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Publications

2014
    Bonhoure, N., Bounova, G., Bernasconi, D., Praz, V., Lammers, F., Canella, D., Willis, I. M., Herr, W., Hernandez, N., Delorenzi, M.: Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Res 2014,
    URL

2013
    Michaud, J., Praz, V., James Faresse, N., Jnbaptiste, C. K., Tyagi, S., Schutz, F., Herr, W.: HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy. Genome Res 2013, 23:907-16. URL

    Lazarus, M. B., Jiang, J., Kapuria, V., Bhuiyan, T., Janetzko, J., Zandberg, W. F., Vocadlo, D. J., Herr, W., Walker, S.: HCF-1 is cleaved in the active site of O-GlcNAc transferase. Science 2013, 342:1235-9. URL

2012
    Park, J., Lammers, F., Herr, W., Song, J. J.: HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation. Proc Natl Acad Sci U S A 2012, 109:17430-5. URL

    Le Martelot, G., Canella, D., Symul, L., Migliavacca, E., Gilardi, F., Liechti, R., Martin, O., Harshman, K., Delorenzi, M., Desvergne, B., Herr, W., Deplancke, B., Schibler, U., Rougemont, J., Guex, N., Hernandez, N., Naef, F.: Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol 2012, 10:e1001442. URL

    Canella, D., Bernasconi, D., Gilardi, F., LeMartelot, G., Migliavacca, E., Praz, V., Cousin, P., Delorenzi, M., Hernandez, N., CycliX Consortium*, *W. Herr is a member of the CycliX Consortium: A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. Genome Res 2012, 22:666-80. URL

2011
    Rodriguez-Jato, S., Busturia, A., Herr, W.: Drosophila melanogaster dHCF Interacts with both PcG and TrxG Epigenetic Regulators. PLoS One 2011, 6:e27479. URL

    Capotosti, F., Guernier, S., Lammers, F., Waridel, P., Cai, Y., Jin, J., Conaway, J. W., Conaway, R. C., Herr, W.: O-GlcNAc Transferase Catalyzes Site-Specific Proteolysis of HCF-1. Cell 2011, 144:376-88. URL

2010
    Mangone, M., Myers, M. P., Herr, W.: Role of the HCF-1 basic region in sustaining cell proliferation. PLoS One 2010, 5:e9020. URL

    Furrer, M., Balbi, M., Albarca-Aguilera, M., Gallant, M., Herr, W., Gallant, P.: Drosophila Myc interacts with host cell factor (dHCF) to activate transcription and control growth. J Biol Chem 2010, 285:39623-36. URL

2009
    Tyagi, S., Herr, W.: E2F1 mediates DNA damage and apoptosis through HCF-1 and the MLL family of histone methyltransferases. Embo J 2009, 28:3185-95. URL

2007
    Tyagi, S., Chabes, A. L., Wysocka, J., Herr, W.: E2F activation of S phase promoters via association with HCF-1 and the MLL family of histone H3K4 methyltransferases. Mol Cell 2007, 27:107-19. URL

    Lee, S., Horn, V., Julien, E., Liu, Y., Wysocka, J., Bowerman, B., Hengartner, M. O., Herr, W.: Epigenetic Regulation of Histone H3 Serine 10 Phosphorylation Status by HCF-1 Proteins in C. elegans and Mammalian Cells. PLoS ONE 2007, 2:e1213. URL

    Capotosti, F., Hsieh, J. J., Herr, W.: Species selectivity of mixed-lineage leukemia/trithorax and HCF proteolytic maturation pathways. Mol Cell Biol 2007, 27:7063-72. URL

2005
    Klejman, M. P., Zhao, X., van Schaik, F. M., Herr, W., Timmers, H. T.: Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants. Nucleic Acids Res 2005, 33:5426-36. URL

2004
    Yokoyama, A., Wang, Z., Wysocka, J., Sanyal, M., Aufiero, D. J., Kitabayashi, I., Herr, W., Cleary, M. L.: Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol Cell Biol 2004, 24:5639-49. URL

    Tubon, T. C., Tansey, W. P., Herr, W.: A nonconserved surface of the TFIIB zinc ribbon domain plays a direct role in RNA polymerase II recruitment. Mol Cell Biol 2004, 24:2863-74. URL

    Julien, E., Herr, W.: A switch in mitotic histone H4 lysine 20 methylation status is linked to M phase defects upon loss of HCF-1. Mol Cell 2004, 14:713-25. URL

2003
    Zhao, X., Schramm, L., Hernandez, N., Herr, W.: A shared surface of TBP directs RNA polymerase II and III transcription via association with different TFIIB family members. Mol Cell 2003, 11:151-61. URL

