Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication
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DOI: 10.1038/s41467-023-41919-x
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- Jason Ernst & Pouya Kheradpour & Tarjei S. Mikkelsen & Noam Shoresh & Lucas D. Ward & Charles B. Epstein & Xiaolan Zhang & Li Wang & Robbyn Issner & Michael Coyne & Manching Ku & Timothy Durham & Mano, 2011. "Mapping and analysis of chromatin state dynamics in nine human cell types," Nature, Nature, vol. 473(7345), pages 43-49, May.
- Jesse R. Dixon & Siddarth Selvaraj & Feng Yue & Audrey Kim & Yan Li & Yin Shen & Ming Hu & Jun S. Liu & Bing Ren, 2012. "Topological domains in mammalian genomes identified by analysis of chromatin interactions," Nature, Nature, vol. 485(7398), pages 376-380, May.
- David Hausmann & Dirk C. Hoffmann & Varun Venkataramani & Erik Jung & Sandra Horschitz & Svenja K. Tetzlaff & Ammar Jabali & Ling Hai & Tobias Kessler & Daniel D. Azoŕin & Sophie Weil & Alexandros Kou, 2023. "Autonomous rhythmic activity in glioma networks drives brain tumour growth," Nature, Nature, vol. 613(7942), pages 179-186, January.
- Jessica Zuin & Gregory Roth & Yinxiu Zhan & Julie Cramard & Josef Redolfi & Ewa Piskadlo & Pia Mach & Mariya Kryzhanovska & Gergely Tihanyi & Hubertus Kohler & Mathias Eder & Christ Leemans & Bas Stee, 2022. "Nonlinear control of transcription through enhancer–promoter interactions," Nature, Nature, vol. 604(7906), pages 571-577, April.
- Alvaro Rada-Iglesias & Ruchi Bajpai & Tomek Swigut & Samantha A. Brugmann & Ryan A. Flynn & Joanna Wysocka, 2011. "A unique chromatin signature uncovers early developmental enhancers in humans," Nature, Nature, vol. 470(7333), pages 279-283, February.
- Giuliano Crispatzu & Rizwan Rehimi & Tomas Pachano & Tore Bleckwehl & Sara Cruz-Molina & Cally Xiao & Esther Mahabir & Hisham Bazzi & Alvaro Rada-Iglesias, 2021. "The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
- Carsten Bahr & Lisa von Paleske & Veli V. Uslu & Silvia Remeseiro & Naoya Takayama & Stanley W. Ng & Alex Murison & Katja Langenfeld & Massimo Petretich & Roberta Scognamiglio & Petra Zeisberger & Ame, 2018. "A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies," Nature, Nature, vol. 553(7689), pages 515-520, January.
- Elphège P. Nora & Bryan R. Lajoie & Edda G. Schulz & Luca Giorgetti & Ikuhiro Okamoto & Nicolas Servant & Tristan Piolot & Nynke L. van Berkum & Johannes Meisig & John Sedat & Joost Gribnau & Emmanuel, 2012. "Spatial partitioning of the regulatory landscape of the X-inactivation centre," Nature, Nature, vol. 485(7398), pages 381-385, May.
- Carsten Bahr & Lisa Paleske & Veli V. Uslu & Silvia Remeseiro & Naoya Takayama & Stanley W. Ng & Alex Murison & Katja Langenfeld & Massimo Petretich & Roberta Scognamiglio & Petra Zeisberger & Amelie , 2018. "Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies," Nature, Nature, vol. 558(7711), pages 4-4, June.
- Humsa S. Venkatesh & Wade Morishita & Anna C. Geraghty & Dana Silverbush & Shawn M. Gillespie & Marlene Arzt & Lydia T. Tam & Cedric Espenel & Anitha Ponnuswami & Lijun Ni & Pamelyn J. Woo & Kathryn R, 2019. "Electrical and synaptic integration of glioma into neural circuits," Nature, Nature, vol. 573(7775), pages 539-545, September.
- Jessica Tome-Garcia & Parsa Erfani & German Nudelman & Alexander M. Tsankov & Igor Katsyv & Rut Tejero & Zhang & Martin Walsh & Roland H. Friedel & Elena Zaslavsky & Nadejda M. Tsankova, 2018. "Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
- Ashot S. Harutyunyan & Brian Krug & Haifen Chen & Simon Papillon-Cavanagh & Michele Zeinieh & Nicolas De Jay & Shriya Deshmukh & Carol C. L. Chen & Jad Belle & Leonie G. Mikael & Dylan M. Marchione & , 2019. "H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
- Varun Venkataramani & Dimitar Ivanov Tanev & Christopher Strahle & Alexander Studier-Fischer & Laura Fankhauser & Tobias Kessler & Christoph Körber & Markus Kardorff & Miriam Ratliff & Ruifan Xie & He, 2019. "Glutamatergic synaptic input to glioma cells drives brain tumour progression," Nature, Nature, vol. 573(7775), pages 532-538, September.
- Joseph Nasser & Drew T. Bergman & Charles P. Fulco & Philine Guckelberger & Benjamin R. Doughty & Tejal A. Patwardhan & Thouis R. Jones & Tung H. Nguyen & Jacob C. Ulirsch & Fritz Lekschas & Kristy Mu, 2021. "Genome-wide enhancer maps link risk variants to disease genes," Nature, Nature, vol. 593(7858), pages 238-243, May.
- Saritha Krishna & Abrar Choudhury & Michael B. Keough & Kyounghee Seo & Lijun Ni & Sofia Kakaizada & Anthony Lee & Alexander Aabedi & Galina Popova & Benjamin Lipkin & Caroline Cao & Cesar Nava Gonzal, 2023. "Glioblastoma remodelling of human neural circuits decreases survival," Nature, Nature, vol. 617(7961), pages 599-607, May.
- Matthias Osswald & Erik Jung & Felix Sahm & Gergely Solecki & Varun Venkataramani & Jonas Blaes & Sophie Weil & Heinz Horstmann & Benedikt Wiestler & Mustafa Syed & Lulu Huang & Miriam Ratliff & Kianu, 2015. "Brain tumour cells interconnect to a functional and resistant network," Nature, Nature, vol. 528(7580), pages 93-98, December.
- Rían W. Manville & Maria Papanikolaou & Geoffrey W. Abbott, 2018. "Direct neurotransmitter activation of voltage-gated potassium channels," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
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