Items where Subject is "bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons"

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Number of items at this level: 67.

A

Aravin, A. A., Sachidanandam, R., Bourc'his, D., Schaefer, C., Pezic, D., Toth, K. F., Bestor, T., Hannon, G. J. (2008) A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice. Molecular Cell, 31 (6). pp. 785-799. ISSN 10972765 (ISSN)

Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K., Hannon, G. J. (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science, 316 (5825). pp. 744-7. ISSN 1095-9203 (Electronic)

B

Barkan, A., Martienssen, R. A. (1991) Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. Proceedings of the National Academy of Sciences of the United States of America, 88 (8). pp. 3502-3506. ISSN 0027-8424

Batut, P. J., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R. (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res, 23 (1). pp. 169-180. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Batut, Philippe (2014) Promoter Evolution in Drosophila: Non-Coding Transcription & Transposon-Driven Innovation. PhD thesis, Cold Spring Harbor Laboratory.

Bortiri, E., Jackson, D. P., Hake, S. (2006) Advances in maize genomics: The emergence of positional cloning. Current Opinion in Plant Biology, 9 (2). pp. 164-171. ISSN 13695266

Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., Hannon, G. J. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128 (6). pp. 1089-103. ISSN 0092-8674 (Print)

Brennecke, J., Malone, C. D., Aravin, A. A., Sachidanandam, R., Stark, A., Hannon, G. J. (2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science, 322 (5906). pp. 1387-92.

Brown, J., Sundaresan, V. (1992) Genetic study of the loss and restoration of Mutator transposon activity in maize: evidence against dominant-negative regulator associated with loss of activity. Genetics, 130 (4). pp. 889-98. ISSN 0016-6731 (Print)0016-6731 (Linking)

Brown, J., Sundaresan, V. (1991) A recombination hotspot in the maize A1 intragenic region. Theor Appl Genet, 81 (2). pp. 185-8. ISSN 0040-5752 (Print)0040-5752 (Linking)

Bukhari, A. I., Froshauer, S. (1978) Insertion of a transposon for chloramphenicol resistance into bacteriophage Mu. Gene, 3 (4). pp. 303-14. ISSN 0378-1119 (Print)0378-1119 (Linking)

C

Chow, L. T., Bukhari, A. I. (1978) Heteroduplex electron microscopy of phage Mu mutants containing IS1 insertions and chloramphenicol resistance transposons. Gene, 3 (4). pp. 333-46. ISSN 0378-1119 (Print)0378-1119 (Linking)

Creasey, K. M., Zhai, J., Borges, F., Van Ex, F., Regulski, M., Meyers, B. C., Martienssen, R. A. (2014) miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature, 508 (7496). pp. 411-415. ISSN 0028-0836

D

Das, L., Martienssen, R. (1995) Site-selected transposon mutagenesis at the hcf106 locus in maize. Plant Cell, 7 (3). pp. 287-294. ISSN 1040-4651

De Bruijn, F. J., Bukhari, A. I. (1978) Analysis of transposable elements inserted in the genomes of bacteriophages Mu and P1. Gene, 3 (4). pp. 315-31. ISSN 0378-1119 (Print)0378-1119 (Linking)

Dellaporta, S. L., Chomet, P. S., Mottinger, J. P., Wood, J. A., Yu, S. M., Hicks, J. B. (1984) Endogenous transposable elements associated with virus infection in maize. Cold Spring Harbor Symposia on Quantitative Biology, 49. pp. 321-328. ISSN 00917451 (ISSN)

Dubnau, J. T. (2012) Talk from Josh Dubnau at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

F

Fagegaltier, D., Falciatori, I., Czech, B., Castel, S., Perrimon, N., Simcox, A., Hannon, G. J. (2016) Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway. Genes Dev, 30 (14). pp. 1623-35. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Fransz, P., Linc, G., Lee, C. R., Aflitos, S. A., Lasky, J. R., Toomajian, C., Ali, H., Peters, J., van Dam, P., Ji, X., Kuzak, M., Gerats, T., Schubert, I., Schneeberger, K., Colot, V., Martienssen, R., Koornneef, M., Nordborg, M., Juenger, T. E., de Jong, H., Schranz, M. E. (2016) Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. Plant J, 88 (2). pp. 159-178. ISSN 1365-313X (Electronic)0960-7412 (Linking)

