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Christopher Benner

Title(s)Assistant Professor In Residence, Medicine
SchoolHealth Sciences
Phone858-534-9449
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    Collapse Biography 
    Collapse Education and Training
    University of California, San Diego, La JollaPhD01/2009Bioinformatics
    University of California, San Diego , La JollaBS06/2002Bioengineering

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Uncovering how transcription and chromatin 3D structure impact one another during cellular activation
    NIH/NIGMS R01GM134366Sep 16, 2019 - Jun 30, 2024
    Role: Principal Investigator

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    Collapse Websites

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers. Cell. 2019 Oct 03; 179(2):373-391.e27. PMID: 31585079.
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    2. López-Moyado IF, Tsagaratou A, Yuita H, Seo H, Delatte B, Heinz S, Benner C, Rao A. Paradoxical association of TET loss of function with genome-wide DNA hypomethylation. Proc Natl Acad Sci U S A. 2019 Aug 01. PMID: 31371502.
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    3. Ramms B, Patel S, Nora C, Pessentheiner AR, Chang MW, Green CR, Golden GJ, Secrest P, Krauss RM, Metallo CM, Benner C, Alexander VJ, Witztum JL, Tsimikas S, Esko JD, Gordts PLSM. ApoC-III ASO Promotes Tissue LPL Activity in Absence of ApoE-Mediated TRL Clearance. J Lipid Res. 2019 May 14. PMID: 31092690.
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    4. Hishida T, Vazquez-Ferrer E, Hishida-Nozaki Y, Sancho-Martinez I, Takahashi Y, Hatanaka F, Wu J, Ocampo A, Reddy P, Wu MZ, Gerken L, Shaw RJ, Rodriguez Esteban C, Benner C, Nakagawa H, Guillen Garcia P, Nuñez Delicado E, Castells A, Campistol JM, Liu GH, Izpisua Belmonte JC. Mutations in foregut SOX2+ cells induce efficient proliferation via CXCR2 pathway. Protein Cell. 2019 Jul; 10(7):485-495. PMID: 31041783.
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    5. Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019 04 03; 10(1):1523. PMID: 30944313.
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    6. Wegner M, Diehl V, Bittl V, de Bruyn R, Wiechmann S, Matthess Y, Hebel M, Hayes MG, Schaubeck S, Benner C, Heinz S, Bremm A, Dikic I, Ernst A, Kaulich M. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome. Elife. 2019 Mar 06; 8. PMID: 30838976.
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    7. Karakus U, Thamamongood T, Ciminski K, Ran W, Günther SC, Pohl MO, Eletto D, Jeney C, Hoffmann D, Reiche S, Schinköthe J, Ulrich R, Wiener J, Hayes MGB, Chang MW, Hunziker A, Yángüez E, Aydillo T, Krammer F, Oderbolz J, Meier M, Oxenius A, Halenius A, Zimmer G, Benner C, Hale BG, García-Sastre A, Beer M, Schwemmle M, Stertz S. MHC class II proteins mediate cross-species entry of bat influenza viruses. Nature. 2019 03; 567(7746):109-112. PMID: 30787439.
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    8. Fonseca GJ, Tao J, Westin EM, Duttke SH, Spann NJ, Strid T, Shen Z, Stender JD, Sakai M, Link VM, Benner C, Glass CK. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun. 2019 01 24; 10(1):414. PMID: 30679424.
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    9. Carlin AF, Wen J, Vizcarra EA, McCauley M, Chaillon A, Akrami K, Kim C, Ngono AE, Lara-Marquez ML, Smith DM, Glass CK, Schooley RT, Benner C, Shresta S. A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela. PLoS Negl Trop Dis. 2018 12; 12(12):e0007053. PMID: 30596671.
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    10. Carlin AF, Vizcarra EA, Branche E, Viramontes KM, Suarez-Amaran L, Ley K, Heinz S, Benner C, Shresta S, Glass CK. Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages. Proc Natl Acad Sci U S A. 2018 09 25; 115(39):E9172-E9181. PMID: 30206152.
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    11. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2018 09; 561(7721):E1. PMID: 29973714.
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    12. Heinz S, Texari L, Hayes MGB, Urbanowski M, Chang MW, Givarkes N, Rialdi A, White KM, Albrecht RA, Pache L, Marazzi I, García-Sastre A, Shaw ML, Benner C. Transcription Elongation Can Affect Genome 3D Structure. Cell. 2018 Sep 06; 174(6):1522-1536.e22. PMID: 30146161.