    Zhao, X., Herr, W.: Role of the inhibitory DNA-binding surface of human TATA-binding protein in recruitment of human TFIIB family members. Mol Cell Biol 2003, 23:8152-60. URL

    Wysocka, J., Myers, M. P., Laherty, C. D., Eisenman, R. N., Herr, W.: Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev 2003, 17:896-911. URL

    Wysocka, J., Herr, W.: The herpes simplex virus VP16-induced complex: the makings of a regulatory switch. Trends Biochem Sci 2003, 28:294-304. URL

    Julien, E., Herr, W.: Proteolytic processing is necessary to separate and ensure proper cell growth and cytokinesis functions of HCF-1. Embo J 2003, 22:2360-9. URL

2002
    Zhao, X., Herr, W.: A regulated two-step mechanism of TBP binding to DNA: a solvent-exposed surface of TBP inhibits TATA box recognition. Cell 2002, 108:615-27. URL

    Reilly, P. T., Wysocka, J., Herr, W.: Inactivation of the retinoblastoma protein family can bypass the HCF-1 defect in tsBN67 cell proliferation and cytokinesis. Mol Cell Biol 2002, 22:6767-78. URL

    Reilly, P. T., Herr, W.: Spontaneous reversion of tsBN67 cell proliferation and cytokinesis defects in the absence of HCF-1 function. Exp Cell Res 2002, 277:119-30. URL

2001
    Wysocka, J., Reilly, P. T., Herr, W.: Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells. Mol Cell Biol 2001, 21:3820-9. URL

    Wysocka, J., Liu, Y., Kobayashi, R., Herr, W.: Developmental and cell-cycle regulation of Caenorhabditis elegans HCF phosphorylation. Biochemistry 2001, 40:5786-94. URL

    Lee, S., Herr, W.: Stabilization but not the transcriptional activity of herpes simplex virus VP16-induced complexes is evolutionarily conserved among HCF family members. J Virol 2001, 75:12402-11. URL

    Babb, R., Huang, C. C., Aufiero, D. J., Herr, W.: DNA recognition by the herpes simplex virus transactivator VP16: a novel DNA-binding structure. Mol Cell Biol 2001, 21:4700-12. URL

2000
    Wilson, A. C., Boutros, M., Johnson, K. M., Herr, W.: HCF-1 amino- and carboxy-terminal subunit association through two separate sets of interaction modules: involvement of fibronectin type 3 repeats. Mol Cell Biol 2000, 20:6721-30. URL

1999
    Liu, Y., Hengartner, M. O., Herr, W.: Selected elements of herpes simplex virus accessory factor HCF are highly conserved in Caenorhabditis elegans. Mol Cell Biol 1999, 19:909-15. URL

    Liu, Y., Gong, W., Huang, C. C., Herr, W., Cheng, X.: Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16. Genes Dev 1999, 13:1692-703. URL

1998
    Hinkley, C. S., Blasco, M. A., Funk, W. D., Feng, J., Villeponteau, B., Greider, C. W., Herr, W.: The mouse telomerase RNA 5"-end lies just upstream of the telomerase template sequence. Nucleic Acids Res 1998, 26:532-6. URL

    Herr, W.: The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation. Cold Spring Harb Symp Quant Biol 1998, 63:599-607. URL

1997
    Wilson, A. C., Freiman, R. N., Goto, H., Nishimoto, T., Herr, W.: VP16 targets an amino-terminal domain of HCF involved in cell cycle progression. Mol Cell Biol 1997, 17:6139-46. URL

    Tansey, W. P., Herr, W.: Selective use of TBP and TFIIB revealed by a TATA-TBP-TFIIB array with altered specificity. Science 1997, 275:829-31. URL

    Tansey, W. P., Herr, W.: TAFs: guilt by association?. Cell 1997, 88:729-32. URL

    Lai, J. S., Herr, W.: Interdigitated residues within a small region of VP16 interact with Oct-1, HCF, and DNA. Mol Cell Biol 1997, 17:3937-46. URL

    Goto, H., Motomura, S., Wilson, A. C., Freiman, R. N., Nakabeppu, Y., Fukushima, K., Fujishima, M., Herr, W., Nishimoto, T.: A single-point mutation in HCF causes temperature-sensitive cell-cycle arrest and disrupts VP16 function. Genes Dev 1997, 11:726-37. URL

    Freiman, R. N., Herr, W.: Viral mimicry: common mode of association with HCF by VP16 and the cellular protein LZIP. Genes Dev 1997, 11:3122-7. URL

