Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor
Deng, Wulan, Lee, Jongjoo, Wang, Hongxin, Miller, Jeff, Reik, Andreas, Gregory, Philip D., Dean, Ann, Blobel, Gerd A.·2012·Cell
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<i>Sox2</i>
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- The 3D enhancer network of the developing T cell genome is shaped by SATB1T. Zelenka, Antonios Klonizakis, Despina Tsoukatou, Dionysios-Alexandros Papamatheakis, S. Franzenburg, Petros Tzerpos, Ioannis-Rafail Tzonevrakis, George Papadogkonas, Manouela Kapsetaki, Christoforos Nikolaou et al. · 2022 · Nature Communications
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- Imaging Transcription: Past, Present, and FutureRobert A. Coleman, Zhe J. Liu, Xavier Darzacq, Robert Tjian, Robert H. Singer, Timothée Lionnet · 2015 · Cold Spring Harbor Symposia on Quantitative Biology
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- Cohesin couples transcriptional bursting probabilities of inducible enhancers and promotersIrene Robles-Rebollo, Sergi Cuartero, Adrià Cañellas-Socias, Sarah Wells, Mohammad Mahdi Karimi, Elisabetta Mereu, Alexandra G. Chivu, Holger Heyn, Chad Whilding, Dirk Dormann et al. · 2022 · Nature Communications
- Communication of genome regulatory elements in a folded chromosomeSergey V. Razin, Alexey A. Gavrilov, Elena S. Ioudinkova, Olga V. Iarovaia · 2013 · FEBS Letters
- The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progressionYuyang Qian, Lei Zhang, Mingyang Cai, Hongxia Li, Heming Xu, Hongzhen Yang, Zhongfang Zhao, Suhn K. Rhie, Peggy Farnham, Jiandang Shi et al. · 2019 · Science Advances
- Enhancer–gene maps in the human and zebrafish genomes using evolutionary linkage conservationYves Clément, Patrick Torbey, Pascale Gilardi‐Hebenstreit, Hugues Roest Crollius · 2019 · Nucleic Acids Research
- Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformationMartín A. Rivas, Cem Meydan, Christopher R. Chin, Matt F. Challman, Daleum Kim, Bhavneet Bhinder, Andreas Kloetgen, Aaron D. Viny, Matt R. Teater, Dylan R. McNally et al. · 2021 · Nature Immunology
- The Stochastic Genome and Its Role in Gene ExpressionChristopher H. Bohrer, Daniel R. Larson · 2021 · Cold Spring Harbor Perspectives in Biology
- Epigenetic Regulation of Individual Modules of the immunoglobulin heavy chain locus 3′ Regulatory RegionBarbara K. Birshtein · 2014 · Frontiers in Immunology
- Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly?Gurumurthy, Aishwarya, Shen, Yong, Gunn, Eliot M., Bungert, Jörg · 2019 · BioEssays
- Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequencesShipra Bhatia, Dirk A. Kleinjan · 2014 · Human Genetics
- Transcriptional enhancers: functional insights and role in human diseaseIrene Miguel-Escalada, Lorenzo Pasquali, Jorge P. Ferrer · 2015 · Current Opinion in Genetics & Development
- Estrogen receptor-mediated long-range chromatin interactions and transcription in breast cancerMei Hui Liu, Edwin Chong Wing Cheung · 2013 · Molecular and Cellular Endocrinology
- From Super-Enhancer Non-coding RNA to Immune Checkpoint: Frameworks to FunctionsManqing Wu, Jun Shen · 2019 · Frontiers in Oncology
- A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blockerYavor K. Bozhilov, D. Downes, J. Telenius, A. M. Oudelaar, Emmanuel N. Olivier, J. Mountford, J. Hughes, R. Gibbons, D. Higgs · 2021 · Nature Communications
- A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genesLei Zhang, An-Shun He, Bo-Han Chen, Jinfang Bi, Jun Chen, Dianhao Guo, Yu-Yang Qian, Wenbin Wang, Tengfei Shi, Zhong-Fang Zhao et al. · 2020 · Genome Research
- Regulation of the Dynamic Chromatin Architecture of the Epidermal Differentiation Complex Is Mediated by a c-Jun/AP-1-Modulated EnhancerInez Y. Oh, Danielle Albea, Zane A. Goodwin, A. Quiggle, Breeana P Baker, Ann M. Guggisberg, Jessica H. Geahlen, Grace M. Kroner, Cristina de Guzman Strong · 2014 · Journal of Investigative Dermatology
