Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data [PDF]
Briefings in Functional Genomics, 2020 Kimberly Mackay, Anthony Kusalik
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Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast [PDF]
Methods, 2020 Surabhi Chowdhary, Amoldeep S Kainth
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3D genome organization and epigenetic regulation in autoimmune diseases
Frontiers in Immunology, 2023 Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin.
Yueqi Qiu +13 more
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Nature Communications, 2023 The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and ...
Ediem Al-jibury +6 more
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Stripenn detects architectural stripes from chromatin conformation data using computer vision
Nature Communications, 2022 Chromosome conformation capture techniques have recently revealed features beyond chromatin loops such as architectural stripes. Here the authors present their stripe detection tool ‘Stripenn’ to detect and quantitate stripes from any type of chromatin ...
Sora Yoon, Aditi Chandra, Golnaz Vahedi
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Identifying and Reducing Systematic Errors in Chromosome Conformation Capture Data. [PDF]
PLoS ONE, 2015 Chromosome conformation capture (3C)-based techniques have recently been used to uncover the mystic genomic architecture in the nucleus. These techniques yield indirect data on the distances between genomic loci in the form of contact frequencies that ...
Seungsoo Hahn, Dongsup Kim
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Characterization of chromosomal architecture in Arabidopsisby chromosome conformation capture [PDF]
Genome Biology, 2013 Abstract Background The packaging of long chromatin fibers in the nucleus poses a major challenge, as it must fulfill both physical and functional requirements. Until recently, insights into the chromosomal architecture of plants were mainly provided by cytogenetic studies. Complementary to these analyses,
Stefan Grob +4 more
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Chromosome Conformation Capture in Bacteria and Archaea
, 2022 The three-dimensional structure of the chromosome is encoded within its sequence and regulates activities such as replication and transcription. This necessitates the study of the spatial organization of the chromosome in relation to the underlying sequence.
Rashid, F.M.Z., Detmar, L., Dame, R.T.
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Novel insights into chromosomal conformations in cancer
Molecular Cancer, 2017 Exploring gene function is critical for understanding the complexity of life. DNA sequences and the three-dimensional organization of chromatin (chromosomal interactions) are considered enigmatic factors underlying gene function, and interactions between
Ruobing Jia +3 more
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Joint profiling of DNA methylation and chromatin architecture in single cells. [PDF]
, 2019 We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the ...
AD Schmitt +31 more
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