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Publications

2014
    Waszak, S. M., Kilpinen, H., Gschwind, A. R., Orioli, A., Raghav, S. K., Witwicki, R. M., Migliavacca, E., Yurovsky, A., Lappalainen, T., Hernandez, N., Reymond, A., Dermitzakis, E. T., Deplancke, B.: Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics 2014, 30:165-71. URL

    Renaud, M., Praz, V., Vieu, E., Florens, L., Washburn, M. P., L'Hote, P., Hernandez, N.: Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res 2014, 24:37-51. URL

    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
    Kilpinen, H., Waszak, S. M., Gschwind, A. R., Raghav, S. K., Witwicki, R. M., Orioli, A., Migliavacca, E., Wiederkehr, M., Gutierrez-Arcelus, M., Panousis, N. I., Yurovsky, A., Lappalainen, T., Romano-Palumbo, L., Planchon, A., Bielser, D., Bryois, J., Padioleau, I., Udin, G., Thurnheer, S., Hacker, D., Core, L. J., Lis, J. T., Hernandez, N., Reymond, A., Deplancke, B., Dermitzakis, E. T.: Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 2013, 342:744-7. URL

2012
    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

    James Faresse, N., Canella, D., Praz, V., Michaud, J., Romascano, D., Hernandez, N.: Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators. PLoS genetics 2012, 8:e1003028. URL

    Raillon, C., Cousin, P., Traversi, F., Garcia-Cordero, E., Hernandez, N., Radenovic, A.: Nanopore Detection of Single Molecule RNAP-DNA Transcription Complex. Nano Lett 2012, 12:1157-64. URL

    Strick, T. R., Hernandez, N.: Eeny meeny miny moe, catch a transcript by the toe, or how to enumerate eukaryotic transcripts. Genes Dev 2012, 26:1643-7. URL

    Canella, D., Bernasconi, D., Gilardi, F., LeMartelot, G., Migliavacca, E., Praz, V., Cousin, P., Delorenzi, M., Hernandez, N.: 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
    Orioli, A., Pascali, C., Quartararo, J., Diebel, K. W., Praz, V., Romascano, D., Percudani, R., van Dyk, L. F., Hernandez, N., Teichmann, M., Dieci, G.: Widespread occurrence of non-canonical transcription termination by human RNA polymerase III. Nucleic Acids Res 2011, 39:5499-5512. URL

    Michels, A. A.: MAF1: a new target of mTORC1. Biochem Soc Trans 2011, 39:487-91. URL

2010
    Canella, D., Praz, V., Reina, J. H., Cousin, P., Hernandez, N.: Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res 2010, 20:710-21. URL

    Michels, A. A., Robitaille, A. M., Buczynski-Ruchonnet, D., Hodroj, W., Reina, J. H., Hall, M. N., Hernandez, N.: mTORC1 directly phosphorylates and regulates human MAF1. Mol Cell Biol 2010, 30:3749-57. URL

2008
    Shanmugam, M., Hernandez, N.: Mitotic functions for SNAP45, a subunit of the small nuclear RNA-activating protein complex SNAPc. J Biol Chem 2008, 283:14845-56. URL

2007
    Reina, J. H., Hernandez, N.: On a roll for new TRF targets. Genes Dev 2007, 21:2855-60. URL

    Denissov, S., van Driel, M., Voit, R., Hekkelman, M., Hulsen, T., Hernandez, N., Grummt, I., Wehrens, R., Stunnenberg, H.: Identification of novel functional TBP-binding sites and general factor repertoires. Embo J 2007, 26:944-54. URL

    Yuan, C. C., Zhao, X., Florens, L., Swanson, S. K., Washburn, M. P., Hernandez, N.: CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription. Mol Cell Biol 2007, 27:8729-38. URL

2006
    Vieu, E., Hernandez, N.: Actin's latest act: polymerizing to facilitate transcription?. Nat Cell Biol 2006, 8:650-1. URL

    Michels, A. A., Hernandez, N.: Does Pol I talk to Pol II? Coordination of RNA polymerases in ribosome biogenesis. Genes Dev 2006, 20:1982-5. URL

    Emran, F., Florens, L., Ma, B., Swanson, S. K., Washburn, M. P., Hernandez, N.: A role for Yin Yang-1 (YY1) in the assembly of snRNA transcription complexes. Gene 2006, 377:96-108. URL

    Reina, J. H., Azzouz, T. N., Hernandez, N.: Maf1, a New Player in the Regulation of Human RNA Polymerase III Transcription. PLoS ONE 2006, 1:e134. URL

2005
    Saxena, A., Ma, B., Schramm, L., Hernandez, N.: Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription. Mol Cell Biol 2005, 25:9406-18. URL

    Kim, Y. S., Kim, J. M., Jung, D. L., Kang, J. E., Lee, S., Kim, J. S., Seol, W., Shin, H. C., Kwon, H. S., Van Lint, C., Hernandez, N., Hur, M. W.: Artificial zinc finger fusions targeting Sp1-binding sites and the trans-activator-responsive element potently repress transcription and replication of HIV-1. J Biol Chem 2005, 280:21545-52. URL

