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259 results on '"Heilig, R."'

1. Comparative and integrated analysis of plasma extracellular vesicle isolation methods in healthy volunteers and patients following myocardial infarction

Author

Paget, D, Checa, A, Zöhrer, B, Heilig, R, Shanmuganathan, M, Dhaliwal, R, Johnson, E, Jørgensen, MM, Bæk, R, Wheelock, CE, Channon, KM, Fischer, R, Anthony, DC, Choudhury, RP, Akbar, N, and (OxAMI), Oxford Acute Myocardial Infarction Study

Subjects
ultracentrifugation, acoustic trapping, immunoaffinity capture, size exclusion chromatography, human, precipitation, plasma, omics
Abstract

Plasma extracellular vesicle (EV) number and composition are altered following myocardial infarction (MI), but to properly understand the significance of these changes it is essential to appreciate how the different isolation methods affect EV characteristics, proteome and sphingolipidome. Here, we compared plasma EV isolated from platelet-poor plasma from four healthy donors and six MI patients at presentation and 1-month post-MI using ultracentrifugation (UC), polyethylene glycol precipitation, acoustic trapping, size-exclusion chromatography (SEC) and immunoaffinity capture. The isolated EV were evaluated by Nanoparticle Tracking Analysis (NTA), Western blot, transmission electron microscopy (TEM), an EV-protein array, untargeted proteomics (LC-MS/MS) and targeted sphingolipidomics (LC-MS/MS). The application of the five different plasma EV isolation methods in patients presenting with MI showed that the choice of plasma EV isolation method influenced the ability to distinguish elevations in plasma EV concentration following MI, enrichment of EV-cargo (EV-proteins and sphingolipidomics) and associations with the size of the infarct determined by cardiac magnetic resonance imaging 6 months post-MI. Despite the selection bias imposed by each method, a core of EV-associated proteins and lipids was detectable using all approaches. However, this study highlights how each isolation method comes with its own idiosyncrasies and makes the comparison of data acquired by different techniques in clinical studies problematic.

Published
2022

8. Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates

Author

Cockman, M. E. (Matthew E.), Lippl, K. (Kerstin), Tian, Y.-M. (Ya-Min), Pegg, H. B. (Hamish B.), Figg Jnr, W. D. (William D.), Abboud, M. I. (Martine I.), Heilig, R. (Raphael), Fischer, R. (Roman), Myllyharju, J. (Johanna), Schofield, C. J. (Christopher J.), Ratcliffe, P. J. (Peter J.), Cockman, M. E. (Matthew E.), Lippl, K. (Kerstin), Tian, Y.-M. (Ya-Min), Pegg, H. B. (Hamish B.), Figg Jnr, W. D. (William D.), Abboud, M. I. (Martine I.), Heilig, R. (Raphael), Fischer, R. (Roman), Myllyharju, J. (Johanna), Schofield, C. J. (Christopher J.), and Ratcliffe, P. J. (Peter J.)

Abstract

Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.

