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39 results on '"Wong, Gane K."'

4. Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics

Author

Gilroy, Kathryn L., Terry, Anne, Naseer, Asif, de Ridder, Jeroen, Allahyar, Amin, Wang, Weiwei, Carpenter, Eric, Mason, Andrew, Wong, Gane K-S., Cameron, Ewan R., Kilbey, Anna, and Neil, James C.

Subjects
Science, Virus Integration, DNA transcription, Gene Expression, Biochemistry, Histones, Gene Types, Cell Line, Tumor, Neoplasms, DNA-binding proteins, Breast Tumors, Breast Cancer, Genetics, Medicine and Health Sciences, Animals, Humans, Gene Regulation, Mammalian Genomics, Chromosome Biology, Leukemia Virus, Feline, Biology and Life Sciences, Proteins, Cancers and Neoplasms, Cell Biology, Genomics, Chromatin, Gene Expression Regulation, Neoplastic, Tumor Virus Infections, Oncology, Animal Genomics, Cats, MCF-7 Cells, Medicine, Regulator Genes, Epigenetics, Transcription Initiation Site, Research Article, Genes, Neoplasm, Retroviridae Infections
Abstract

Retroviruses have been foundational in cancer research since early studies identified protooncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types. Analysis of FeLV insertion sites in the MCF-7 mammary carcinoma cell line revealed strong bias towards active chromatin marks with no evidence of significant post-integration growth selection. The most prominent FeLV integration targets had little overlap with the most abundantly expressed transcripts, but were strongly enriched for annotated cancer genes. A meta-analysis based on several gamma-retrovirus integration profiling (GRIP) studies in human cells (CD34+, K562, HepG2) revealed a similar cancer gene bias but also remarkable cell-type specificity, with prominent exceptions including a universal integration hotspot at the long non-coding RNA MALAT1. Comparison of GRIP targets with databases of super-enhancers from the same cell lines showed that these have only limited overlap and that GRIP provides unique insights into the upstream drivers of cell growth. These observations elucidate the oncogenic potency of the gamma-retroviruses and support the wider application of GRIP to identify the genes and growth regulatory circuits that drive distinct cancer types.

Published
2016

12. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Author

Yan, Zhixiang, Larsson, Anders, Shaw, A Jonathan, Thomas, Philip, Der, Joshua P., Ruhsam, Markus., Villarreal, Juan C., Soltis, Douglas E., Deyholos, Michael K., Sun, Xiao, Li, Fay-Wei, Pokorny, Lisa, Tian, Zhijian, Chen, Li, Melkonian, Michael, Windham, Michael D., Sigel, Erin M., Wang, Jun, Weststrand, Stina, Carpenter, Eric, Stevenson, Dennis W., Zhu, Ying, Frangedakis, Eftychios, Graham, Sean W., Pryer, Kathleen M., Chen, Tao, Crandall-Stotler, Barbara J., Pittermann, Jarmila, Rothfels, Carl J., Langdale, Jane A., Zhang, Yong, Kelly, Steven, Wong, Gane K., Mathews, Sarah, and Burge, Dylan O

Published
2015
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20. Data access for the 1,000 Plants (1KP) project

Author

Wu, Xiaolei, Wafula, Eric, Yan, Zhixiang, Kutchan, Toni M., Gitzendanner, Matthew A, Shaw, Jonathan A., Chen, Tao., Wickett, Norman J., Nguyen, Nam, Burleigh, J Gordon, Miles, Nicholas W., Soltis, Pamela S., Melkonian, Michael, Deyholos, Michael K., Matasci, Naim, DeGironimo, Lisa, Samudrala, Ram, Leebens-Mack, Jim, Mirarab, Siavash, Barker, Michael, Sun, Xiao, Soltis, Douglas E., Rolf, Megan, Tian, Zhijian, Wong, Gane K, Rothfels, Carl, Pokorny, Lisa, Zhang, Yong, Ayyampalayam, Saravanaraj, Graham, Sean W., Roure, Béatrice, Der, Joshua P., Wang, Jun, Mathews, Sarah, Surek, Barbara, Baucom, Regina S., Ruhfel, Brad R., Villarreal, Juan C., Stevenson, Dennis W., Hung, Ling-Hong, Warnow, Tandy, Philippe, Hervé, and Carpenter, Eric J.

Published
2014
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24. A Genome Triplication associated with early diversification of the core eudicots

Author

Wong, Gane K., Wickett, Norman J., Ruzicka, Daniel R., Leebens-Mack, Jim, Deyholos, Michael K., DePamphilis, Claude W., Zhang, Yeting, Chanderbali, Andre S., McCombie, Richard, Ayyampalayam, Saravanaraj, Kutchan, Toni M., Wu, Xiaolei, Stevenson, Dennis W., Wafula, Eric, Pires, J Chris, McNeal, Joel, Zhang, Yong, Wang, Jun, Rolf, Megan, Soltis, Pamela S., Soltis, Douglas E., Carpenter, Eric J., Jiao, YN, McKain, Michael R., and Bowers, John E.