2004
    Hu, P., Samudre, K., Wu, S., Sun, Y., Hernandez, N.: CK2 phosphorylation of Bdp1 executes cell cycle-specific RNA polymerase III transcription repression. Mol Cell 2004, 16:81-92. URL

    Hu, P., Wu, S., Hernandez, N.: A role for beta-actin in RNA polymerase III transcription. Genes Dev 2004, 18:3010-5. URL

2003
    Hu, P., Wu, S., Hernandez, N.: A minimal RNA polymerase III transcription system from human cells reveals positive and negative regulatory roles for CK2. Mol Cell 2003, 12:699-709. URL

    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

    Pessler, F., Hernandez, N.: Flexible DNA binding of the BTB/POZ-domain protein FBI-1. J Biol Chem 2003, 278:29327-35. URL

2002
    Schramm, L., Hernandez, N.: Recruitment of RNA polymerase III to its target promoters. Genes Dev 2002, 16:2593-620. URL

    Ma, B., Hernandez, N.: Redundant cooperative interactions for assembly of a human U6 transcription initiation complex. Mol Cell Biol 2002, 22:8067-78. URL

    Hu, P., Wu, S., Sun, Y., Yuan, C. C., Kobayashi, R., Myers, M. P., Hernandez, N.: Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits. Mol Cell Biol 2002, 22:8044-55. URL

    Pendergrast, P. S., Wang, C., Hernandez, N., Huang, S.: FBI-1 can stimulate HIV-1 Tat activity and is targeted to a novel subnuclear domain that includes the Tat-P-TEFb-containing nuclear speckles. Mol Biol Cell 2002, 13:915-29. URL

2001
    Zhao, X., Pendergrast, P. S., Hernandez, N.: A positioned nucleosome on the human U6 promoter allows recruitment of SNAPc by the Oct-1 POU domain. Mol Cell 2001, 7:539-49. URL

    Chong, S. S., Hu, P., Hernandez, N.: Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J Biol Chem 2001, 276:20727-34. URL

    Hernandez, N.: Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J Biol Chem 2001, 276:26733-6. URL

    Ma, B., Hernandez, N.: A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc. J Biol Chem 2001, 276:5027-35. URL

2000
    Schramm, L., Pendergrast, P. S., Sun, Y., Hernandez, N.: Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters. Genes Dev 2000, 14:2650-63. URL

1999
    Morrison, D. J., Pendergrast, P. S., Stavropoulos, P., Colmenares, S. U., Kobayashi, R., Hernandez, N.: FBI-1, a factor that binds to the HIV-1 inducer of short transcripts (IST), is a POZ domain protein. Nucleic Acids Res 1999, 27:1251-62. URL

    Kuhlman, T. C., Cho, H., Reinberg, D., Hernandez, N.: The general transcription factors IIA, IIB, IIF, and IIE are required for RNA polymerase II transcription from the human U1 small nuclear RNA promoter. Mol Cell Biol 1999, 19:2130-41. URL

    Mittal, V., Ma, B., Hernandez, N.: SNAP(c): a core promoter factor with a built-in DNA-binding damper that is deactivated by the Oct-1 POU domain. Genes Dev 1999, 13:1807-21. URL

1998
    Henry, R. W., Mittal, V., Ma, B., Kobayashi, R., Hernandez, N.: SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III. Genes Dev 1998, 12:2664-72. URL

    Ford, E., Strubin, M., Hernandez, N.: The Oct-1 POU domain activates snRNA gene transcription by contacting a region in the SNAPc largest subunit that bears sequence similarities to the Oct-1 coactivator OBF-1. Genes Dev 1998, 12:3528-40. URL

    Wong, M. W., Henry, R. W., Ma, B., Kobayashi, R., Klages, N., Matthias, P., Strubin, M., Hernandez, N.: The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1. Mol Cell Biol 1998, 18:368-77. URL

    Pessler, F., Hernandez, N.: The HIV-1 inducer of short transcripts activates the synthesis of 5,6-dichloro-1-beta-D-benzimidazole-resistant short transcripts in vitro. J Biol Chem 1998, 273:5375-84. URL

    Henry, R. W., Ford, E., Mital, R., Mittal, V., Hernandez, N.: Crossing the line between RNA polymerases: transcription of human snRNA genes by RNA polymerases II and III. Cold Spring Harb Symp Quant Biol 1998, 63:111-20. URL

1997
    Sepehri, S., Hernandez, N.: The largest subunit of human RNA polymerase III is closely related to the largest subunit of yeast and trypanosome RNA polymerase III. Genome Res 1997, 7:1006-19. URL

    Ford, E., Hernandez, N.: Characterization of a trimeric complex containing Oct-1, SNAPc, and DNA. J Biol Chem 1997, 272:16048-55. URL

    Pessler, F., Pendergrast, P. S., Hernandez, N.: Purification and characterization of FBI-1, a cellular factor that binds to the human immunodeficiency virus type 1 inducer of short transcripts. Mol Cell Biol 1997, 17:3786-98. URL