Published
2019

14. Initial sequencing and analysis of the human genome

Author

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M, FitzHugh, W, Funke, R, Gage, D, Harris, K, Heaford, A, Howland, J, Kann, L, Lehoczky, J, LeVine, R, McEwan, P, McKernan, K, Meldrim, J, Mesirov, JP, Miranda, C, Morris, W, Naylor, J, Raymond, C, Rosetti, M, Santos, R, Sheridan, A, Sougnez, C, Stange-Thomann, N, Stojanovic, N, Subramanian, A, Wyman, D, Rogers, J, Sulston, J, Ainscough, R, Beck, S, Bentley, D, Burton, J, Clee, C, Carter, N, Coulson, A, Deadman, R, Deloukas, P, Dunham, A, Dunham, I, Durbin, R, French, L, Grafham, D, Gregory, S, Hubbard, T, Humphray, S, Hunt, A, Jones, M, Lloyd, C, McMurray, A, Matthews, L, Mercer, S, Milne, S, Mullikin, JC, Mungall, A, Plumb, R, Ross, M, Shownkeen, R, Sims, S, Waterston, RH, Wilson, RK, Hillier, LW, McPherson, JD, Marra, MA, Mardis, ER, Fulton, LA, Chinwalla, AT, Pepin, KH, Gish, WR, Chissoe, SL, Wendl, MC, Delehaunty, KD, Miner, TL, Delehaunty, A, Kramer, JB, Cook, LL, Fulton, RS, Johnson, DL, Minx, PJ, Clifton, SW, Hawkins, T, Branscomb, E, Predki, P, Richardson, P, Wenning, S, Slezak, T, Doggett, N, Cheng, JF, Olsen, A, Lucas, S, Elkin, C, Uberbacher, E, Frazier, M, Gibbs, RA, Muzny, DM, Scherer, SE, Bouck, JB, Sodergren, EJ, Worley, KC, Rives, CM, Gorrell, JH, Metzker, ML, Naylor, SL, Kucherlapati, RS, Nelson, DL, Weinstock, GM, Sakaki, Y, Fujiyama, A, Hattori, M, Yada, T, Toyoda, A, Itoh, T, Kawagoe, C, Watanabe, H, Totoki, Y, Taylor, T, Weissenbach, J, Heilig, R, Saurin, W, Artiguenave, F, Brottier, P, Bruls, T, Pelletier, E, Robert, C, Wincker, P, Smith, DR, Doucette-Stamm, L, Rubenfield, M, Weinstock, K, Lee, HM, Dubois, J, Rosenthal, A, Platzer, M, Nyakatura, G, Taudien, S, Rump, A, Yang, H, Yu, J, Wang, J, Huang, G, Gu, J, Hood, L, Rowen, L, Madan, A, Qin, S, Davis, RW, Federspiel, NA, Abola, AP, Proctor, MJ, Myers, RM, Schmutz, J, Dickson, M, Grimwood, J, Cox, DR, Olson, MV, Kaul, R, Shimizu, N, Kawasaki, K, Minoshima, S, Evans, GA, Athanasiou, M, Schultz, R, Roe, BA, Chen, F, Pan, H, Ramser, J, Lehrach, H, Reinhardt, R, McCombie, WR, de la Bastide, M, Dedhia, N, Blöcker, H, Hornischer, K, Nordsiek, G, Agarwala, R, Aravind, L, Bailey, JA, Bateman, A, Batzoglou, S, Birney, E, Bork, P, Brown, DG, Burge, CB, Cerutti, L, Chen, HC, Church, D, Clamp, M, Copley, RR, Doerks, T, Eddy, SR, Eichler, EE, Furey, TS, Galagan, J, Gilbert, JG, Harmon, C, Hayashizaki, Y, Haussler, D, Hermjakob, H, Hokamp, K, Jang, W, Johnson, LS, Jones, TA, Kasif, S, Kaspryzk, A, Kennedy, S, Kent, WJ, Kitts, P, Koonin, EV, Korf, I, Kulp, D, Lancet, D, Lowe, TM, McLysaght, A, Mikkelsen, T, Moran, JV, Mulder, N, Pollara, VJ, Ponting, CP, Schuler, G, Schultz, J, Slater, G, Smit, AF, Stupka, E, Szustakowski, J, Thierry-Mieg, D, Thierry-Mieg, J, Wagner, L, Wallis, J, Wheeler, R, Williams, A, Wolf, YI, Wolfe, KH, Yang, SP, Yeh, RF, Collins, F, Guyer, MS, Peterson, J, Felsenfeld, A, Wetterstrand, KA, Patrinos, A, Morgan, MJ, de Jong, P, Catanese, JJ, Osoegawa, K, Shizuya, H, Choi, S, Chen, YJ, and Szustakowki, J