G

Gao, M. Q., Li, G. Y., McCombie, W. R., Quiros, C. F. (2005) Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A-thaliana. Theoretical and Applied Genetics, 111 (5). pp. 949-955. ISSN 0040-5752

Geurts, A. M., Collier, L. S., Geurts, J. L., Oseth, L. L., Bell, M. L., Mu, David, Lucito, R., Godbout, S. A., Green, L. E., Lowe, S. W., Hirsch, B. A., Leinwand, L. A., Largaespada, D. A. (2006) Gene mutations and genomic rearrangements in the mouse as a result of transposon mobilization from chromosomal concatemers. PLoS Genetics, 2 (9). pp. 1413-1423. ISSN 15537390

Gill, N., SanMiguel, P., Dhillon, B. D. S., Abernathy, B., Kim, H., Stein, L. D., Ware, D. H., Wing, R., Jackson, S. A. (2010) Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents. Rice, 3 (4). pp. 251-269.

Girard, A. (2008) Mammalian Piwi proteins and transposon silencing in the male germline. PhD thesis, Cold Spring Harbor Laboratory.

K

Kamp, D., Chow, L. T., Broker, T. R., Kwoh, D., Zipser, D., Kahmann, R. (1979) Site-specific recombination in phage mu. Cold Spring Harb Symp Quant Biol, 43 (2). pp. 1159-67. ISSN 0091-7451 (Print)0091-7451 (Linking)

Keng, V. W., Villanueva, A., Chiang, D. Y., Dupuy, A. J., Ryan, B. J., Matise, I., Silverstein, K. A. T., Sarver, A., Starr, T. K., Akagi, K., Tessarollo, L., Collier, L. S., Powers, S., Lowe, S. W., Jenkins, N. A., Copeland, N. G., Llovet, J. M., Largaespada, D. A. (2009) A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nature Biotechnology, 27 (3). pp. 264-274. ISSN 1087-0156

Klar, A. J. S., Strathern, J. N., Hicks, J. B. (1981) A position-effect control for gene transposition: State of expression of yeast mating-type genes affects their ability to switch. Cell, 25 (2). pp. 517-524.

Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W. W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., Dubnau, J. (2017) Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet, 13 (3). e1006635. ISSN 1553-7390

L

Lalanne, E., Michaelidis, C., Moore, J. M., Gagliano, W., Johnson, A., Patel, R., Howden, R., Vielle-Calzada, J. P., Grossniklaus, U., Twell, D. (2004) Analysis of transposon insertion mutants highlights the diversity of mechanisms underlying male progamic development in arabidopsis. Genetics, 167 (4). pp. 1975-1986. ISSN 0016-6731

Li, W. H., Jin, Y., Prazak, L., Hammell, M., Dubnau, J. (2012) Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders. PLoS ONE, 7 (9). ISSN 1932-6203

Lippman, Z., May, B., Yordan, C., Singer, T., Martienssen, R. (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS biology, 1 (3). pp. 420-428. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Lippman, Z. B. (2004) Transposons, heterochromatin, and epigenetic landscapes in Arabidopsis thaliana. PhD thesis, Cold Spring Harbor Laboratory.

Lister, C., Jackson, D., Martin, C. (1993) Transposon-induced inversion in Antirrhinum modifies nivea gene expression to give a novel flower color pattern under the control of cycloidearadialis. Plant Cell, 5 (11). pp. 1541-53. ISSN 1040-4651 (Print)1040-4651

Lu, X. W., Wontakal, S. N., Kavi, H., Kim, B. J., Guzzardo, P. M., Emelyanov, A. V., Xu, N., Hannon, G. J., Zavadil, J., Fyodorov, D. V., Skoultchi, A. I. (2013) Drosophila H1 Regulates the Genetic Activity of Heterochromatin by Recruitment of Su(var)3-9. Science, 340 (6128). pp. 78-81. ISSN 0036-8075

M

Malone, C. D. (2010) Evolution, Inheritance and Specialization of Transposon Control Pathways in Drosophila. PhD thesis, Cold Spring Harbor Laboratory.

