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

Hagège, Hélène, Klous, Petra, Braem, Caroline, Splinter, Erik, Dekker, Job, Cathala, Guy, de Laat, Wouter, Forné, Thierry·2007·Nature Protocols

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Items 201–300 of 747

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  2. Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition
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  3. Direct Interactions of OCA-B and TFII-I Regulate Immunoglobulin Heavy-Chain Gene Transcription by Facilitating Enhancer-Promoter Communication
    Xiaodi Ren, Rachael Siegel, Unkyu Kim, Robert G. Roeder · 2011 · Molecular Cell
  4. Enhancer RNA-driven looping enhances the transcription of the long noncoding RNA DHRS4-AS1, a controller of the DHRS4 gene cluster
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  5. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes
    Daniel Andergassen, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kuliński, Hans‐Christian Theussl, Takahiko Shimizu, Josef Martin Penninger, Florian M. Pauler, Quanah James Hudson · 2019 · PLoS Genetics
  6. The Genome in Three Dimensions: A New Frontier in Human Brain Research
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  7. Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions
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  8. Epigenetic Deregulation of the LMP1/LMP2 Locus of Epstein-Barr Virus by Mutation of a Single CTCF-Cohesin Binding Site
    Horng-Shen Chen, Kayla A. Martin, Fang Ying Lu, Lena N. Lupey-Green, Joshua M. Mueller, Paul M. Lieberman, Italo Tempera · 2013 · Journal of Virology
  9. The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription
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  10. Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the β-globin locus
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  11. Irf6 directly regulates Klf17 in zebrafish periderm and Klf4 in murine oral epithelium, and dominant-negative KLF4 variants are present in patients with cleft lip and palate
    Huan Liu, Elizabeth J. Leslie, Zhonglin Jia, Tiffany Smith, Mekonen A. Eshete, Azeez Butali, Martine Dunnwald, Jeffrey Clark Murray, Robert A. Cornell · 2015 · Human Molecular Genetics
  12. Adipocyte Long-Noncoding RNA Transcriptome Analysis of Obese Mice Identified Lnc-Leptin, Which Regulates Leptin
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  13. RUNX3 regulates cell cycle-dependent chromatin dynamics by functioning as a pioneer factor of the restriction-point
    Lee, Jung-Won, Kim, Da-Mi, Jang, Ju-Won, Park, Tae-Geun, Song, Soo-Hyun, Lee, You-Soub, Chi, Xin-Zi, Park, Il Yeong, Hyun, Jin-Won, Ito, Yoshiaki et al. · 2019 · Nature Communications
  14. Myod and H19-Igf2 locus interactions are required for diaphragm formation in the mouse
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  15. Interplay between SIN3A and STAT3 Mediates Chromatin Conformational Changes and GFAP Expression during Cellular Differentiation
    Pei-Yi Cheng, Yuping Lin, Yaling Chen, Yi‐Ching Lee, Chia-Chen Tai, Yi-Ting Wang, Yu‐Ju Chen, Cheng-Fu Kao, John Yu · 2011 · PLoS ONE
  16. A discrete chromatin loop in the murine Tcra-Tcrd locus shapes the TCRδ and TCRα repertoires
    Liang Chen, Z. Carico, H. Shih, M. Krangel · 2015 · Nature Immunology
  17. Twist1 Regulates Ifng Expression in Th1 Cells by Interfering with Runx3 Function
    Duy Pham, Joshua W. Vincentz, Anthony B. Firulli, Mark H. Kaplan · 2012 · The Journal of Immunology
  18. Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element
    Kinjal Majumder, Olivia I. Koues, Elizabeth Chan, Katherine E. Kyle, Julie E. Horowitz, Katherine S Yang-Iott, Craig H. Bassing, Ichiro Taniuchi, Michael S. Krangel, Eugene M. Oltz · 2014 · The Journal of Experimental Medicine
  19. Unifying model for molecular determinants of the preselection Vβ repertoire
    Suhasni Gopalakrishnan, Kinjal Majumder, Alexander V. Predeus, Yue Huang, Olivia I. Koues, Jiyoti Verma‐Gaur, Salvatore Loguercio, Andrew I. Su, Ann J. Feeney, Maxim N. Artyomov et al. · 2013 · Proceedings of the National Academy of Sciences
  20. EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence
    Sima Kheradmand Kia, Parham Solaimani Kartalaei, Elnaz Farahbakhshian, Farzin Pourfarzad, Marieke v. Lindern, C. Peter Verrijzer · 2009 · Epigenetics & Chromatin
  21. Glia-specific enhancers and chromatin structure regulate NFIA expression and glioma tumorigenesis
    Stacey M. Glasgow, Jeffrey C. Carlson, Wenyi Zhu, Lesley S. Chaboub, Peng Kang, Hyun Kyoung Lee, Yoanne M. Clovis, Brittney Lozzi, Robert J. McEvilly, Michael G. Rosenfeld et al. · 2017 · Nature Neuroscience
  22. LINC00941 promotes oral squamous cell carcinoma progression via activating CAPRIN2 and canonical WNT/β‐catenin signaling pathway
    Yilong Ai, Siyuan Wu, Chen Zou, Haigang Wei · 2020 · Journal of Cellular and Molecular Medicine
  23. Androgen receptor-driven chromatin looping in prostate cancer
    Dayong Wu, Chunpeng Zhang, Yanping Shen, Kenneth P. Nephew, Qianben Wang · 2011 · Trends in Endocrinology and Metabolism
  24. HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis
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  25. Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition
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  26. Amplification of Distant Estrogen Response Elements Deregulates Target Genes Associated with Tamoxifen Resistance in Breast Cancer