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    13. Zhu Q, Hoong N, Aslanian A, Hara T, Benner C, Heinz S, Miga KH, Ke E, Verma S, Soroczynski J, Yates JR, Hunter T, Verma IM. Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer. Mol Cell. 2018 06 07; 70(5):842-853.e7. PMID: 29861157.
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    14. Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 03 01; 69(5):915. PMID: 29499140.
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    15. Prohaska TA, Que X, Diehl CJ, Hendrikx S, Chang MW, Jepsen K, Glass CK, Benner C, Witztum JL. Massively Parallel Sequencing of Peritoneal and Splenic B Cell Repertoires Highlights Unique Properties of B-1 Cell Antibodies. J Immunol. 2018 03 01; 200(5):1702-1717. PMID: 29378911.
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    16. Neal S, Jaeger PA, Duttke SH, Benner C, K Glass C, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 01 18; 69(2):306-320.e4. PMID: 29351849.
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    17. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2017 12 21; 552(7685):430. PMID: 29168501.
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    18. Franks TM, McCloskey A, Shokirev MN, Benner C, Rathore A, Hetzer MW. Nup98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes Dev. 2017 11 15; 31(22):2222-2234. PMID: 29269482.
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    19. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2017 11 16; 551(7680):340-345. PMID: 29144460.
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    20. Kelso TWR, Porter DK, Amaral ML, Shokhirev MN, Benner C, Hargreaves DC. Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers. Elife. 2017 10 02; 6. PMID: 28967863.
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    21. Rahnamoun H, Lu H, Duttke SH, Benner C, Glass CK, Lauberth SM. Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling. Nat Commun. 2017 09 29; 8(1):754. PMID: 28963538.
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    22. Arnoult N, Correia A, Ma J, Merlo A, Garcia-Gomez S, Maric M, Tognetti M, Benner CW, Boulton SJ, Saghatelian A, Karlseder J. Regulation of DNA repair pathway choice in S and G2 phases by the NHEJ inhibitor CYREN. Nature. 2017 09 20; 549(7673):548-552. PMID: 28959974.
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    23. Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer MW. Corrigendum: Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev. 2017 04 15; 31(8):845. PMID: 28512238.
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    24. Koyama Y, Wang P, Liang S, Iwaisako K, Liu X, Xu J, Zhang M, Sun M, Cong M, Karin D, Taura K, Benner C, Heinz S, Bera T, Brenner DA, Kisseleva T. Mesothelin/mucin 16 signaling in activated portal fibroblasts regulates cholestatic liver fibrosis. J Clin Invest. 2017 Apr 03; 127(4):1254-1270. PMID: 28287406.
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    25. Ibarra A, Benner C, Tyagi S, Cool J, Hetzer MW. Nucleoporin-mediated regulation of cell identity genes. Genes Dev. 2016 Oct 15; 30(20):2253-2258. PMID: 27807035.
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    26. Hetzel J, Duttke SH, Benner C, Chory J. Nascent RNA sequencing reveals distinct features in plant transcription. Proc Natl Acad Sci U S A. 2016 10 25; 113(43):12316-12321. PMID: 27729530.
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    27. Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature. 2016 08 11; 536(7615):205-9. PMID: 27487209.
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    28. Meitinger F, Anzola JV, Kaulich M, Richardson A, Stender JD, Benner C, Glass CK, Dowdy SF, Desai A, Shiau AK, Oegema K. 53BP1 and USP28 mediate p53 activation and G1 arrest after centrosome loss or extended mitotic duration. J Cell Biol. 2016 07 18; 214(2):155-66. PMID: 27432897.
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    29. Franks TM, Benner C, Narvaiza I, Marchetto MC, Young JM, Malik HS, Gage FH, Hetzer MW. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev. 2016 05 15; 30(10):1155-71. PMID: 27198230.
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    30. Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JSY, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, Merad M, Jin J, Weirauch M, Heinz S, Benner C, van Bakel H, Basler C, García-Sastre A, Bukreyev A, Marazzi I. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science. 2016 May 27; 352(6289):aad7993. PMID: 27127234.