    Mittal, V., Hernandez, N.: Role for the amino-terminal region of human TBP in U6 snRNA transcription. Science 1997, 275:1136-40. URL

    Pendergrast, P. S., Hernandez, N.: RNA-targeted activators, but not DNA-targeted activators, repress the synthesis of short transcripts at the human immunodeficiency virus type 1 long terminal repeat. J Virol 1997, 71:910-7. 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

    Ruppert, S. M., McCulloch, V., Meyer, M., Bautista, C., Falkowski, M., Stunnenberg, H. G., Hernandez, N.: Monoclonal antibodies directed against the amino-terminal domain of human TBP cross-react with TBP from other species. Hybridoma 1996, 15:55-68. URL

    Henry, R. W., Ma, B., Sadowski, C. L., Kobayashi, R., Hernandez, N.: Cloning and characterization of SNAP50, a subunit of the snRNA-activating protein complex SNAPc. Embo J 1996, 15:7129-36. URL

    Mital, R., Kobayashi, R., Hernandez, N.: RNA polymerase III transcription from the human U6 and adenovirus type 2 VAI promoters has different requirements for human BRF, a subunit of human TFIIIB. Mol Cell Biol 1996, 16:7031-42. URL

    Pendergrast, P. S., Morrison, D., Tansey, W. P., Hernandez, N.: Mutations in the carboxy-terminal domain of TBP affect the synthesis of human immunodeficiency virus type 1 full-length and short transcripts similarly. J Virol 1996, 70:5025-34. URL

    Sadowski, C. L., Henry, R. W., Kobayashi, R., Hernandez, N.: The SNAP45 subunit of the small nuclear RNA (snRNA) activating protein complex is required for RNA polymerase II and III snRNA gene transcription and interacts with the TATA box binding protein. Proc Natl Acad Sci U S A 1996, 93:4289-93. URL

1995
    Henry, R. W., Sadowski, C. L., Kobayashi, R., Hernandez, N.: A TBP-TAF complex required for transcription of human snRNA genes by RNA polymerase II and III. Nature 1995, 374:653-6. URL

1994
    Lobo, S., Hernandez, N. : Transcription of snRNA genes by RNA polymerases II and III. In Transcription, Mechanisms and Regulation, Raven Press Series on Molecular and Cellular Biology Edited by Conaway, R.C., Conaway, J.W.,; Raven Press ; 1994: 127-159.

1993
    Hernandez, N.: TBP, a universal eukaryotic transcription factor?. Genes Dev 1993, 7:1291-308. URL

    Sheldon, M., Ratnasabapathy, R., Hernandez, N.: Characterization of the inducer of short transcripts, a human immunodeficiency virus type 1 transcriptional element that activates the synthesis of short RNAs. Mol Cell Biol 1993, 13:1251-63. URL

    Sadowski, C. L., Henry, R. W., Lobo, S. M., Hernandez, N.: Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE. Genes Dev 1993, 7:1535-48. URL

1992
    Lobo, S. M., Tanaka, M., Sullivan, M. L., Hernandez, N.: A TBP complex essential for transcription from TATA-less but not TATA-containing RNA polymerase III promoters is part of the TFIIIB fraction. Cell 1992, 71:1029-40. URL

    Hernandez, N. : Transcription of snRNA genes and related genes In Transcriptional regulation Edited by Yamamoto, K.R., McKnight, S.L. ; Cold Spring Harbor; 1992: 281-283.

1991
    Lobo, S. M., Lister, J., Sullivan, M. L., Hernandez, N.: The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro. Genes Dev 1991, 5:1477-89. URL

1990
    Lobo, S. M., Ifill, S., Hernandez, N.: cis-acting elements required for RNA polymerase II and III transcription in the human U2 and U6 snRNA promoters. Nucleic Acids Res 1990, 18:2891-9. URL

    Ratnasabapathy, R., Sheldon, M., Johal, L., Hernandez, N.: The HIV-1 long terminal repeat contains an unusual element that induces the synthesis of short RNAs from various mRNA and snRNA promoters. Genes Dev 1990, 4:2061-74. URL

1989
    Lobo, S. M., Hernandez, N.: A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter. Cell 1989, 58:55-67. URL

1988
    Hernandez, N., Lucito, R.: Elements required for transcription initiation of the human U2 snRNA gene coincide with elements required for snRNA 3' end formation. Embo J 1988, 7:3125-34. URL

    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

1986
    Hernandez, N., Weiner, A. M.: Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements. Cell 1986, 47:249-58. URL

1985
    Hernandez, N.: Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region. Embo J 1985, 4:1827-37. URL

1983
    Cattaneo, R., Will, H., Hernandez, N., Schaller, H.: Signals regulating hepatitis B surface antigen transcription. Nature 1983, 305:336-8. URL

    Hernandez, N., Keller, W.: Splicing of in vitro synthesized messenger RNA precursors in HeLa cell extracts. Cell 1983, 35:89-99. URL
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