Nouria Hernandez - Selected publications#

Co-corresponding author: *

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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