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    31. Ding N, Hah N, Yu RT, Sherman MH, Benner C, Leblanc M, He M, Liddle C, Downes M, Evans RM. BRD4 is a novel therapeutic target for liver fibrosis. Proc Natl Acad Sci U S A. 2015 Dec 22; 112(51):15713-8. PMID: 26644586.
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    32. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Perspectives on Unidirectional versus Divergent Transcription. Mol Cell. 2015 Nov 05; 60(3):348-9. PMID: 26545075.
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    33. Denli AM, Narvaiza I, Kerman BE, Pena M, Benner C, Marchetto MC, Diedrich JK, Aslanian A, Ma J, Moresco JJ, Moore L, Hunter T, Saghatelian A, Gage FH. Primate-specific ORF0 contributes to retrotransposon-mediated diversity. Cell. 2015 Oct 22; 163(3):583-93. PMID: 26496605.
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    34. Benner C, Isoda T, Murre C. New roles for DNA cytosine modification, eRNA, anchors, and superanchors in developing B cell progenitors. Proc Natl Acad Sci U S A. 2015 Oct 13; 112(41):12776-81. PMID: 26417104.
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    35. Wu MZ, Chen SF, Nieh S, Benner C, Ger LP, Jan CI, Ma L, Chen CH, Hishida T, Chang HT, Lin YS, Montserrat N, Gascon P, Sancho-Martinez I, Izpisua Belmonte JC. Hypoxia Drives Breast Tumor Malignancy through a TET-TNFa-p38-MAPK Signaling Axis. Cancer Res. 2015 Sep 15; 75(18):3912-24. PMID: 26294212.
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    36. Jacinto FV, Benner C, Hetzer MW. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes Dev. 2015 Jun 15; 29(12):1224-38. PMID: 26080816.
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    37. Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015 May 21; 521(7552):316-21. PMID: 25945737.
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    38. Estarás C, Benner C, Jones KA. SMADs and YAP compete to control elongation of ß-catenin:LEF-1-recruited RNAPII during hESC differentiation. Mol Cell. 2015 Jun 04; 58(5):780-93. PMID: 25936800.
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    39. Puto LA, Benner C, Hunter T. The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer. Oncoscience. 2015; 2(4):362-72. PMID: 26097870.
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    40. Kashyap MK, Kumar D, Villa R, La Clair JJ, Benner C, Sasik R, Jones H, Ghia EM, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Targeting the spliceosome in chronic lymphocytic leukemia with the macrolides FD-895 and pladienolide-B. Haematologica. 2015 Jul; 100(7):945-54. PMID: 25862704.
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    41. Miller MS, Rialdi A, Ho JS, Tilove M, Martinez-Gil L, Moshkina NP, Peralta Z, Noel J, Melegari C, Maestre AM, Mitsopoulos P, Madrenas J, Heinz S, Benner C, Young JA, Feagins AR, Basler CF, Fernandez-Sesma A, Becherel OJ, Lavin MF, van Bakel H, Marazzi I. Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis. Nat Immunol. 2015 May; 16(5):485-94. PMID: 25822250.
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    42. Chang AT, Liu Y, Ayyanathan K, Benner C, Jiang Y, Prokop JW, Paz H, Wang D, Li HR, Fu XD, Rauscher FJ, Yang J. An evolutionarily conserved DNA architecture determines target specificity of the TWIST family bHLH transcription factors. Genes Dev. 2015 Mar 15; 29(6):603-16. PMID: 25762439.
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    43. Kurian L, Aguirre A, Sancho-Martinez I, Benner C, Hishida T, Nguyen TB, Reddy P, Nivet E, Krause MN, Nelles DA, Esteban CR, Campistol JM, Yeo GW, Belmonte JCI. Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development. Circulation. 2015 Apr 07; 131(14):1278-1290. PMID: 25739401.
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    44. Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015 Mar; 16(3):144-54. PMID: 25650801.
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    45. Duttke SHC, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Human promoters are intrinsically directional. Mol Cell. 2015 Feb 19; 57(4):674-684. PMID: 25639469.
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    46. Hah N, Benner C, Chong LW, Yu RT, Downes M, Evans RM. Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):E297-302. PMID: 25564661.