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  27. Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression
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  28. Enhancer-Promoter Interaction of SELF PRUNING 5G Shapes Photoperiod Adaptation
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  29. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy
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  30. Progesterone receptor integrates the effects of mutated MED12 and altered DNA methylation to stimulate RANKL expression and stem cell proliferation in uterine leiomyoma
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  31. ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3
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  32. Chromatin remodeling mediated by the FOXA1/A2 transcription factors activatesCFTRexpression in intestinal epithelial cells
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  33. Long non-coding RNA LncKdm2b regulates cortical neuronal differentiation by cis-activating Kdm2b
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  34. Epigenetic landscape reveals MECOM as an endothelial lineage regulator
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  35. Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition
    Mitchell Robert Vollger, Jonas Korlach, Kiara C. Eldred, Elliott G. Swanson, Jason G. Underwood, Stephanie C. Bohaczuk, Yizi Mao, Yong-Han Hank Cheng, Jane E. Ranchalis, Elizabeth Blue et al. · 2025 · Nature Genetics
  36. The distinctive roles of erythroid specific activator GATA-1 and NF-E2 in transcription of the human fetal γ-globin genes
    Yea Woon Kim, Seoyeon Kim, Chul Geun Kim, AeRi Kim · 2011 · Nucleic Acids Research
  37. CTCF-mediated chromatin looping in EGR2 regulation and SUZ12 recruitment critical for peripheral myelination and repair
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  38. Convergence of oncogenic and hormone receptor pathways promotes metastatic phenotypes
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  39. Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression
    Yichi Xu, Weimin Guo, Ping Li, Yan Zhang, Meng Liang Zhao, Zenghua Fan, Zhihu Zhao, Jun Yan · 2016 · PLoS Genetics
  40. Tcrd Rearrangement Redirects a Processive Tcra Recombination Program to Expand the Tcra Repertoire
    Zachary M. Carico, Kingshuk Roy Choudhury, Baojun Zhang, Yuan Zhuang, Michael S. Krangel · 2017 · Cell Reports
  41. Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation
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  42. ZNF382 controls mouse neuropathic pain via silencer-based epigenetic inhibition of Cxcl13 in DRG neurons
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  43. Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus
    Nehal Gosalia, Daniel S. Neems, Jenny L. Kerschner, Steven T. Kosak, Ann Harris · 2014 · Nucleic Acids Research
  44. Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation
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  45. G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture
    Jun Yuan, Xiao-Mei He, Yin-Sheng Wang · 2023 · Nucleic Acids Research
  46. Pdx1 and BETA2/NeuroD1 Participate in a Transcriptional Complex That Mediates Short-range DNA Looping at the Insulin Gene
    Daniella A. Babu, Swarup K. Chakrabarti, James C. Garmey, Raghavendra G. Mirmira · 2008 · Journal of Biological Chemistry
  47. Dynamic Reconfiguration of Long Human Genes during One Transcription Cycle
    Joshua D. Larkin, Peter R. Cook, Argyris Papantonis · 2012 · Molecular and Cellular Biology
  48. Farnesoid X Receptor Activation Mediates Head-to-Tail Chromatin Looping in theNr0b2Gene Encoding Small Heterodimer Partner
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  49. Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML
    Cihangir Duy, Matt R. Teater, Francine E. Garrett-Bakelman, Tak C. Lee, Cem Meydan, Jacob Lowell Glass, Meng Li, Johannes C. Hellmuth, Helai P. Mohammad, Kimberly N. Smitheman et al. · 2019 · Cancer Discovery
  50. Per1/Per2–Igf2 axis–mediated circadian regulation of myogenic differentiation
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  51. Epstein-Barr Virus Proteins EBNA3A and EBNA3C Together Induce Expression of the Oncogenic MicroRNA Cluster miR-221/miR-222 and Ablate Expression of Its Target p57KIP2
    Quentin Bazot, Kostas Paschos, Lenka Skalska, Jens Kalchschmidt, Gillian A. Parker, Martin J. Allday · 2015 · PLoS Pathogens
  52. Active opsin loci adopt intrachromosomal loops that depend on the photoreceptor transcription factor network
    Guang-Hua Peng, Shiming Chen · 2011 · Proceedings of the National Academy of Sciences
  53. Direct Evidence for Pitavastatin Induced Chromatin Structure Change in the KLF4 Gene in Endothelial Cells
    Takashi Maejima, Tsuyoshi Inoue, Yasuharu Kanki, Takahide Kohro, Guoliang Li, Yoshihiro Ohta, Hiroshi Kimurâ, Mika Kobayashi, Akashi Taguchi, Shuichi Tsutsumi et al. · 2014 · PLoS ONE
  54. Effective Blocking of the White Enhancer Requires Cooperation between Two Main Mechanisms Suggested for the Insulator Function
    Olga Kyrchanova, Oksana G Maksimenko, Viacheslav Stakhov, Tatyana Ivlieva, Alexander Parshikov, Vasily M. Studitsky, Pavel G Georgiev · 2013 · PLoS Genetics