Published
2012
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25. Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

Author

Zhang, Yong, Wu, Xiaolei, Patterson, Jordan, Villarreal, Juan C., Jordon-Thaden, Ingrid, Bruskiewich, Richard, Sage, Rowan F., Goh, Falicia, Wong, Gane K., Chase, Mark W., Stewart Jr, C Neal, Clarke, Neil D., Burris, Jason N., Ralph, Paula, Tian, Zhijian, Myburg, Henrietta, Surek, Barbara., Rolf, Megan., Graham, Sean, Thomsen, Christina J., Johnson, Marc TJ., Miles, Nicholas, Carrigan, Charlotte T., Greiner, Stephan, Soltis, Pamela, Leebens-Mack, James, Edger, Patrick P., Soltis, Douglas, Kutchan, Toni M., Melkonian, Michael, Covshoff, Sarah, Carpenter, Eric J., Deyholos, Michael K., Pires, J Chris, Hibberd, Julian M., and Stevenson, Dennis

Published
2012
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26. Large Insert Genome Analysis (LIGAN) Technology Detects Structural Variation in Pseudomonas aeruginosa Clinical Strains from Cystic Fibrosis Patients1

Author

Hayden, Hillary S., Gillett, Will, Saenphimmachak, Channakhone, Lim, Regina, Zhou, Yang, Jacobs, Michael A., Chang, Jean, Rohmer, Laurence, D’Argenio, David A., Palmieri, Anthony, Levy, Ruth, Haugen, Eric, Wong, Gane K., Brittnacher, Mitch J., Burns, Jane L., Miller, Samuel I., Olson, Maynard V., and Kaul, Rajinder

Subjects
Recombination, Genetic, Mutagenesis, Insertional, Base Sequence, Cystic Fibrosis, DNA Mutational Analysis, Molecular Sequence Data, Pseudomonas aeruginosa, Genetic Variation, Humans, DNA Fingerprinting, Article, Genome, Bacterial, Sequence Deletion
Abstract

Large Insert Genome Analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools in order to pinpoint locations of insertions, deletions and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 742,869 bp containing 651 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement break points and 220 kb of deleted sequences were also identified. Our study expands the “genome universe” of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphism than structural variation.

Published
2008

30. Origin and evolution of new exons in rodents

Author

Samudrala, Ram, Zheng, Hongkun, Li, Jun, Yang, Shuang, Zhang, Jianguo, Yu, Haijing, McDermott, Jason, Wang, Wen, Yang, Huanming, Jiang, Huifeng, Yang, Lei, Wang, Jian, Wong, Gane K., Kristiansen, Karsten, Su, Jianning, and Yu, Jun

Published
2005
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37. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Author

Li, Fay-Wei, Nishiyama, Tomoaki, Waller, Manuel, Frangedakis, Eftychios, Keller, Jean, Li, Zheng, Fernandez-Pozo, Noe, Barker, Michael S, Bennett, Tom, Blázquez, Miguel A, Cheng, Shifeng, Cuming, Andrew C, De Vries, Jan, De Vries, Sophie, Delaux, Pierre-Marc, Diop, Issa S, Harrison, C Jill, Hauser, Duncan, Hernández-García, Jorge, Kirbis, Alexander, Meeks, John C, Monte, Isabel, Mutte, Sumanth K, Neubauer, Anna, Quandt, Dietmar, Robison, Tanner, Shimamura, Masaki, Rensing, Stefan A, Villarreal, Juan Carlos, Weijers, Dolf, Wicke, Susann, Wong, Gane K-S, Sakakibara, Keiko, and Szövényi, Péter

Subjects
2. Zero hunger, Embryophyta, Anthocerotophyta, 15. Life on land, Biological Evolution, Life History Traits, Genome, Plant
Abstract

Funder: National Institute for Basic Biology (NIBB) Collaborative Research Program (13-710), Funder: The Forschungskredit of the University of Zurich The University Research Priority Program “Evolution in Action” of the University of Zurich The Georges and Antoine Claraz Foundation (Switzerland), Funder: Spanish Ministry of Science, Innovation and Universities (BFU2016-80621-P), Funder: The Georges and Antoine Claraz Foundation (Switzerland) The Research Priority Program “Evolution in Action” of the University of Zurich, Funder: Foundation of German Business (sdw), Georges and Antoine Claraz Foundation, URPP Evolution in Action of the University of Zurich, Funder: Special Grant for Innovation in Research Program of the Technical University of Dresden (Germany)., Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

