Cell Reports Resource The NFk B Genomic Landscape in Lymphoblastoid B Cells

Bo Zhao,1,2,9 Luis A. Barrera,3,4,5,6,7,9 Ina Ersing,1,2 Bradford Willox,1 Stefanie C.S. Schmidt,1,2 Hannah Greenfeld,1 Hufeng Zhou,1,2 Sarah B. Mollo,1,2 Tommy T. Shi,1 Kaoru Takasaki,1 Sizun Jiang,1,2 Ellen Cahir-McFarland,1 Manolis Kellis,7 Martha L. Bulyk,3,4,5,6,8,10,* Elliott Kieff,1,2,10 and Benjamin E. Gewurz1,2,10,* 1Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA 2Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA 3Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA 4Harvard Medical School, Boston, MA 02115, USA 5Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA 6Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA 7Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 8Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA 9Co-first author 10Co-senior author *Correspondence: mbulyk@receptor.med.harvard.edu (M.L.B.), bgewurz@partners.org (B.E.G.) http://dx.doi.org/10.1016/j.celrep.2014.07.037 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

[1]  Yuqi Cai,et al.  Foxm1 transcription factor is required for the initiation of lung tumorigenesis by oncogenic KrasG12D , 2014, Oncogene.

[2]  Yan Li,et al.  A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.

[3]  C. Glass,et al.  Impact of natural genetic variation on enhancer selection and function , 2013, Nature.

[4]  Brian J. Smith,et al.  Identification of Candidate B-Lymphoma Genes by Cross-Species Gene Expression Profiling , 2013, PloS one.

[5]  D. Odom,et al.  CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets , 2013, Cell.

[6]  A. Gartel,et al.  FOX(M1) News—It Is Cancer , 2013, Molecular Cancer Therapeutics.

[7]  X. Chen,et al.  The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism , 2012, Molecular and Cellular Biology.

[8]  Marc D. Perry,et al.  ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.

[9]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[10]  K. Al-Kuraya,et al.  Overexpression of FoxM1 offers a promising therapeutic target in diffuse large B-cell lymphoma , 2012, Haematologica.

[11]  L. Staudt,et al.  Pathogenetic importance and therapeutic implications of NF‐κB in lymphoid malignancies , 2012, Immunological reviews.

[12]  J. Decaprio,et al.  The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression. , 2012, Genes & development.

[13]  R. Sen,et al.  NF‐κB function in B lymphocytes , 2012, Immunological reviews.

[14]  S. Ghosh,et al.  NF-κB, the first quarter-century: remarkable progress and outstanding questions. , 2012, Genes & development.

[15]  J. Ragoussis,et al.  Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding , 2011, Nature Immunology.

[16]  Michael Karin,et al.  Inflammation meets cancer, with NF-κB as the matchmaker , 2011, Nature Immunology.

[17]  S. Smale.  Hierarchies of NF-κB target-gene regulation , 2011, Nature Immunology.

[18]  John Quackenbush,et al.  Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth , 2011, Proceedings of the National Academy of Sciences.

[19]  R. Lea,et al.  Integrative genomic profiling reveals conserved genetic mechanisms for tumorigenesis in common entities of non‐Hodgkin's lymphoma , 2011, Genes, chromosomes & cancer.

[20]  G. McFadden,et al.  Modulation of NF-κB signalling by microbial pathogens , 2011, Nature Reviews Microbiology.

[21]  Tao Ye,et al.  seqMINER: an integrated ChIP-seq data interpretation platform , 2010, Nucleic acids research.

[22]  Vsevolod J. Makeev,et al.  Deep and wide digging for binding motifs in ChIP-Seq data , 2010, Bioinform..

[23]  Mariano J. Alvarez,et al.  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers , 2010, Molecular systems biology.

[24]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[25]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[26]  M. Gerstein,et al.  Variation in Transcription Factor Binding Among Humans , 2010, Science.

[27]  J. Ragoussis,et al.  Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. , 2010, Immunity.

[28]  Gioacchino Natoli,et al.  Control of NF-kappaB-dependent transcriptional responses by chromatin organization. , 2009, Cold Spring Harbor perspectives in biology.

[29]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[30]  L. Staudt,et al.  Stromal gene signatures in large-B-cell lymphomas. , 2008, The New England journal of medicine.

[31]  P. Park,et al.  Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.

[32]  Joshy George,et al.  Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. , 2007, Molecular cell.

[33]  S. Gerondakis,et al.  Unravelling the complexities of the NF-κB signalling pathway using mouse knockout and transgenic models , 2006, Oncogene.

[34]  Richard G. Jenner,et al.  Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[35]  A. Hoffmann,et al.  Unique CD40-mediated biological program in B cell activation requires both type 1 and type 2 NF-kappaB activation pathways. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  T. Yamazaki,et al.  Contribution of BCAP to maintenance of mature B cells through c-Rel , 2003, Nature Immunology.

[37]  Jiajian Liu,et al.  Distinct Pathways for NF-κB Regulation Are Associated with Aberrant Macrophage IL-12 Production in Lupus- and Diabetes-Prone Mouse Strains1 , 2003, The Journal of Immunology.

[38]  K. Yamamoto,et al.  The glucocorticoid receptor inhibits NFkappaB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. , 2000, Genes & development.

[39]  E. Kieff,et al.  NF-kappa B inhibition causes spontaneous apoptosis in Epstein-Barr virus-transformed lymphoblastoid cells. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[40]  W. Tam,et al.  c-Rel is a target of pentoxifylline-mediated inhibition of T lymphocyte activation. , 1997, Immunity.

[41]  U. Nater,et al.  Epstein-Barr virus. , 1991, The Journal of family practice.

[42]  Alexander Hoffmann,et al.  A single NFκB system for both canonical and non-canonical signaling , 2011, Cell Research.

[43]  Shao-Cong Sun,et al.  Non-canonical NF-κB signaling pathway , 2011, Cell Research.

[44]  M. Lenardo,et al.  The nuclear signaling of NF-κB: current knowledge, new insights, and future perspectives , 2010, Cell Research.

[45]  S. Smale,et al.  Selectivity of the NF- k B Response , 2010 .

[46]  A. Hoffmann,et al.  One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. , 2004, Cell.

[47]  M. Karin,et al.  The two NF-kappaB activation pathways and their role in innate and adaptive immunity. , 2004, Trends in immunology.

[48]  Mark Gerstein,et al.  Distribution of NF-kappaB-binding sites across human chromosome 22. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[49]  S. Saccani,et al.  Modulation of NF-kappaB activity by exchange of dimers. , 2003, Molecular cell.

[50]  C. Glass,et al.  Exchange of N-CoR corepressor and Tip60 coactivator complexes links gene expression by NF-kappaB and beta-amyloid precursor protein. , 2002, Cell.

[51]  N. Kudo,et al.  A nuclear export signal in the N-terminal regulatory domain of IkappaBalpha controls cytoplasmic localization of inactive NF-kappaB/IkappaBalpha complexes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[52]  F. E. Chen,et al.  Regulation of DNA binding by Rel/NF-kappaB transcription factors: structural views. , 1999, Oncogene.

[53]  R. Hay,et al.  Nuclear retention of IkappaBalpha protects it from signal-induced degradation and inhibits nuclear factor kappaB transcriptional activation. , 1999, The Journal of biological chemistry.

[54]  S. Harrison,et al.  Structure of the NF-kappa B p50 homodimer bound to DNA. , 1995, Nature.

[55]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[56]  U. Klein,et al.  Article Transcriptional Regulation of Germinal Center B and Plasma Cell Fates by Dynamical Control of Irf4 , 2022 .