- Enhancer-like long-range transcriptional activation by λ CI-mediated DNA loopingLun Cui, Iain Murchland, Keith Edward Shearwin, Ian B. Dodd · 2013 · Proceedings of the National Academy of Sciences
- Transcription in the context of the 3D nucleusKerstin S. Wendt, Frank G. Grosveld · 2014 · Current Opinion in Genetics & Development
- Genetic therapies for sickle cell diseaseErica B. Esrick, Daniel E. Bauer · 2018 · Seminars in Hematology
- Core pluripotency factors promote glycolysis of human embryonic stem cells by activating GLUT1 enhancerLili Yu, Kaiyuan Ji, Jian Zhang, Yan‐Xia Xu, Ying Yue, Taoyi Mai, Shuxiang Xu, Qian-bing Zhang, Kai‐Tai Yao, Yang Xu · 2019 · Protein & Cell
- Gene Therapy of the HemoglobinopathiesJoachim B. Kunz, Andreas E. Kulozik · 2020 · HemaSphere
- Understanding and Engineering Chromatin as a Dynamical System across Length and TimescalesChristopher P. Johnstone, Nathan Wang, Stuart A. Sevier, Kate E. Galloway · 2020 · Cell Systems
- iEnhancer-RF: Identifying enhancers and their strength by enhanced feature representation using random forestDae Yeong Lim, Jhabindra Khanal, Hilal Tayara, Kil To Chong · 2021 · Chemometrics and Intelligent Laboratory Systems
- 3D spatial genome organization in the nervous system: From development and plasticity to diseaseYuki Fujita, Sarshan R. Pather, Guo‐li Ming, Hongjun Song · 2022 · Neuron
- Ex Uno Plures: Molecular Designs for Embryonic PluripotencyKyle M. Loh, Bing Lim, Lay Teng Ang · 2014 · Physiological Reviews
- Nuclear Compartments, Genome Folding, and Enhancer-Promoter CommunicationSergey V. Ulianov, Alexey A. Gavrilov, Sergey V. Razin · 2015 · International review of cytology
- Mining 3D genome structure populations identifies major factors governing the stability of regulatory communitiesChao Dai, Wenyuan Li, Harianto Tjong, Shengli Hao, Yonggang Zhou, Qingjiao Li, Lin Chen, Bing Zhu, Frank Alber, Xianghong Jasmine Zhou · 2016 · Nature Communications
- Revisiting 3D chromatin architecture in cancer development and progressionYuliang Feng, Siim Pauklin · 2020 · Nucleic Acids Research
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- Enhancer TalkValentina Snetkova, Jane A. Skok · 2018 · Epigenomics
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- lncRNA and gene loopingYoutaro Shibayama, Stephanie Fanucchi, Loretta Magagula, Musa M. Mhlanga · 2014 · Transcription
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- A genome editing primer for the hematologistMegan D. Hoban, Daniel E. Bauer · 2016 · Blood
- RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter InteractionAnetta Ptasinska, Anna Pickin, Salam Adli Assi, Paulynn Suyin Chin, Luke Ames, Roberto Avellino, Stefan Gröschel, Ruud Delwel, Peter N. Cockerill, Cameron S. Osborne et al. · 2019 · Cell Reports
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- Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model SystemsOlga Kyrchanova, Vladimir Sokolov, Pavel G Georgiev · 2023 · International Journal of Molecular Sciences
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- Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and EvolutionRafael Galupa, Édith Heard · 2017 · Cold Spring Harbor Symposia on Quantitative Biology
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- Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and DrosophilaKyrchanova, Olga V., Bylino, Oleg V., Georgiev, Pavel G. · 2022 · Frontiers in Genetics
- Genome organization at different scales: nature, formation and functionJacques Serizay, Julie Ahringer · 2018 · Current Opinion in Cell Biology
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- Regulatory Domains and Their MechanismsNezha S. Benabdallah, Wendy A. Bickmore · 2015 · Cold Spring Harbor Symposia on Quantitative Biology
- Unraveling architecture of the pluripotent genomeJennifer E. Phillips‐Cremins · 2014 · Current Opinion in Cell Biology