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Alexander J. Federation
Researcher at Harvard University
Publications - 31
Citations - 2919
Alexander J. Federation is an academic researcher from Harvard University. The author has contributed to research in topics: Chromatin & Enhancer. The author has an hindex of 15, co-authored 30 publications receiving 2342 citations. Previous affiliations of Alexander J. Federation include Broad Institute & University of Rochester.
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Journal ArticleDOI
NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis
Jonathan D. Brown,Charles Y. Lin,Qiong Duan,Qiong Duan,Gabriel K. Griffin,Alexander J. Federation,Ronald M. Paranal,Steven M. Bair,Gail Newton,Andrew H. Lichtman,Andrew L. Kung,Andrew L. Kung,Tianlun Yang,Hong Wang,Francis W. Luscinskas,Kevin Croce,James E. Bradner,Jorge Plutzky +17 more
TL;DR: A chemical genetic approach reveals a requirement for BET bromodomains in communicating enhancer remodeling to RNA Polymerase II and orchestrating the transition to the inflammatory cell state, demonstrated in activated endothelium and macrophages.
Journal ArticleDOI
RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity.
Evangelos Pefanis,Jiguang Wang,Gerson Rothschild,Junghyun Lim,David Kazadi,Jianbo Sun,Alexander J. Federation,Jaime Chao,Oliver Elliott,Zhi-Ping Liu,Aris N. Economides,James E. Bradner,Raul Rabadan,Uttiya Basu +13 more
TL;DR: It is proposed that the RNA exosome protects divergently transcribed lncRNA expressing enhancers by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function.
Journal ArticleDOI
Active medulloblastoma enhancers reveal subgroup-specific cellular origins
Charles Y. Lin,Charles Y. Lin,Serap Erkek,Yiai Tong,Linlin Yin,Alexander J. Federation,Marc Zapatka,Parthiv Haldipur,Daisuke Kawauchi,Thomas Risch,Hans-Jörg Warnatz,Barbara C. Worst,Bensheng Ju,Brent A. Orr,Rhamy Zeid,Donald R. Polaski,Maia Segura-Wang,Sebastian M. Waszak,David T.W. Jones,Marcel Kool,Volker Hovestadt,Ivo Buchhalter,Laura Sieber,Pascal Johann,Lukas Chavez,Stefan Gröschel,Marina Ryzhova,Andrey Korshunov,Andrey Korshunov,Wenbiao Chen,Victor V. Chizhikov,Kathleen J. Millen,Kathleen J. Millen,Vyacheslav Amstislavskiy,Hans Lehrach,Marie-Laure Yaspo,Roland Eils,Roland Eils,Peter Lichter,Jan O. Korbel,Stefan M. Pfister,Stefan M. Pfister,James E. Bradner,Paul A. Northcott +43 more
TL;DR: In this article, using H3K27ac and BRD4 chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with tissue-matched DNA methylation and transcriptome data, the authors describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens.
Journal ArticleDOI
Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors
Wenyu Yu,Emma J. Chory,Emma J. Chory,Amy K. Wernimont,Wolfram Tempel,Alex Scopton,Alexander J. Federation,Jason J. Marineau,Jun Qi,Dalia Barsyte-Lovejoy,Joanna Yi,Richard Marcellus,Roxana E. Iacob,John R. Engen,Carly Griffin,Ahmed Aman,Erno Wienholds,Fengling Li,Javier Pineda,Javier Pineda,Guillermina Estiu,Tatiana Shatseva,Taraneh Hajian,Rima Al-awar,John E. Dick,Masoud Vedadi,Peter Brown,Cheryl H. Arrowsmith,James E. Bradner,Matthieu Schapira,Matthieu Schapira +30 more
TL;DR: The three-dimensional structure of the protein methyl transferase DOT1L bound to EPZ004777, the first S-adenosylmethionine-competitive inhibitor of a protein methyltransferase with in vivo efficacy, and those of four new analogues reveal remodelling of the catalytic site.
Journal ArticleDOI
Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability.
Fei-Long Meng,Zhou Du,Zhou Du,Alexander J. Federation,Jiazhi Hu,Qiao Wang,Kyong-Rim Kieffer-Kwon,Robin M. Meyers,Corina Amor,Caitlyn R. Wasserman,Donna Neuberg,Rafael Casellas,Michel C. Nussenzweig,James E. Bradner,X. Shirley Liu,Frederick W. Alt +15 more
TL;DR: It is reported that most robust AID off-target translocations occur within highly focal regions of target genes in which sense and antisense transcription converge, and it is found that such AID-targeting "convergent" transcription arises fromantisense transcription that emanates from super-enhancers within sense transcribed gene bodies.