
PLoS Genetics, 2023 While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood.
Madeleine L Ball +5 more
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Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes [PDF]
Communications BiologyChromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-
Karolina Buka +7 more
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