Subjects
Genetics, Cancer genome sequencing, Chimpanzee genome project, Multidisciplinary, Cancer Genome Project, Gene density, DNA sequencing theory, Hybrid genome assembly, Computational biology, Biology, Genome, Personal genomics
Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2016

18. STRUCTURE AND EXPRESSION OF OVALBUMIN AND CLOSELY RELATED CHICKEN GENES

Author

Chambon, P., primary, Perrin, F., additional, O'Hare, K., additional, Mandel, J.L., additional, LePennec, J.P., additional, LeMeur, M., additional, Krust, A., additional, Heilig, R., additional, Gerlinger, P., additional, Gannon, F., additional, Cochet, M., additional, Breathnach, R., additional, and Benoist, C., additional

Published
1979
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19. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi

Author

Cohen, G., Barbe, V., Flament, D., Galperin, M., Heilig, R., Lecompte, O., Prieur, D., Poch, O., Querellou, J., Thierry, J.C., van der Oost, J., Weissenbach, J., Zivanovic, Y., and Forterre, P.

Subjects
inorganic chemicals, transfer-rna synthetase, phylogenetic characterization, horizontal gene exchange, thermus-thermophilus, hydrothermal vent, Microbiology, bacterial hyperthermophiles, replication factor-c, Microbiologie, dna-polymerases, biochemical-characterization, transcription factor, VLAG
Abstract

The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii , whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.

