Genome Function Publications
Brookes, E., Pombo, A., (2012). Code breaking: The RNAPII modification code in pluripotency. Cell cycle 11 (7). Abstract
Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A (2012) Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs. Cell Stem Cell, in press. Abstract
Moeller A, Xie SQ, Hosp F, Lang, B, Phatnani HP, James S, Ramirez F, Collin GB, Naggert JK, Babu MM, Greenleaf AL, Selbach M, Pombo A (2011) Proteomic analysis of mitotic RNA polymerase IIreveals novel interactors and association withproteins dysfunctional in disease. Molecular & Cell Proteomics, in press. Abstract
Stock JK, Brookes E, Pombo A (2011) Phospho-sensitive chromatin immunoprecipitation of RNA Polymerase II. EpigeneSys Protocol. | Full text
Chotalia M, Pombo A (2011) Polycomb targets seek closest neighbours. PLoS Genetics 7 (3). Abstract
Pombo A, Starr DA (2011) Nuclear Cell Biology. Molecular Biology of the Cell 22 (6). Abstract
Alder O, Lavial F, Helness A, Brookes E, Pinho S, Chandrashekran A, Arnaud P, Pombo A, O'Neill L, Azuara V (2010) Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment. Development, 137 2483–92. Abstract
Pombo A, Gilbert DM (2010) Nucleus and gene expression: the structure and function conundrum. Current Opinion in Cell Biology 22, 269–270.
Landeira D, Sauer S, Poot R, Dvorkina M, Mazzarella L, Jørgensen HF, Pereira CF, Leleu M, Piccolo F, Spivakov M, Brookes E, Pombo A, Fisher C, Skarnes WC, Snoek T, Bezstarosti K, Demmers J, Klose RJ, Casanova M, Tavares L, Brockdorff N, Merkenschlager M, Fisher AG (2010) JARID2 is a PRC2 component in embryonic stem cells required for multilineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulator genes. Nature Cell Biology 12, 618–624. Abstract
Kanhere AS, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte W, Pereira CF, Brookes E, Walker K, Bell GW, Pombo A, Fisher AG, Young RA , Jenner RG (2010) Short RNAs are transcribed from repressed Polycomb target genes and interact with Polycomb Repressive Complex-2. Molecular Cell 38, 675–688. Abstract
Xie SQ, Lavitas LM, Pombo A (2010) CryoFISH: Fluorescence in situ hybridization in thin cryosections. Methods Mol Biol. 659, 219–230. Abstract
Morris K, Chotalia L, Pombo A (2010) Nuclear architecture in stem cells. Adv Exp Med Biol 695, 14–25. Click here to download chapter PDF
Ferrai C, de Castro IJ, Lavitas L, Chotalia M, Pombo A (2010) Gene positioning. Cold Spring Harb Perspect Biol 2, a000588. Abstract
Ferrai, C., Xie, S. Q., Luraghi, P., Munari, D., Ramirez, F., Branco, M. R., Pombo, A., Crippa, M. P. (2010). Poised Transcription Factories Prime Silent uPA Gene Prior to Activation. PLoS Biol. 8(1): e1000270 Abstract
Brookes, E. & Pombo, A. (2009). Modifications of RNA polymerase II are pivotal in regulating gene expression states. EMBO reports 10 (11), 1213–1219. Abstract
Hiragami-Hamada, K. H., Xie, S., Saveliev, A., Lewis, S. U., Pombo, A., Festenstein, R., 2009. The molecular basis for stability of heterochromatin-mediated silencing in mammals. Epigenetics & Chromatin 2 (1), 14+. Abstract | Full text
Baddeley, D., Chagin, V., Schermelleh, L., Martin, S., Pombo, A., Gahl, A., Domaing, P., Birk, U., Leonhardt, H., Cremer, C., Cardoso, M. C. (2009). Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucl. Ac. Res., in press.
