R
Raman P. Nagarajan
Researcher at University of California, San Francisco
Publications - 41
Citations - 5047
Raman P. Nagarajan is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: DNA methylation & Chemistry. The author has an hindex of 19, co-authored 27 publications receiving 4551 citations. Previous affiliations of Raman P. Nagarajan include GlaxoSmithKline & University of California, Davis.
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Journal ArticleDOI
Conserved role of intragenic DNA methylation in regulating alternative promoters
Alika K. Maunakea,Raman P. Nagarajan,Mikhail Bilenky,Tracy J. Ballinger,Cletus D'Souza,Shaun D. Fouse,Brett E. Johnson,Chibo Hong,Cydney B. Nielsen,Yongjun Zhao,Gustavo Turecki,Allen Delaney,Richard Varhol,Nina Thiessen,Ksenya Shchors,Ksenya Shchors,Vivi M. Heine,David H. Rowitch,Xiaoyun Xing,Chris Fiore,Maximiliaan Schillebeeckx,Steven J.M. Jones,David Haussler,Marco A. Marra,Martin Hirst,Ting Wang,Ting Wang,Joseph F. Costello +27 more
TL;DR: An in-depth investigation of the human SHANK3 locus and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo.
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
R. Alan Harris,Ting Wang,Cristian Coarfa,Raman P. Nagarajan,Chibo Hong,Sara L. Downey,Brett E. Johnson,Shaun D. Fouse,Allen Delaney,Yongjun Zhao,Adam B. Olshen,Tracy J. Ballinger,Xin Zhou,Kevin J. Forsberg,Junchen Gu,Lorigail Echipare,Henriette O'Geen,Ryan Lister,Mattia Pelizzola,Yuanxin Xi,Charles B. Epstein,Bradley E. Bernstein,R. David Hawkins,Bing Ren,Wen-Yu Chung,Hongcang Gu,Christoph Bock,Andreas Gnirke,Michael Q. Zhang,David Haussler,Joseph A. Ecker,Wei Li,Peggy J. Farnham,Robert A. Waterland,Alexander Meissner,Marco A. Marra,Martin Hirst,Aleksandar Milosavljevic,Joseph F. Costello +38 more
TL;DR: This work combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost and detected regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with Monoallelic epigenetic marks and monoallelic expression.
Journal ArticleDOI
The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer
Robert J.A. Bell,H. Tomas Rube,Alex Kreig,Andrew Mancini,Shaun D. Fouse,Raman P. Nagarajan,Serah Choi,Chibo Hong,Daniel He,Melike Pekmezci,John K. Wiencke,Margaret Wrensch,Susan M. Chang,Kyle M. Walsh,Sua Myong,Jun S. Song,Joseph F. Costello +16 more
TL;DR: Cancer-associated mutations in the promoter of the telomerase gene allow increased activation by transcription factor binding, and GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.
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Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
Dag H. Yasui,Sailaja Peddada,Mark Bieda,Roxanne O. Vallero,Amber Hogart,Raman P. Nagarajan,Karen N. Thatcher,Peggy J. Farnham,Janine M. LaSalle +8 more
TL;DR: Integrated genome-wide promoter analysis of MeCP2 binding, CpG methylation, and gene expression revealed that 63% of Me CP2-bound promoters are actively expressed and that only 6% are highly methylated.
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Reduced MeCP2 expression is frequent in autism frontal cortex and correlates with aberrant MECP2 promoter methylation.
TL;DR: The results suggest that both genetic and epigenetic defects lead to reduced MeCP2 expression and may be important in the complex etiology of autism.