Published
2003

21. Initial sequencing and analysis of the human genome

Author

Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI 48109 USA, Univ Michigan, Sch Med, Dept Internal Med, Ann Arbor, MI 48109 USA, Whitehead Inst Biomed Res, Ctr Genome Res, Cambridge, MA 02142 USA, Sanger Ctr, Hinxton CB10 1RQ, Cambs, England, Washington Univ, Genome Sequencing Ctr, St Louis, MO 63108 USA, US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA, Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA, Univ Texas, Hlth Sci Ctr, Dept Cellular & Struct Biol, San Antonio, TX 78229 USA, Yeshiva Univ Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA, Univ Texas, Sch Med, Dept Microbiol & Mol Genet, Houston, TX 77225 USA, RIKEN, Genom Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan, Genoscope, F-91057 Evry, France, CNRS, UMR 8030, F-91057 Evry, France, Genome Therapeut Corp, GTC Sequencing Ctr, Waltham, MA 02453 USA, Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany, Chinese Acad Sci, Inst Genet, Ctr Human Genome, Beijing Genom Inst, Beijing 100101, Peoples R China, So China Natl Human Genome Res Ctr, Shanghai 201203, Peoples R China, No China Natl Human Genome Res Ctr, Beijing 100176, Peoples R China, Inst Syst Biol, Multimegabase Sequencing Ctr, Seattle, WA 98105 USA, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA, Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA, Stanford Univ, Stanford Human Genome Ctrr, Sch Med, Stanford, CA 94305 USA, Univ Washington, Genome Ctr, Seattle, WA 98195 USA, Keio Univ, Sch Med, Dept Biol Mol, Shinjuku Ku, Tokyo 1608582, Japan, Univ Texas, SW Med Ctr, Dallas, TX 75235 USA, Univ Oklahoma, Adv Ctr Genome Technol, Dept Chem & Biochem, Norman, OK 73019 USA, Max Planck Inst Mol Genet, D-14195 Berlin, Germany, Cold Spring Harbor Lab, Lita Annenberg Hazen Genome Ctr, Cold Spring Harbor, NY 11724 USA, GBF, German Res Ctr Biotechnol, D-38124 Braunschweig, Germany, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA, Case Western Reserve Univ, Sch Med, Dept Genet, Cleveland, OH 44106 USA, Univ Hosp Cleveland, Cleveland, OH 44106 USA, EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England, Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany, MIT, Dept Biol, Cambridge, MA 02139 USA, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA, Univ Calif Santa Cruz, Dept Comp Sci, Santa Cruz, CA 95064 USA, Affymetrix Inc, Berkeley, CA 94710 USA, RIKEN, Yokoham Inst, Genom Sci Ctr, Genom Explorat Res Grp, Tsurumi Ku, Kanagawa 2300045, Japan, Univ Calif Santa Cruz, Dept Comp Sci, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA, Univ Dublin Trinity Coll, Dept Genet, Smurfit Inst, Dublin 2, Ireland, Compaq Comp Corp, Cambridge Res Lab, Cambridge, MA 02142 USA, MIT, Genome Ctr, Cambridge, MA 02142 USA, Univ Calif Santa Cruz, Dept Math, Santa Cruz, CA 95064 USA, Univ Calif Santa Cruz, Dept Biol, Santa Cruz, CA 95064 USA, Weizmann Inst Sci, Crown Human Genet Ctr, IL-71600 Rehovot, Israel, Weizmann Inst Sci, Dept Mol Genet, IL-71600 Rehovot, Israel, Univ Oxford, Dept Human Anat & Genet, MRC, Funct Genet Unit, Oxford OX1 3QX, England, Inst Syst Biol, Seattle, WA 98105 USA, NHGRI, NIH, Bethesda, MD 20892 USA, US Dept Energy, Off Sci, Germantown, MD 20874 USA, Wellcome Trust, London NW1 2BE, England, Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, John D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E.C., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H.Q., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., De la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, Jgr, Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W.H., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J.R., Slater, G., Smit, A.F.A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., Morgan, M.J., Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI 48109 USA, Univ Michigan, Sch Med, Dept Internal Med, Ann Arbor, MI 48109 USA, Whitehead Inst Biomed Res, Ctr Genome Res, Cambridge, MA 02142 USA, Sanger Ctr, Hinxton CB10 1RQ, Cambs, England, Washington Univ, Genome Sequencing Ctr, St Louis, MO 63108 USA, US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA, Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA, Univ Texas, Hlth Sci Ctr, Dept Cellular & Struct Biol, San Antonio, TX 78229 USA, Yeshiva Univ Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA, Univ Texas, Sch Med, Dept Microbiol & Mol Genet, Houston, TX 77225 USA, RIKEN, Genom Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan, Genoscope, F-91057 Evry, France, CNRS, UMR 8030, F-91057 Evry, France, Genome Therapeut Corp, GTC Sequencing Ctr, Waltham, MA 02453 USA, Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany, Chinese Acad Sci, Inst Genet, Ctr Human Genome, Beijing Genom Inst, Beijing 100101, Peoples R China, So China Natl Human Genome Res Ctr, Shanghai 201203, Peoples R China, No China Natl Human Genome Res Ctr, Beijing 100176, Peoples R China, Inst Syst Biol, Multimegabase Sequencing Ctr, Seattle, WA 98105 USA, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA, Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA, Stanford Univ, Stanford Human Genome Ctrr, Sch Med, Stanford, CA 94305 USA, Univ Washington, Genome Ctr, Seattle, WA 98195 USA, Keio Univ, Sch Med, Dept Biol Mol, Shinjuku Ku, Tokyo 1608582, Japan, Univ Texas, SW Med Ctr, Dallas, TX 75235 USA, Univ Oklahoma, Adv Ctr Genome Technol, Dept Chem & Biochem, Norman, OK 73019 USA, Max Planck Inst Mol Genet, D-14195 Berlin, Germany, Cold Spring Harbor Lab, Lita Annenberg Hazen Genome Ctr, Cold Spring Harbor, NY 11724 USA, GBF, German Res Ctr Biotechnol, D-38124 Braunschweig, Germany, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA, Case Western Reserve Univ, Sch Med, Dept Genet, Cleveland, OH 44106 USA, Univ Hosp Cleveland, Cleveland, OH 44106 USA, EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England, Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany, MIT, Dept Biol, Cambridge, MA 02139 USA, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA, Univ Calif Santa Cruz, Dept Comp Sci, Santa Cruz, CA 95064 USA, Affymetrix Inc, Berkeley, CA 94710 USA, RIKEN, Yokoham Inst, Genom Sci Ctr, Genom Explorat Res Grp, Tsurumi Ku, Kanagawa 2300045, Japan, Univ Calif Santa Cruz, Dept Comp Sci, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA, Univ Dublin Trinity Coll, Dept Genet, Smurfit Inst, Dublin 2, Ireland, Compaq Comp Corp, Cambridge Res Lab, Cambridge, MA 02142 USA, MIT, Genome Ctr, Cambridge, MA 02142 USA, Univ Calif Santa Cruz, Dept Math, Santa Cruz, CA 95064 USA, Univ Calif Santa Cruz, Dept Biol, Santa Cruz, CA 95064 USA, Weizmann Inst Sci, Crown Human Genet Ctr, IL-71600 Rehovot, Israel, Weizmann Inst Sci, Dept Mol Genet, IL-71600 Rehovot, Israel, Univ Oxford, Dept Human Anat & Genet, MRC, Funct Genet Unit, Oxford OX1 3QX, England, Inst Syst Biol, Seattle, WA 98105 USA, NHGRI, NIH, Bethesda, MD 20892 USA, US Dept Energy, Off Sci, Germantown, MD 20874 USA, Wellcome Trust, London NW1 2BE, England, Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, John D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E.C., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H.Q., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., De la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, Jgr, Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W.H., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J.R., Slater, G., Smit, A.F.A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., and Morgan, M.J.

Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2009

22. Physical and genetic mapping of polymorphic loci in Xq28 (DXS15, DXS52 and DXS134): analysis of a cosmid clone and a yeast artificial chromosome

Author

Feil, R., Giuseppe Palmieri, D Urso, M., Heilig, R., Oberlé, I., and Mandel, J. L.

Subjects
Genetic Markers, Male, X Chromosome, Restriction Mapping, Saccharomyces cerevisiae, Cosmids, Pedigree, Humans, Female, Chromosomes, Fungal, Cloning, Molecular, DNA Probes, Polymorphism, Restriction Fragment Length, Gene Library, Research Article
Abstract

Sequences corresponding to the Xq28 loci DXS15, DXS52, DXS134, and DXS130 were shown to be present in a 140-kb yeast artificial chromosome (YAC XY58, isolated by Little et al.). This YAC clone appears to contain a faithful copy of this genomic region, as shown by comparison with human DNA and with a cosmid clone that contains probes St14c (part of the DXS52 sequences) and cpX67 (DXS134). cpX67 and St14c are contained in 11 kb and detect the same MspI RFLP polymorphism. A comparison of the YAC restriction map and pulsed-field gel electrophoresis data leads us to propose the following order of loci: DXS52(VNTR)-DXS33-DXF22S3-DXS130-DXS134 -DXS52-DXS15-DXS52, this whole cluster being comprised within 575 kb. The physical proximity of the DXS15, DXS52, and DXS134 loci led us to reinvestigate recombination events that had been reported between these loci in families from the Centre d'Etude du Polymorphisme Humain. Our results do not support the assumption that this region shows increased recombination.

Published
1990

23. A human homologue of the Drosophila eyes absent gene underlies branchio-oto-renal (BOR) syndrome and identifies a novel gene family.

Author

Abdelhak, S, Kalatzis, V, Heilig, R, Compain, S, Samson, D, Vincent, C. M., Weil, D, Cruaud, C., Sahly, I, Leibovici, M, Bitner-Glindzicz, M, Francis, Michael, Lacombe, Denis, Vigneron, Jean-Robert, Charachon, R, Boven, K, Bedbeder, P, Van Regemorter, Nicole, Weissenbach, J., Petit, Christine, Abdelhak, S, Kalatzis, V, Heilig, R, Compain, S, Samson, D, Vincent, C. M., Weil, D, Cruaud, C., Sahly, I, Leibovici, M, Bitner-Glindzicz, M, Francis, Michael, Lacombe, Denis, Vigneron, Jean-Robert, Charachon, R, Boven, K, Bedbeder, P, Van Regemorter, Nicole, Weissenbach, J., and Petit, Christine