Malone, C. D., Hannon, G. J. (2010) Molecular Evolution of piRNA and Transposon Control Pathways in Drosophila. Cold Spring Harb Symp Quant Biol. pp. 225-234. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Malone, C. D., Hannon, G. J. (2009) Small RNAs as Guardians of the Genome. Cell, 136 (4). pp. 656-668. ISSN 0092-8674

Martienssen, R. (1998) Transposons, DNA methylation and gene control. Trends in Genetics, 14 (7). pp. 263-264. ISSN 0168-9525

Martienssen, R., Baron, A. (1994) Coordinate suppression of mutations caused by Robertson's mutator transposons in maize. Genetics, 136 (3). pp. 1157-1170. ISSN 0016-6731

Martienssen, R., Lippman, Z., May, B., Ronemus, M., Vaughn, M. (2004) Transposons, tandem repeats, and the silencing of imprinted genes. Cold Spring Harbor symposia on quantitative biology, 69. pp. 371-9. ISSN 0091-7451 (Print)0091-7451 (Linking)

Martienssen, R. A. (1998) Functional genomics: Probing plant gene function and expression with transposons. Proceedings of the National Academy of Sciences of the United States of America, 95 (5). pp. 2021-2026. ISSN 0027-8424

Martienssen, R. A. (2010) Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytologist, 186 (1). pp. 46-53. ISSN 0028-646X

Martienssen, R. A., Baulcombe, D. C. (1989) An unusual wheat insertion sequence (WIS1) lies upstream of an alpha-amylase gene in hexaploid wheat, and carries a "minisatellite" array. Mol Gen Genet, 217 (2-3). pp. 401-410. ISSN 0026-8925

Matsumoto, T., Wu, J. Z., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B. A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R., Hamada, M., Harada, C., Hayashi, A., Hijishita, S., Honda, M., Hosokawa, S., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, K., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Kurita, K., Katagiri, S., Kikuta, A., Kobayashi, H., Kobayashi, N., Machita, K., Maehara, T., Masukawa, M., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nagata, Y., Naito, S., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Meguro, A., Negishi, M., Ohta, I., Ohta, T., Okamoto, M., Ono, N., Saji, S., Sakaguchi, M., Sakai, K., Shibata, M., Shimokawa, T., Song, J. Y., Takazaki, Y., Terasawa, K., Tsugane, M., Tsuji, K., Ueda, S., Waki, K., Yamagata, H., Yamamoto, M., Yamamoto, S., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H. S., Yano, M., Sasaki, T., Yuan, Q. P., Shu, O. T., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Bera, J., Fadrosh, D., Jin, S. H., Johri, S., Kim, M., Overton, L., Reardon, M., Tsitrin, T., Vuong, H., Weaver, B. (2005) The map-based sequence of the rice genome. Nature, 436 (7052). pp. 793-800. ISSN 0028-0836

May, B. P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P. D., Roh, D., Pan, X. K., Stein, L., Freeling, M., Alexander, D., Martienssen, R. (2003) Maize-targeted mutagenesis: A knockout resource for maize. Proceedings of the National Academy of Sciences of the United States of America, 100 (20). pp. 11541-11546. ISSN 0027-8424

May, B. P., Martienssen, R. A. (2003) Transposon mutagenesis in the study of plant development. Critical Reviews in Plant Sciences, 22 (1). pp. 1-35. ISSN 0735-2689

McCombie, W. R., Hansen, J. B., Zylstra, G. J., Maurer, B., Olsen, R. H. (1983) Pseudomonas Streptomycin Resistance Transposon Associated with R-Plasmid Mobilization. Journal of Bacteriology, 155 (1). pp. 40-48. ISSN 0021-9193

Muerdter, F., Guzzardo, P. M., Gillis, J., Luo, Y., Yu, Y., Chen, C., Fekete, R., Hannon, G.J. (2013) A Genome-wide RNAi Screen Draws a Genetic Framework for Transposon Control and Primary piRNA Biogenesis in Drosophila. Molecular Cell, 50 (5). pp. 736-748. ISSN 1097-4164

N

Ngo, Q. A., Moore, J. M., Baskar, R., Grossniklaus, U., Sundaresan, V. (2007) Arabidopsis GLAUCE promotes fertilization-independent endosperm development and expression of paternally inherited alleles. Development, 134 (22). pp. 4107-4117. ISSN 0950-1991

