Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Items 301–400 of 1,052

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4. B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity
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5. The pluripotent genome in three dimensions is shaped around pluripotency factors
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6. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
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8. Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes
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9. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
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10. Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms
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11. Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila
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12. Long-Range Chromatin Interactions
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13. Bipartite structure of the inactive mouse X chromosome
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14. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression
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15. Xist RNA in action: Past, present, and future
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16. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs
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17. Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders
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18. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells
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19. Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
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20. Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries
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21. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
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22. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research
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23. De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture
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24. The role of transcription in shaping the spatial organization of the genome
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25. Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin
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26. A statistical approach for inferring the 3D structure of the genome
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27. Enhancer Function: Mechanistic and Genome-Wide Insights Come Together
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28. Transcription Factories: Genome Organization and Gene Regulation
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29. X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation
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30. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co‐aligned active and inactive nuclear compartments
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31. 3D imaging of Sox2 enhancer clusters in embryonic stem cells
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32. The formation and function of the cardiac conduction system
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33. Codon usage of highly expressed genes affects proteome-wide translation efficiency
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34. Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
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35. Multiplex chromatin interactions with single-molecule precision
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36. Systematic evaluation of chromosome conformation capture assays
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37. Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development
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38. Dissecting super-enhancer hierarchy based on chromatin interactions
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39. PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation
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40. 3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions
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41. Lamins Organize the Global Three-Dimensional Genome from the Nuclear Periphery
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42. Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes
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43. Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
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44. Gene Insertion Into Genomic Safe Harbors for Human Gene Therapy
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45. High-throughput mapping of regulatory DNA
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46. Identification of significant chromatin contacts from HiChIP data by FitHiChIP
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47. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
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48. Untangling the roles of TOP2A and TOP2B in transcription and cancer
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49. Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9
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50. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function
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51. Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism
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52. Chromosome organization in bacteria: mechanistic insights into genome structure and function
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53. CTCF: the protein, the binding partners, the binding sites and their chromatin loops
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54. MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification
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55. Nuclear compartmentalization as a mechanism of quantitative control of gene expression
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56. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
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57. Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors
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58. Enhancer hubs and loop collisions identified from single-allele topologies
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59. HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types
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60. Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer
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61. Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
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62. Chromatin Compaction Protects Genomic DNA from Radiation Damage
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63. TAD disruption as oncogenic driver
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64. Comparison of computational methods for the identification of topologically associating domains
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65. Genome organization controls transcriptional dynamics during development
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66. Three-dimensional modeling of theP. falciparumgenome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
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67. Transcription in Living Cells: Molecular Mechanisms of Bursting
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68. Identification of alternative topological domains in chromatin
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69. Evolutionary dynamics of coding and non-coding transcriptomes
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70. Topology, structures, and energy landscapes of human chromosomes
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71. Two major mechanisms of chromosome organization
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72. The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
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73. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk
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74. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo
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75. C2H2 Zinc Finger Proteins: The Largest but Poorly Explored Family of Higher Eukaryotic Transcription Factors
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76. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II
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77. Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia
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78. Chromatin as dynamic 10-nm fibers
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79. An Overview of Genome Organization and How We Got There: from FISH to Hi-C
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80. Joint profiling of DNA methylation and chromatin architecture in single cells
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81. Evaluating Enhancer Function and Transcription
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82. Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
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83. Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines
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84. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes
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85. Transcription shapes 3D chromatin organization by interacting with loop extrusion
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86. Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
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87. Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming
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88. Polymer physics predicts the effects of structural variants on chromatin architecture
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89. CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention
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90. DNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner
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91. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
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92. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans
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93. HiCPlotter integrates genomic data with interaction matrices
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94. Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment
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95. Cancer, metastasis, and the epigenome
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96. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes
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97. Chromatin Insulators: Linking Genome Organization to Cellular Function
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98. Regulation of the Human Telomerase Gene TERT by Telomere Position Effect—Over Long Distances (TPE-OLD): Implications for Aging and Cancer
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99. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton
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100. CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
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