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    47. Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, Liang G, Tang Z, Mathé E, Benner C, Dubois W, Nelson S, Vian L, Oliveira TY, Jankovic M, Hakim O, Gazumyan A, Pavri R, Awasthi P, Song B, Liu G, Chen L, Zhu S, Feigenbaum L, Staudt L, Murre C, Ruan Y, Robbiani DF, Pan-Hammarström Q, Nussenzweig MC, Casellas R. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell. 2014 Dec 18; 159(7):1524-37. PMID: 25483777.
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    48. Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. Nucleic Acids Res. 2014 Nov 10; 42(20):12570-84. PMID: 25352550.
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    49. Li X, Liang Y, LeBlanc M, Benner C, Zheng Y. Function of a Foxp3 cis-element in protecting regulatory T cell identity. Cell. 2014 Aug 14; 158(4):734-748. PMID: 25126782.
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    50. Benner C, van der Meulen T, Cacéres E, Tigyi K, Donaldson CJ, Huising MO. The transcriptional landscape of mouse beta cells compared to human beta cells reveals notable species differences in long non-coding RNA and protein-coding gene expression. BMC Genomics. 2014 Jul 22; 15:620. PMID: 25051960.
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    51. Liu GH, Suzuki K, Li M, Qu J, Montserrat N, Tarantino C, Gu Y, Yi F, Xu X, Zhang W, Ruiz S, Plongthongkum N, Zhang K, Masuda S, Nivet E, Tsunekawa Y, Soligalla RD, Goebl A, Aizawa E, Kim NY, Kim J, Dubova I, Li Y, Ren R, Benner C, Del Sol A, Bueren J, Trujillo JP, Surralles J, Cappelli E, Dufour C, Esteban CR, Belmonte JCI. Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. Nat Commun. 2014 Jul 07; 5:4330. PMID: 24999918.
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    52. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 03; 15(1):31-6. PMID: 24996168.
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    53. Crotti A, Benner C, Kerman BE, Gosselin D, Lagier-Tourenne C, Zuccato C, Cattaneo E, Gage FH, Cleveland DW, Glass CK. Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. Nat Neurosci. 2014 Apr; 17(4):513-21. PMID: 24584051.
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    54. Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Izpisua Belmonte JC. Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell. 2014 Jan; 5(1):59-68. PMID: 24474197.
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    55. Benner C, Konovalov S, Mackintosh C, Hutt KR, Stunnenberg R, Garcia-Bassets I. Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions. PLoS Genet. 2013 Nov; 9(11):e1003906. PMID: 24244184.
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    56. Marchetto MCN, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola ACM, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH. Differential L1 regulation in pluripotent stem cells of humans and apes. Nature. 2013 Nov 28; 503(7477):525-529. PMID: 24153179.
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    57. Almenar-Queralt A, Kim SN, Benner C, Herrera CM, Kang DE, Garcia-Bassets I, Goldstein LS. Presenilins regulate neurotrypsin gene expression and neurotrypsin-dependent agrin cleavage via cyclic AMP response element-binding protein (CREB) modulation. J Biol Chem. 2013 Dec 06; 288(49):35222-36. PMID: 24145027.
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    58. Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. Effect of natural genetic variation on enhancer selection and function. Nature. 2013 Nov 28; 503(7477):487-92. PMID: 24121437.
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    59. Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Belmonte JC. Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell. 2013 Aug 27. PMID: 23982742.
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    60. Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell. 2013 Aug 08; 51(3):310-25. PMID: 23932714.
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    61. Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature. 2013 Jun 27; 498(7455):511-5. PMID: 23728303.
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    62. Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W, Längst G, Benner C, Rehli M. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. 2013 Jul; 41(13):6391-402. PMID: 23658224.
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    63. Mansson R, Welinder E, Åhsberg J, Lin YC, Benner C, Glass CK, Lucas JS, Sigvardsson M, Murre C. Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate. Proc Natl Acad Sci U S A. 2012 Dec 18; 109(51):21028-33. PMID: 23213261.
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    64. Lin YC, Benner C, Mansson R, Heinz S, Miyazaki K, Miyazaki M, Chandra V, Bossen C, Glass CK, Murre C. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol. 2012 Dec; 13(12):1196-204. PMID: 23064439.
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    65. Kisseleva T, Cong M, Paik Y, Scholten D, Jiang C, Benner C, Iwaisako K, Moore-Morris T, Scott B, Tsukamoto H, Evans SM, Dillmann W, Glass CK, Brenner DA. Myofibroblasts revert to an inactive phenotype during regression of liver fibrosis. Proc Natl Acad Sci U S A. 2012 Jun 12; 109(24):9448-53. PMID: 22566629.