Abstract

A candidate gene for Branchio-Oto-Renal (BOR) syndrome was identified at chromosome 8q13.3 by positional cloning and shown to underlie the disease. This gene is a human homologue of the Drosophila eyes absent gene (eya), and was therefore called EYA1. A highly conserved 271-amino acid C-terminal region was also found in the products of two other human genes (EYA2 and EYA3), demonstrating the existence of a novel gene family. The expression pattern of the murine EYA1 orthologue, Eya1, suggests a role in the development of all components of the inner ear, from the emergence of the otic placode. In the developing kidney, the expression pattern is indicative of a role for Eya1 in the metanephric cells surrounding the 'just-divided' ureteric branches., Comparative Study, Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
1997

34. Nucleotide sequence of the mouse preprosomatostatin gene

Author

Kempf J, Heilig R, A. Ebel, and Guy Fuhrmann

Subjects
Genetics, Base Sequence, Molecular Sequence Data, Prohormone, Protein primary structure, Nucleic acid sequence, DNA, Biology, Mice, chemistry.chemical_compound, Somatostatin, Genes, chemistry, medicine, Animals, Base sequence, Amino Acid Sequence, Protein Precursors, Gene, Peptide sequence, medicine.drug
Published
1990

40. Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea.

Author

Lecompte, O, Ripp, R, Puzos-Barbe, V, Duprat, S, Heilig, R, Dietrich, J, Thierry, J C, and Poch, O

Abstract

We have compared three complete genomes of closely related hyperthermophilic species of Archaea belonging to the Pyrococcus genus: Pyrococcus abyssi, Pyrococcus horikoshii, and Pyrococcus furiosus. At the genomic level, the comparison reveals a differential conservation among four regions of the Pyrococcus chromosomes correlated with the location of genetic elements mediating DNA reorganization. This discloses the relative contribution of the major mechanisms that promote genomic plasticity in these Archaea, namely rearrangements linked to the replication terminus, insertion sequence-mediated recombinations, and DNA integration within tRNA genes. The combination of these mechanisms leads to a high level of genomic plasticity in these hyperthermophilic Archaea, at least comparable to the plasticity observed between closely related bacteria. At the proteomic level, the comparison of the three Pyrococcus species sheds light on specific selection pressures acting both on their coding capacities and evolutionary rates. Indeed, thanks to two independent methods, the "reciprocal best hits" approach and a new distance ratio analysis, we detect the false orthology relationships within the Pyrococcus lineage. This reveals a high amount of differential gains and losses of genes since the divergence of the three closely related species. The resulting polymorphism is probably linked to an adaptation of these free-living organisms to differential environmental constraints. As a corollary, we delineate the set of orthologous genes shared by the three species, that is, the genes that may characterize the Pyrococcus genus. In this conserved core, the amino acid substitution rate is equal between P. abyssi and P. horikoshii for most of their shared proteins, even for fast-evolving ones. In contrast, strong discrepancies exist among the substitution rates observed in P. furiosus relative to the two other species, which is in disagreement with the molecular clock hypothesis.

Published
2001
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41. The chicken dystrophin cDNA: striking conservation of the C‐terminal coding and 3′ untranslated regions between man and chicken.

Author

Lemaire, C., Heilig, R., and Mandel, J. L.