    Cleary, M. A., Pendergrast, P. S., Herr, W.: Structural flexibility in transcription complex formation revealed by protein-DNA photocrosslinking. Proc Natl Acad Sci U S A 1997, 94:8450-5. URL

    Babb, R., Cleary, M. A., Herr, W.: OCA-B is a functional analog of VP16 but targets a separate surface of the Oct-1 POU domain. Mol Cell Biol 1997, 17:7295-305. URL

    Atanasoski, S., Schreiber, E., Fontana, A., Herr, W.: N-Oct 5 is generated by in vitro proteolysis of the neural POU-domain protein N-Oct 3. Oncogene 1997, 14:1287-94. URL

1996
    Mittal, V., Cleary, M. A., Herr, W., Hernandez, N.: The Oct-1 POU-specific domain can stimulate small nuclear RNA gene transcription by stabilizing the basal transcription complex SNAPc. Mol Cell Biol 1996, 16:1955-65. URL

    LaMarco, K., Wilson, A.C., and Herr, W.: Herpes simplex virus drug screen. 1996,


    Huang, C. C., Herr, W.: Differential control of transcription by homologous homeodomain coregulators. Mol Cell Biol 1996, 16:2967-76. URL

1995
    Wilson, A. C., Peterson, M. G., Herr, W.: The HCF repeat is an unusual proteolytic cleavage signal. Genes Dev 1995, 9:2445-58. URL

    Wilson, A. C., Parrish, J. E., Massa, H. F., Nelson, D. L., Trask, B. J., Herr, W.: The gene encoding the VP16-accessory protein HCF (HCFC1) resides in human Xq28 and is highly expressed in fetal tissues and the adult kidney. Genomics 1995, 25:462-8. URL

    Tansey, W. P., Herr, W.: The ability to associate with activation domains in vitro is not required for the TATA box-binding protein to support activated transcription in vivo. Proc Natl Acad Sci U S A 1995, 92:10550-4. URL

    LaMarco, K., Wilson, A.C., and Herr, W.: Eukaryotic transcription protein; host cell factor. 1995,


    Herr, W. and Kingston, R. : Chromosomes and expression mechanisms: Editorial overview.. Curr. Opin. Genet. Dev. 1995,


    Herr, W., Kingston, R. : Chromosomes and expression mechanisms: Editorial overview. Curr. Opin. Genet. Dev. 1995, 5:151-152. URL

    Herr, W., Cleary, M. A.: The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev 1995, 9:1679-93. URL

    Das, G., Hinkley, C. S., Herr, W.: Basal promoter elements as a selective determinant of transcriptional activator function. Nature 1995, 374:657-60. URL

    Cleary, M. A., Herr, W.: Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain. Mol Cell Biol 1995, 15:2090-100. URL

1994
    Tansey, W. P., Ruppert, S., Tjian, R., Herr, W.: Multiple regions of TBP participate in the response to transcriptional activators in vivo. Genes Dev 1994, 8:2756-69. URL

    Tanaka, M., Herr, W.: Reconstitution of transcriptional activation domains by reiteration of short peptide segments reveals the modular organization of a glutamine-rich activation domain. Mol Cell Biol 1994, 14:6056-67. URL

    Tanaka, M., Clouston, W. M., Herr, W.: The Oct-2 glutamine-rich and proline-rich activation domains can synergize with each other or duplicates of themselves to activate transcription. Mol Cell Biol 1994, 14:6046-55. URL

    Klemm, J. D., Rould, M. A., Aurora, R., Herr, W., Pabo, C. O.: Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 1994, 77:21-32. URL

1993
    Wilson, A. C., LaMarco, K., Peterson, M. G., Herr, W.: The VP16 accessory protein HCF is a family of polypeptides processed from a large precursor protein. Cell 1993, 74:115-25. URL

    Wilson, A. C., Cleary, M. A., Lai, J. S., LaMarco, K., Peterson, M. G., Herr, W.: Combinatorial control of transcription: the herpes simplex virus VP16-induced complex. Cold Spring Harb Symp Quant Biol 1993, 58:167-78. URL

    Herr, W. : The SV40 enhancer: Transcriptional regulation through a hierarchy of combinatorial interactions. In Seminars in Virology 1993: 3-13.