Maya-Mendoza, A., Tang, C. W., Pombo, A., Jackson, D. A. (2009). Mechanisms regulating S phase progression in mammalian cells. Frontiers in bioscience 14, 4199–4213. Abstract
Ferrai, C. & Pombo, A. (2009). 3D chromatin regulation of Sonic hedgehog in the limb buds. Developmental Cell (16) 1, 9–11. Abstract | Full text
Branco, M. R., Branco, T., Ramirez, F. & Pombo, A. (2008). Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH. Chromosome Research 16, 413-426. Abstract
Madan-Babu, M., Janga, S. C., de Santiago, I. & Pombo, A. (2008). Eukaryotic gene regulation in three dimensions and its impact on genome evolution. Current Opinion in Genetics & Development 18, 571–582. Abstract
Noordermeer, D., Branco, M. R., Splinter, E., Klous, P., van Ijcken, W., Swagemakers, S., Koutsourakis, M., van der Spek, P., Pombo, A. & de Laat, W. (2008). Transcription and chromatin organization of a housekeeping gene cluster containing an integrated β-globin locus control region. PLoS Genetics 4, e1000016. Abstract | Full text
Branco, M. R. & Pombo, A. (2007). Chromosome organization: new facts, new models. Trends in Cell Biology 17, 127-134. Abstract
Piercy, R. J., Zhou, H., Feng, L., Pombo, A., Muntoni, F. & Brown, S. C. (2007). Desmin immunolocalisation in autosomal dominant Emery-Dreifuss muscular dystrophy. Neuromuscular Disorders 17, 297-305. Abstract
Pombo, A. (2007). Advances in imaging the interphase nucleus using thin cryosections. Histochemistry and Cell Biology 128, 97-104. Abstract
Pombo, A. & Branco, M. R. (2007). Functional organisation of the genome during interphase. Current Opinion in Genetics & Development 17, 451-455. Abstract
Stock, J. K., Giardrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., Brockdorff, N., Fisher, A. G. & Pombo, A. (2007). Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nature Cell Biology 9, 1428-1435. Abstract
Branco M. R. & Pombo A. (2006). Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biology 4, e138. Abstract | Full text
Branco, M. R., Xie, S. Q., Martin, S. & Pombo, A. (2006). Correlative microscopy using Tokuyasu cryosections: applications for immunogold labelling and in situ hybridisation. In Cell Imaging (Methods Express Series). ed. Stephens, D., pp. 201-217. Bloxham: Scion Publishing Ltd.
Xie, S. Q., Martin, S., Guillot, P. V., Bentley, D. L. & Pombo, A. (2006). Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain. Molecular Biology of the Cell 17, 1723-1733. Abstract
Xie, S. Q., & Pombo, A. (2006). Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study. Histochemistry and Cell Biology 125, 21-31. Abstract
Chow, C.-M., Georgiou, A., Szutorisz, H., Maia e Silva, A., Pombo, A., Barahona, I., Dargelos, E., Canzonetta, C. & Dillon, N. (2005). Variant histone H3.3 marks promotors of transcriptionally active genes during cell division. EMBO Reports 6, 354-360. Abstract | Full text
Guillot, P. V., Martin, S. & Pombo, A. (2005). The organization of transcription in the nucleus of mammalian cells. In Visions of the Cell Nucleus ed. Hemmerich, P. & Diekmann, S., pp. 95-105. California: American Scientific Publishers.
Ribeiro, A. C., Maia e Silva, A., Santa-Marta, M., Pombo, A., Moniz-Pereira, J., Goncalves, J. & Barahona, I. (2005). Functional analysis of Vif protein shows less restriction of human immunodeficiency virus type 2 by APOBEC3G. Journal of Virolology 79, 823-833. Abstract | Full text
Guillot, P. V., Xie, S. Q., Hollinshead, M. & Pombo, A. (2004). Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells. Experimental Cell Research 295, 460-468. Abstract
Kenny, E., Mason, D., Saoudi, A., Pombo, A. & Ramirez, F. (2004). Cellular immune response CD8α is an activation marker for a subset of peripheral CD4 T cells. European Journal of Immunology 34, 1262-1271. Abstract
Martin, S., Failla, A. V., Spöri, U., Cremer, C. & Pombo, A. (2004). Measuring the size of biological nanostructures with spatially modulated illumination microscopy; transcription factories. Molecular Biology of the Cell 15, 2449-2455. Abstract | Full text
Boyd, D. C., Pombo, A. & Murphy, S. (2003). Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo. Gene 315, 103-112. Abstract
Martin, S. & Pombo, A. (2003). Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Research 11, 461-470. Abstract
