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3D Genome Architecture in the Mammalian Nucleus
Epigenomics, 2013Advances in DNA-sequencing technologies have made it possible to study the spatial hierarchy of genomic organization across different eukaryotic systems. Although genetic information is encrypted in the linear DNA sequence, a growing body of research suggests that the 3D genome plays an essential role in gene regulation [1].
Badam, Enkhmandakh +1 more
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Gene regulation by non-coding RNAs in the 3D genome architecture
Current Opinion in Genetics & Development, 2020Appropriate gene expression is essential for producing the correct amount of proteins at the right time, which is critical for living organisms. In the three-dimensional (3D) space of the nucleus, genomes are folded into higher order chromatin structures that are intimately associated with epigenetic factors, including histone modifications and nuclear
Hiroaki Tachiwana +2 more
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Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture
Current Opinion in Genetics & Development, 2020Cohesin is a complex conserved in evolution that entraps DNA. Originally identified for its role in sister chromatid cohesion, it is currently considered a key player in 3D genome organization. In vertebrates, two paralog genes encode two versions of the SA/STAG subunit of cohesin, STAG1 and STAG2.
Ana, Cuadrado, Ana, Losada
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3D genome architecture from populations to single cells
Current Opinion in Genetics & Development, 2015Dominated by microscopy for decades the nuclear genome organization field has recently undergone a dramatic transition fuelled by new next generation sequencing technologies that are beginning to bridge the gap between microscopic observations and molecular scale studies. It is no longer in doubt that the nucleus is spatially compartmentalized and that
Mayra, Furlan-Magaril +3 more
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Computational Approaches for Understanding Sequence Variation Effects on the 3D Genome Architecture
Annual Review of Biomedical Data Science, 2022Decoding how genomic sequence and its variations affect 3D genome architecture is indispensable for understanding the genetic architecture of various traits and diseases. The 3D genome organization can be significantly altered by genome variations and in turn impact the function of the genomic sequence.
Pavel, Avdeyev, Jian, Zhou
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Evolutionary dynamics of 3D genome architecture following polyploidization in cotton
Nature Plants, 2018The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor.
Maojun Wang +9 more
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CRISPR Double Cutting through the Labyrinthine Architecture of 3D Genomes
Journal of Genetics and Genomics, 2016The genomes are organized into ordered and hierarchical topological structures in interphase nuclei. Within discrete territories of each chromosome, topologically associated domains (TADs) play important roles in various nuclear processes such as gene regulation.
Haiyan, Huang, Qiang, Wu
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The role of nuclear matrix protein HNRNPU in maintaining the architecture of 3D genome
Seminars in Cell & Developmental Biology, 2019The complexity of higher eukaryote genomes is far from being explained by linear information. There is a need to understand roles of genome regulation at the organism level through defining a comprehensive profile of chromosomal organization. Chromosome conformation capture (3C)-based studies reveal that higher-order of chromatin include not only long ...
Linlin, Zhang +3 more
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Technologies for Capturing 3D Genome Architecture in Plants
Trends in Plant Science, 2021Weizhi, Ouyang +3 more
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How computer science can help in understanding the 3D genome architecture
Briefings in Bioinformatics, 2015Chromosome conformation capture techniques are producing a huge amount of data about the architecture of our genome. These data can provide us with a better understanding of the events that induce critical regulations of the cellular function from small changes in the three-dimensional genome architecture. Generating a unified view of spatial, temporal,
Shavit +7 more
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