  55. Crosstalk of the Androgen Receptor with Transcriptional Collaborators: Potential Therapeutic Targets for Castration-Resistant Prostate Cancer
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  56. Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML
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  57. MED1 Regulates BMP/TGF-β in Endothelium: Implication for Pulmonary Hypertension
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  58. Chromatin Conformation Signatures: Ideal Human Disease Biomarkers?
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  59. Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture
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  60. Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection
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  61. Regions of very low H3K27me3 partition the Drosophila genome into topological domains
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  62. Spatial configuration of the chicken α-globin gene domain: immature and active chromatin hubs
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  63. SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription
    Anil K. Panigrahi, Charles E. Foulds, Rainer B. Lanz, Ross A. Hamilton, Ping Yi, David Michael Lonard, Ming‐Jer Tsai, Sophia Y. Tsai, Bert W. O’Malley · 2018 · Molecular Cell
  64. Chromosome Conformation Capture
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  65. Discovering genome regulation with 3C and 3C-related technologies
    Sylvain D. Ethier, Hisashi Miura, Josée Dostie · 2011 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
  66. Chromatin insulator bodies are nuclear structures that form in response to osmotic stress and cell death
    Todd Andrew Schoborg, Ryan A. Rickels, Joshua P. Barrios, Mariano Labrador · 2013 · The Journal of Cell Biology
  67. Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells
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  68. Aberrant activation of CYR61 enhancers in colorectal cancer development
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  69. Androgen Receptor-Activated Enhancers Simultaneously Regulate Oncogene TMPRSS2 and lncRNA PRCAT38 in Prostate Cancer
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  70. Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex
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  71. Regulation of miR-200c/141 expression by intergenic DNA-looping and transcriptional read-through
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  72. TIP48/Reptin and H2A.Z Requirement for Initiating Chromatin Remodeling in Estrogen-Activated Transcription
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  73. Molecular mechanisms controlling CFTR gene expression in the airway
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  74. Enhancer variants reveal a conserved transcription factor network governed by PU.1 during osteoclast differentiation
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  78. Phosphorylation of the androgen receptor at Ser81 is co‐sustained by CDK1 and CDK9 and leads to AR‐mediated transactivation in prostate cancer
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  80. Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor
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  81. Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer
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  82. Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus
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  83. DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes
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  84. MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer
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  85. PRMT1 Is Required for the Maintenance of Mature β-Cell Identity
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  88. Centromere/kinetochore is assembled through CENP-C oligomerization
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  89. Regulation of the Dynamic Chromatin Architecture of the Epidermal Differentiation Complex Is Mediated by a c-Jun/AP-1-Modulated Enhancer
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  90. Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip
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  92. Core pluripotency factors promote glycolysis of human embryonic stem cells by activating GLUT1 enhancer
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  93. Genomic Matrix Attachment Region and Chromosome Conformation Capture Quantitative Real Time PCR Assays Identify Novel Putative Regulatory Elements at the Imprinted Dlk1/Gtl2 Locus
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  94. Noncoding origins of anthropoid traits and a new null model of transposon functionalization
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  95. Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus
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  96. Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish
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  97. miRNA-independent function of long noncoding pri-miRNA loci
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  98. Functional elements of the cis-regulatory lincRNA-p21
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  99. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates
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