O'Brien, T. P., Bult, C. J., Cremer, C., Grunze, M., Knowles, B. B., Langowshi, J., McNally, J., Pederson, T., Politz, J. C., Pombo, A., Schmahl, G., Spatz, J. P. & van Driel, R. (2003). Genome function and nuclear architecture: from gene expression to nanoscience. Genome Research 13, 1029-1041. Abstract | Full text
Politz, J., van Driel, R., Sauer, M. & Pombo, A. (2003). From linear genome sequence to three-dimensional organization of the cell nucleus. Genome Biology 4, 310-311. Abstract | Full text
Pombo, A. (2003). Cellular genomics: which genes are transcribed when and where? Trends in Biochemical Science 28, 6-9. Abstract
Politz, J. & Pombo, A. (2002). Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters. Genome Biology 3, 4007.1-4007.3. Abstract | Full text
Robinson, J. M., Takizawa, T., Pombo, A. & Cook, P. R. (2001). Integrated fluorescence and electron microscopy on ultrathin cryosections: bridging he resolution gap. Journal of Histochemistry and Cytochemistry 49, 803-808. Abstract | Full text
Jackson, D. A., Pombo, A. & Iborra, F. (2000). The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells. The FASEB Journal 14, 242-254. Abstract | Full text
Kenny, E., Mason, D., Pombo, A. & Ramirez, F. (2000). Phenotypic analysis of peripheral CD4+CD8+ T cells in the rat. Immunology 101, 178-184. Abstract | Full text
Pombo, A., Jackson, D. A., Iborra, F. J., Hollinshead, M., Kimura, H., Sugaya, K. & Cook, P. R. (2000). Transcription factories. Proceeding of the 12th European Congress on Electron Microscope Volume I Biological Sciences, B461-B464.
Pombo, A., Jones, E., Iborra, F. J., Kimura, H. J., Sugaya, K., Cook, P. R. & Jackson, D. A. (2000). Specialized transcription factories within mammalian nuclei. Critical Reviews in Eukaryotic Gene Expression 10, 21-29. Abstract
McDowell, T. L., Gibbons, R. J., O'Rourke, D., Sutherland, H., Bickmore, W. A., Pombo, A., Turley, H., Gatter, K., Picketts, D., Buckle, V. J., Chapman, L., Rhodes, D. & Higgs, D. R. (1999). Localizaton of a putative transcriptional regulator (ATRX) at pericentric heterochromatin and the tips of acrocentric chromosomes. Proceedings of the National Academy of Sciences of the United States of America 96, 13983-13988. Abstract | Full text
Pombo, A., Hollinshead, M. & Cook, P. R. (1999). Bridging the resolution gap: Imaging the same transcription factories in cryosections by light and electron microscopy. Journal of Histochemistry and Cytochemistry 47, 471-480. Abstract | Full text
Pombo, A., Jackson, D. A., Hollinshead, M., Wang, Z., Roeder, R. G. & Cook, P. R. (1999). Regional specialization in the nucleus: visualization of discrete sites of transcription by RNA polymerase III. The EMBO Journal 18, 2241-2253. Abstract | Full text
Jackson, D. A. & Pombo, A. (1998). Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase cells in human cells. Journal of Cell Biology 140, 1285-1295. Abstract | Full text
Pombo, A., Cuello, P., Schul, W., Yoon, J.-B., Roeder, R. G., Cook, P. R. & Murphy, S. (1998). Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle. The EMBO Journal 17, 1768-1778. Abstract | Full text
Wykes, M., Pombo, A., Jenkins, C., MacPherson, G. G. (1998). Dendritic cells interact with naive B lymphocytes to transfer antigen and initiate class-switching in a primary T-dependent response. The Journal of Immunology 161, 1313-1319. Abstract | Full text
Iborra, F. J., Pombo, A. & Jackson, D. A. (1997). Dedicated sites of gene expression in the nuclei of mammalian cells. Gene Therapy and Molecular Biology 1, 495-508. Abstract | Full text
Pombo, A., McMannus, J., Hughes, T. A., Iborra, F. J., Jackson, D. A. & Cook, P. R. (1997). Transcription factories and chromosome structure. In Chromosomes Today ed. Henriques-Gil, N., Parker, J. S. & Puertas, M. J., vol. 12, pp. 147-160. London: Chapman & Hall.
Iborra, F. J., Pombo, A., Jackson, D. A. & Cook, P. R. (1996). Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. Journal of Cell Science 109, 1427-1436. Abstract | Full text
Iborra, F. J., Pombo, A., McMannus, J., Jackson, D. A. & Cook, P. R. (1996). The topology of transcription by immobilized polymerases. Experimental Cell Research 229, 167-173. Abstract
Pombo, A., Cook, P. R. (1996). The localization of sites containing nascent RNA and splicing factors. Experimental Cell Research 229, 201-203. Abstract
