Quantitative analysis of chromosome conformation capture assays (3C-qPCR)

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Items 401–500 of 747

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4. Quantitative Analysis of Intra-chromosomal Contacts: The 3C-qPCR Method
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5. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
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6. Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics
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11. RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription
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14. A model for the 3D chromatin architecture of pro and eukaryotes
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15. Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation
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16. Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster
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17. Activation of Mouse Tcrb: Uncoupling RUNX1 Function from Its Cooperative Binding with ETS1
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18. Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast
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19. Profiling the epigenetic interplay of lncRNA RUNXOR and oncogenic RUNX1 in breast cancer cells by gene in situ cis-activation.
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20. Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor
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21. Profound alterations of the chromatin architecture at chromosome 11p15.5 in cells from Beckwith-Wiedemann and Silver-Russell syndromes patients
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22. Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4+ T cell identity and function
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23. Genome-wide screens identify specific drivers of mutant hTERT promoters
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24. Histone acetylation contributes to chromatin looping between the locus control region and globin gene by influencing hypersensitive site formation
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25. The immunoglobulin heavy chain gene 3′ enhancers induce Bcl2 deregulation and lymphomagenesis in murine B cells
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26. 3C Technologies in plants
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27. Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
    Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Albert Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak · 2020 · International Journal of Molecular Sciences
28. Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years
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29. BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer
    Ge Sun, Yuntao Wei, Baosheng Zhou, Manlin Wang, Ruina Luan, Yu Bai, Hao Li, Shan Wang, Dantong Zheng, Chunyu Wang et al. · 2023 · Cell Death and Differentiation
30. Functional characteristics of novel pancreatic Pax6 regulatory elements
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31. Spatial organization of the chicken beta-globin gene domain in erythroid cells of embryonic and adult lineages
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32. Long Noncoding RNAs as Targets and Regulators of Nuclear Receptors
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33. Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data
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34. Diet-dependent natriuretic peptide receptor C expression in adipose tissue is mediated by PPARγ via long-range distal enhancers
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35. Colorectal cancer risk variant rs7017386 modulates two oncogenic lncRNAs expression via ATF1-mediated long-range chromatin loop
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36. Characterization of the Unusual Bidirectional ves Promoters Driving VESA1 Expression and Associated with Antigenic Variation in Babesia bovis
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37. The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing
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38. Fibroblast growth factors (FGFs) prime the limb specific Shh enhancer for chromatin changes that balance histone acetylation mediated by E26 transformation-specific (ETS) factors
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39. A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors
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40. Risk single-nucleotide polymorphism-mediated enhancer–promoter interaction drives keloids through long noncoding RNA down expressed in keloids
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41. ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis
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42. Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding
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43. Erythroid specific activator GATA-1-dependent interactions between CTCF sites around the β-globin locus
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44. Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments–an evaluation and review framework of the 3D genome organization
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45. Identification of a pituitary ERα-activated enhancer triggering the expression of Nr5a1, the earliest gonadotrope lineage-specific transcription factor
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46. Cis-acting regulatory elements regulating CYP3A4 transcription in human liver
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47. Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
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48. An APOO Pseudogene on Chromosome 5q Is Associated With Low-Density Lipoprotein Cholesterol Levels
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50. Upregulation of YY1 in M2 macrophages promotes secretion of exosomes containing hsa-circ-0000326 via super-enhancers to facilitate prostate cancer progression
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51. CTCF demarcates chicken embryonic α-globingene autonomous silencing and contributes to adult stage-specific gene expression
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52. Regulation of Human CYP2C9 Expression by Electrophilic Stress Involves Activator Protein 1 Activation and DNA Looping
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54. Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors
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55. Transcriptional repression and DNA looping associated with a novel regulatory element in the final exon of the lymphotoxin-β gene
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56. The MYC 3′ Wnt-Responsive Element Drives Oncogenic MYC Expression in Human Colorectal Cancer Cells
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57. Unbiased Interrogation of 3D Genome Topology Using Chromosome Conformation Capture Coupled to High-Throughput Sequencing (4C-Seq)
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58. Disruption of a −35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells
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    Yinfei Tan, Eleonora Sementino, Jinfei Xu, Jianming Pei, Zemin Liu, Timothy K. Ito, Kathy Qi Cai, Suraj Peri, Andres J. Klein–Szanto, David L. Wiest et al. · 2017 · Oncotarget
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