38. Data access for the 1,000 Plants (1KP) project

Author

Matasci, Naim, Hung, Ling-Hong, Yan, Zhixiang, Carpenter, Eric J, Wickett, Norman J, Mirarab, Siavash, Nguyen, Nam, Warnow, Tandy, Ayyampalayam, Saravanaraj, Barker, Michael, Burleigh, J G, Gitzendanner, Matthew A, Wafula, Eric, Der, Joshua P, DePamphilis, Claude W, Roure, Béatrice, Philippe, Hervé, Ruhfel, Brad R, Miles, Nicholas W, Graham, Sean W, Mathews, Sarah, Surek, Barbara, Melkonian, Michael, Soltis, Douglas E, Soltis, Pamela S, Rothfels, Carl, Pokorny, Lisa, Shaw, Jonathan A, DeGironimo, Lisa, Stevenson, Dennis W, Villarreal, Juan C, Chen, Tao, Kutchan, Toni M, Rolf, Megan, Baucom, Regina S, Deyholos, Michael K, Samudrala, Ram, Tian, Zhijian, Wu, Xiaolei, Sun, Xiao, Zhang, Yong, Wang, Jun, Leebens-Mack, Jim, and Wong, Gane K

Subjects
15. Life on land
Abstract

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

39. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Author

Isabel Monte, Pierre-Marc Delaux, Zheng Li, Dolf Weijers, Noe Fernandez-Pozo, Jan de Vries, Alexander Kirbis, Shifeng Cheng, Tanner A. Robison, Keiko Sakakibara, Jill C. Harrison, Sumanth K. Mutte, Péter Szövényi, Stefan A. Rensing, Tomoaki Nishiyama, Sophie de Vries, Masaki Shimamura, Tom Bennett, Miguel A. Blázquez, Eftychios Frangedakis, Jorge Hernández-García, Manuel Waller, Duncan A. Hauser, Juan Carlos Villarreal, John C. Meeks, Gane Ka-Shu Wong, Jean Keller, Dietmar Quandt, Michael S. Barker, Fay-Wei Li, Susann Wicke, Andrew C. Cuming, Issa S. Diop, Anna Neubauer, Boyce Thompson Institute [Ithaca], Cornell University [New York], Kanazawa University (KU), Universität Zürich [Zürich] = University of Zurich (UZH), Department of Plant, University of Oxford [Oxford], Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Orange Labs, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Campus de Teatinos s/n, Universidad de Málaga [Málaga] = University of Málaga [Málaga], Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Instituto de Biología Molecular y Celular de Plantas, Chinese Academy of Agricultural Sciences (CAAS), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), University of Bristol [Bristol], Nees Institut for Plant Biodiversity, Rheinische Friedrich-Wilhelms-Universität Bonn, Faculty of Biology, University of Freiburg [Freiburg], Wageningen University and Research Centre (WUR), Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Li, Fay-Wei [0000-0002-0076-0152], Nishiyama, Tomoaki [0000-0003-1279-7806], Keller, Jean [0000-0002-5198-0331], Fernandez-Pozo, Noe [0000-0002-6489-5566], Barker, Michael S [0000-0001-7173-1319], Bennett, Tom [0000-0003-1612-4019], Blázquez, Miguel A [0000-0001-5743-0448], Cuming, Andrew C [0000-0003-2562-2052], de Vries, Jan [0000-0003-3507-5195], de Vries, Sophie [0000-0002-5267-8935], Delaux, Pierre-Marc [0000-0002-6211-157X], Hernández-García, Jorge [0000-0003-2526-8639], Monte, Isabel [0000-0002-7058-8343], Mutte, Sumanth K [0000-0003-3376-2354], Rensing, Stefan A [0000-0002-0225-873X], Villarreal, Juan Carlos [0000-0002-0770-1446], Weijers, Dolf [0000-0003-4378-141X], Wicke, Susann [0000-0001-5785-9500], Wong, Gane K-S [0000-0001-6108-5560], Sakakibara, Keiko [0000-0003-4420-9351], Szövényi, Péter [0000-0002-0324-4639], Apollo - University of Cambridge Repository, University of Zurich, and Li, Fay-Wei

Subjects
MESH: Genome, Plant, Crop and Pasture Production, 0106 biological sciences, Anthoceros, Evolution, [SDV]Life Sciences [q-bio], Lineage (evolution), Biochemie, Plant Biology, MESH: Biological Evolution, Anthocerotophyta, Plant Science, 580 Plants (Botany), Biology, Biochemistry, 01 natural sciences, Genome, Article, Pyrenoid, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Hornwort, 03 medical and health sciences, 1110 Plant Science, Genetics, Life Science, 10211 Zurich-Basel Plant Science Center, MESH: Anthocerotophyta / genetics, Clade, Life History Traits, 030304 developmental biology, 0303 health sciences, MESH: Life History Traits, Sporophyte, Plant, Genomics, 15. Life on land, biology.organism_classification, Biological Evolution, 10121 Department of Systematic and Evolutionary Botany, Evolutionary biology, Embryophyta, Bryophyte, MESH: Embryophyta / physiology, EPS, Plant sciences, Genome, Plant, 010606 plant biology & botany
Abstract

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants., Analyses of three high-quality genomes of Anthoceros hornworts place hornworts as a sister clade to the lineage including liverworts and mosses, and provide insights into the unique biological features of hornworts.

Published
2020

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