Abstract

Dystrophin is a very large muscle protein (approximately 400 kd) the deficiency of which is responsible for Duchenne muscular dystrophy. Its function is unknown at present. In order to know whether different domains of the protein are differentially conserved during evolution, we have cloned and sequenced the chicken dystrophin cDNA. The protein coding sequence has almost the same size as in man. The N‐terminal region that resembles the actin binding domain of alpha actinin, as well as the large spectrin like domain show 80% and 75% conservation respectively between chicken and man. In contrast, the C‐terminal region shows 95% identity over 627 aa suggesting that it is an important region of interaction with other proteins. Comparison of the amino acid sequence of this C‐terminal region to other protein sequences shows only marginally significant similarities. Finally we have found a striking conservation of three segments of the 3′ untranslated sequence (85% homology over a total of 920 nt) between chicken and man. These also appear to be conserved in other mammals. This high conservation is not linked to open reading frames.

Published
1988
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42. Actin‐like sequences are present on human X and Y chromosomes.

Author

Heilig, R., Hanauer, A., Grzeschik, K.H., Hors‐Cayla, M.C., and Mandel, J.L.

Abstract

The human genome contains greater than 20 actin‐related sequences, six of which at least are expressed as protein. We have shown by blot hybridization the presence of actin‐like sequences on both the X and the Y chromosomes. These sequences can be detected in HindIII digests of genomic DNA, using as probe cDNA clones corresponding to human alpha skeletal actin or to a hamster (beta or gamma) cytoskeletal actin; they show more homology to the latter probe. The actin probes also detect a polymorphic DNA fragment showing autosomal inheritance with a frequency for the major allele of 0.55 in the population studied. The X‐linked actin sequence has been assigned to a centromeric region between Xp11 and Xq11 by hybridization to DNAs from a panel of human‐mouse hybrid cell lines, and thus lies outside the postulated region of homology between the X and Y chromosomes. The Y‐linked actin sequence can serve as a marker to analyse anomalies of sex determination or of gametogenesis in man. It was found in all XY males studied but was absent from the genomic DNA of four unrelated ‘XX male’ subjects and two XX hermaphrodites. This shows that the region of chromosome Y which contains the actin sequence is not translocated onto the X chromosome (or onto autosomes) in these patients.

Published
1984
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43. Additional polymorphisms at marker loci D9S5 and D9S15 generate extended haplotypes in linkage disequilibrium with Friedreich ataxia.

Author

Fujita, R, Hanauer, A, Sirugo, G, Heilig, R, and Mandel, J L

Abstract

The gene for Friedreich ataxia (FA), a severe recessive neurodegenerative disease, has previously been shown to be tightly linked to the polymorphic markers D9S15 and D9S5 on human chromosome 9. In addition, the observation of linkage disequilibrium suggested that D9S15 is within 1 centimorgan (cM) of the disease locus, FRDA. Although D9S5 did not show recombination with FRDA, its localization was less precise (0-5 cM) due to its lower informativeness. We have now identified additional polymorphisms at both marker loci. Two cosmids spanning 50 kilobases around D9S5 were isolated, and a probe derived from one of them detects an informative three-allele polymorphism. We have found a highly polymorphic microsatellite sequence at D9S15 which is rapidly typed by the DNA polymerase chain reaction. The polymorphism information contents at the D9S5 and D9S15 loci have been increased from 0.14 to 0.60 and from 0.33 to 0.74, respectively. With the additional polymorphisms the lod (log10 odds ratio) score for the D9S15-FRDA linkage is now 48.10 at recombination fraction theta = 0.005 and for D9S5-FRDA, the lod score is 27.87 at theta = 0.00. We have identified a recombinant between D9S15 and FRDA. However, due to the family structure, it will be of limited usefulness for more precise localization of FRDA. The linkage disequilibrium previously observed between D9S15 and FRDA is strengthened by analysis of the haplotypes using the microsatellite polymorphism, while weaker but significant disequilibrium is found between D9S5 and FRDA. Extended haplotypes that encompass D9S5 and D9S15 show a strikingly different distribution between chromosomes that carry the FA mutation and normal chromosomes. This suggests that both marker loci are less than 1 cM from the FRDA gene and that a small number of mutations account for the majority of FA cases in the French population studied. D9S5 and D9S15 are thus excellent start points to isolate the disease gene.

Published
1990
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