    Herr, W. , Seminars in Virology : The SV40 enhancer: Transcriptional regulation through a hierarchy of combinatorial interactions.. 1993,


    Das, G., Herr, W.: Enhanced activation of the human histone H2B promoter by an Oct-1 variant generated by alternative splicing. J Biol Chem 1993, 268:25026-32. URL

    Cleary, M. A., Stern, S., Tanaka, M., Herr, W.: Differential positive control by Oct-1 and Oct-2: activation of a transcriptionally silent motif through Oct-1 and VP16 corecruitment. Genes Dev 1993, 7:72-83. URL

    Assa-Munt, N., Mortishire-Smith, R. J., Aurora, R., Herr, W., Wright, P. E.: The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage lambda repressor DNA-binding domain. Cell 1993, 73:193-205. URL

1992
    Tanaka, M., Lai, J. S., Herr, W.: Promoter-selective activation domains in Oct-1 and Oct-2 direct differential activation of an snRNA and mRNA promoter. Cell 1992, 68:755-67. URL

    Phares, W., Franza, B. R., Jr., Herr, W.: The kappa B enhancer motifs in human immunodeficiency virus type 1 and simian virus 40 recognize different binding activities in human Jurkat and H9 T cells: evidence for NF-kappa B-independent activation of the kappa B motif. J Virol 1992, 66:7490-8. URL

    Lai, J. S., Herr, W.: Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations. Proc Natl Acad Sci U S A 1992, 89:6958-62. URL

    Lai, J. S., Cleary, M. A., Herr, W.: A single amino acid exchange transfers VP16-induced positive control from the Oct-1 to the Oct-2 homeo domain. Genes Dev 1992, 6:2058-65. URL

    Herr, W.: Oct-1 and Oct-2: Differential transcriptional regulation by proteins that bind to the same DNA sequence In Transcriptional Regulation Edited by McKnight, SL,, Yamamoto, KR; Cold Spring Harbor Laboratory Press; 1992:

    Aurora, R., Herr, W.: Segments of the POU domain influence one another's DNA-binding specificity. Mol Cell Biol 1992, 12:455-67. URL

1991
    Stern, S., Herr, W.: The herpes simplex virus trans-activator VP16 recognizes the Oct-1 homeo domain: evidence for a homeo domain recognition subdomain. Genes Dev 1991, 5:2555-66. URL

    Phares, W., Herr, W.: Functional similarities between human immunodeficiency virus type 1 and simian virus 40 kappa B proto-enhancers. J Virol 1991, 65:2200-10. URL

    Ondek, B., Herr, W.: Stable growth of simian virus 40 recombinants containing multimerized enhancers. J Virol 1991, 65:1596-9. URL

    Herr, W.: Regulation of eukaryotic RNA polymerase II transcription by sequence-specific DNA-binding proteins In The Hormonal Control of Gene Expression Edited by Cohen, P, and Foulkes, J.G.; 1991: 25-56.

    Herr, W.: Gene activation. An agent of suppression. Nature 1991, 350:554-5. URL

1990
    Tanaka, M., Herr, W.: Differential transcriptional activation by Oct-1 and Oct-2: interdependent activation domains induce Oct-2 phosphorylation. Cell 1990, 60:375-86. URL

    Hsieh, C. L., Sturm, R., Herr, W., Francke, U.: The gene for the ubiquitous octamer-binding protein Oct-1 is on human chromosome 1, region cen-q32, and near Ly-22 and Ltw-4 on mouse chromosome 1. Genomics 1990, 6:666-72. URL

1989
    Stern, S., Tanaka, M., Herr, W.: The Oct-1 homoeodomain directs formation of a multiprotein-DNA complex with the HSV transactivator VP16. Nature 1989, 341:624-30. URL

1988
    Tanaka, M., Grossniklaus, U., Herr, W., Hernandez, N.: Activation of the U2 snRNA promoter by the octamer motif defines a new class of RNA polymerase II enhancer elements. Genes Dev 1988, 2:1764-78. URL

    Sturm, R. A., Herr, W.: The POU domain is a bipartite DNA-binding structure. Nature 1988, 336:601-4. URL

    Sturm, R. A., Das, G., Herr, W.: The ubiquitous octamer-binding protein Oct-1 contains a POU domain with a homeo box subdomain. Genes Dev 1988, 2:1582-99. URL

    Shepard, A., Clarke, J., Herr, W.: Simian virus 40 revertant enhancers exhibit restricted host ranges for enhancer function. J Virol 1988, 62:3364-70. URL

    Ondek, B., Gloss, L., Herr, W.: The SV40 enhancer contains two distinct levels of organization. Nature 1988, 333:40-5. URL

    Herr, W., Sturm, R. A., Clerc, R. G., Corcoran, L. M., Baltimore, D., Sharp, P. A., Ingraham, H. A., Rosenfeld, M. G., Finney, M., Ruvkun, G., et al.,: The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes Dev 1988, 2:1513-6. URL