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    66. Pham TH, Benner C, Lichtinger M, Schwarzfischer L, Hu Y, Andreesen R, Chen W, Rehli M. Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. Blood. 2012 Jun 14; 119(24):e161-71. PMID: 22550342.
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    67. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet. 2011 Dec; 7(12):e1002401. PMID: 22174696.
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    68. Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity. 2011 Sep 23; 35(3):413-25. PMID: 21903424.
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    69. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature. 2011 May 15; 474(7351):390-4. PMID: 21572438.
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    70. Sullivan AL, Benner C, Heinz S, Huang W, Xie L, Miano JM, Glass CK. Serum response factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages. Mol Cell Biol. 2011 Feb; 31(4):861-75. PMID: 21135125.
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    71. Barish GD, Yu RT, Karunasiri M, Ocampo CB, Dixon J, Benner C, Dent AL, Tangirala RK, Evans RM. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev. 2010 Dec 15; 24(24):2760-5. PMID: 21106671.
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    72. Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, Liu WT, Ohgi KA, Benner C, Garcia-Bassets I, Aggarwal AK, Desai A, Dorrestein PC, Glass CK, Rosenfeld MG. PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature. 2010 Jul 22; 466(7305):508-12. PMID: 20622854.
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    73. Stender JD, Kim K, Charn TH, Komm B, Chang KC, Kraus WL, Benner C, Glass CK, Katzenellenbogen BS. Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol. 2010 Aug; 30(16):3943-55. PMID: 20547749.
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    74. Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul; 11(7):635-43. PMID: 20543837.
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    75. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28; 38(4):576-89. PMID: 20513432.
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    76. Wiesner P, Choi SH, Almazan F, Benner C, Huang W, Diehl CJ, Gonen A, Butler S, Witztum JL, Glass CK, Miller YI. Low doses of lipopolysaccharide and minimally oxidized low-density lipoprotein cooperatively activate macrophages via nuclear factor kappa B and activator protein-1: possible mechanism for acceleration of atherosclerosis by subclinical endotoxemia. Circ Res. 2010 Jul 09; 107(1):56-65. PMID: 20489162.
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    77. Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M, Dietmaier W, Thiede C, Holler E, Andreesen R, Rehli M. General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res. 2010 Feb 15; 70(4):1398-407. PMID: 20145141.
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    78. El Chartouni C, Benner C, Eigner M, Lichtinger M, Rehli M. Transcriptional effects of colony-stimulating factor-1 in mouse macrophages. Immunobiology. 2010 Jun; 215(6):466-74. PMID: 19758725.
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    79. Ghisletti S, Huang W, Jepsen K, Benner C, Hardiman G, Rosenfeld MG, Glass CK. Cooperative NCoR/SMRT interactions establish a corepressor-based strategy for integration of inflammatory and anti-inflammatory signaling pathways. Genes Dev. 2009 Mar 15; 23(6):681-93. PMID: 19299558.
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    80. Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA. In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics. 2008 Feb 07; 9:70. PMID: 18257930.
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    81. Hevener AL, Olefsky JM, Reichart D, Nguyen MT, Bandyopadyhay G, Leung HY, Watt MJ, Benner C, Febbraio MA, Nguyen AK, Folian B, Subramaniam S, Gonzalez FJ, Glass CK, Ricote M. Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones. J Clin Invest. 2007 Jun; 117(6):1658-69. PMID: 17525798.
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    82. Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan JB, Duan L, Glass CK, Rosenfeld MG, Fu XD. Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A. 2007 Mar 20; 104(12):4852-7. PMID: 17360330.
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    83. Maurya MR, Benner C, Pradervand S, Glass C, Subramaniam S. Systems biology of macrophages. Adv Exp Med Biol. 2007; 598:62-79. PMID: 17892205.
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    84. Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC, Ribeiro AA, Murphy RC, Ulevitch RJ, Fearns C, Reichart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA. Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4. J Lipid Res. 2006 May; 47(5):1097-111. PMID: 16479018.
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    85. Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell. 2005 Sep 09; 122(5):707-21. PMID: 16143103.
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    86. Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. BMC Bioinformatics. 2004 Apr 20; 5:42. PMID: 15099405.
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