    Baumruker, T., Sturm, R., Herr, W.: OBP100 binds remarkably degenerate octamer motifs through specific interactions with flanking sequences. Genes Dev 1988, 2:1400-13. URL

1987
    Sturm, R., Baumruker, T., Franza, B. R., Jr., Herr, W.: A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer. Genes Dev 1987, 1:1147-60. URL

    Ondek, B., Shepard, A., Herr, W.: Discrete elements within the SV40 enhancer region display different cell-specific enhancer activities. Embo J 1987, 6:1017-25. URL

    Clarke, J., Herr, W.: Activation of mutated simian virus 40 enhancers by amplification of wild-type enhancer elements. J Virol 1987, 61:3536-42. URL

1986
    Herr, W.,, Clarke, J.,, Ondek, B.,, Shepard, A.,, Fox, H.: Duplications within mutated SV40 enhancers that restore enhancer function In Cancer Cells 4: DNA Tumor Viruses Edited by Botchan, M., , Grodzicker, T.,, Sharp, P. A.,; Cold Spring Harbor Laboratory Press; 1986: 95-101.

    Herr, W., Clarke, J., Ondek, B., Shepard, A., Fox, H.: Duplications within mutated SV40 enhancers that restore enhancer function.. Cancer Cells 4/DNA Tumor Viruses 1986,
    95-101.

    Herr, W., Clarke, J.: The SV40 enhancer is composed of multiple functional elements that can compensate for one another. Cell 1986, 45:461-70. URL

1985
    Herr, W., Gluzman, Y.: Duplications of a mutated simian virus 40 enhancer restore its activity. Nature 1985, 313:711-4. URL

    Herr, W.: Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA. Proc Natl Acad Sci U S A 1985, 82:8009-13. URL

1984
    Herr, W., Gilbert, W.: Free and integrated recombinant murine leukemia virus DNAs appear in preleukemic thymuses of AKR/J mice. J Virol 1984, 50:155-62. URL

    Herr, W.: Nucleotide sequence of AKV murine leukemia virus. J Virol 1984, 49:471-8. URL

1983
    Herr, W., Schwartz, D., Gilbert, W.: Isolation and mapping of cDNA hybridization probes specific for ecotropic and nonecotropic murine leukemia proviruses. Virology 1983, 125:139-54. URL

    Herr, W., Perlmutter, A. P., Gilbert, W.: Monoclonal AKR/J thymic leukemias contain multiple JH immunoglobulin gene rearrangements. Proc Natl Acad Sci U S A 1983, 80:7433-6. URL

    Herr, W., Gilbert, W.: Somatically acquired recombinant murine leukemia proviruses in thymic leukemias of AKR/J mice. J Virol 1983, 46:70-82. URL

1982
    Herr, W., Gilbert, W.: Germ-line MuLV reintegrations in AKR/J mice. Nature 1982, 296:865-8. URL

    Herr, W., Corbin, V., Gilbert, W.: Nucleotide sequence of the 3' half of AKV. Nucleic Acids Res 1982, 10:6931-44. URL

1981
    Peattie, D. A., Herr, W.: Chemical probing of the tRNA--ribosome complex. Proc Natl Acad Sci U S A 1981, 78:2273-7. URL

    Noller, H. F., Kop, J., Wheaton, V., Brosius, J., Gutell, R. R., Kopylov, A. M., Dohme, F., Herr, W., Stahl, D. A., Gupta, R., Waese, C. R.: Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res 1981, 9:6167-89. URL

1979
    Herr, W., Noller, H. F.: Protection of specific sites in 23 S and 5 S RNA from chemical modification by association of 30 S and 50 S ribosomes. J Mol Biol 1979, 130:421-32. URL

    Herr, W., Chapman, N. M., Noller, H. F.: Mechanism of ribosomal subunit association: discrimination of specific sites in 16 S RNA essential for association activity. J Mol Biol 1979, 130:433-49. URL

1978
    Herr, W., Noller, H. F.: Nucleotide sequences of accessible regions of 23S RNA in 50S ribosomal subunits. Biochemistry 1978, 17:307-15. URL

1975
    Herr, W., Noller, H. F.: A fragment of 23S RNA containing a nucleotide sequence complementary to a region of 5S RNA. FEBS Lett 1975, 53:248-52. URL

1974
    Noller, H. F., Herr, W.: Nucleotide sequence of the 3' terminus of E. coli 16S ribosomal RNA. Mol Biol Rep 1974, 1:437-9. URL

    Noller, H. F., Herr, W.: Letters to the editor: Accessibility of 5 S RNA in 50 S ribosomal subunits. J Mol Biol 1974, 90:181-4. URL
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