Nussaume, L., Harrison, K., Klimyuk, V., Martienssen, R., Sundaresan, V., Jones, J. D. G. (1995) Analysis of splice donor and acceptor site function in a transposable gene trap derived from the maize element Activator. Molecular & General Genetics, 249 (1). pp. 91-101. ISSN 0026-8925

O

Ong-Abdullah, M., Ordway, J. M., Jiang, N., Ooi, S. E., Kok, S. Y., Sarpan, N., Azimi, N., Hashim, A. T., Ishak, Z., Rosli, S. K., Malike, F. A., Bakar, N. A., Marjuni, M., Abdullah, N., Yaakub, Z., Amiruddin, M. D., Nookiah, R., Singh, R., Low, E. L., Chan, K. L., Azizi, N., Smith, S. W., Bacher, B., Budiman, M. A., Van Brunt, A., Wischmeyer, C., Beil, M., Hogan, M., Lakey, N., Lim, C. C., Arulandoo, X., Wong, C. K., Choo, C. N., Wong, W. C., Kwan, Y. Y., Alwee, S. S., Sambanthamurthi, R., Martienssen, R. A. (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature, 525. pp. 533-537. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

P

Page, D. R., Kohler, C., da Costa-Nunes, J. A., Baroux, C., Moore, J. M., Grossniklaus, U. (2004) Intrachromosomal excision of a hybrid Ds element induces large genomic deletions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 101 (9). pp. 2969-2974. ISSN 0027-8424

Petersen, M., Brodersen, P., Naested, H., Andreasson, E., Lindhart, U., Johansen, B., Nielsen, H. B., Lacy, M., Austin, M. J., Parker, J. E., Sharma, S. B., Klessig, D. F., Martienssen, R., Mattsson, O., Jensen, A. B., Mundy, J. (2000) Arabidopsis MAP kinase 4 negatively regulates systemic acquired resistance. Cell, 103 (7). pp. 1111-1120. ISSN 0092-8674

R

Rabinowicz, P. D. (2000) Are obese plant genomes on a diet? Genome Research, 10 (7). pp. 893-894. ISSN 1088-9051

Rabinowicz, P. D., Palmer, L. E., May, B. P., Hemann, M. T., Lowe, S. W., McCombie, W. R., Martienssen, R. A. (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Research, 13 (12). pp. 2658-64. ISSN 1088-9051

Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics, 23 (3). pp. 305-308. ISSN 10614036 (ISSN)

Rozhkov, N. V., Aravin, A. A., Zelentsova, E. S., Schostak, N. G., Sachidanandam, R., McCombie, W. R., Hannon, G. J., Evgen'ev, M. B. (2010) Small RNA-based silencing strategies for transposons in the process of invading Drosophila species. RNA, 16 (8). pp. 1634-1645. ISSN 1355-8382

Rozhkov, N. V., Hammell, M., Hannon, G. J. (2013) Multiple roles for Piwi in silencing Drosophila transposons. Genes and Development, 27 (4). pp. 400-412. ISSN 08909369 (ISSN)

S

Scholl, R., Sachs, M. M., Ware, D. (2003) Maintaining collections of mutants for plant functional genomics. Methods in Molecular Biology, 236. pp. 311-26. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Settles, A. M., Baron, A., Barkan, A., Martienssen, R. A. (2001) Duplication and suppression of chloroplast protein translocation genes in maize. Genetics, 157 (1). pp. 349-360. ISSN 0016-6731

Singer, T., Yordan, C., Martienssen, R. A. (2001) Robertson's Mutator transposons in A-thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes & Development, 15 (5). pp. 591-602. ISSN 0890-9369

Singh, P. K., Bourque, G., Craig, N. L., Dubnau, J. T., Feschotte, C., Flasch, D. A., Gunderson, K. L., Malik, H. S., Moran, J. V., Peters, J. E., Slotkin, R. K., Levin, H. L. (2014) Mobile genetic elements and genome evolution 2014. Mobile DNA, 5. ISSN 1759-8753

Springer, P. S., McCombie, W. R., Sundaresan, V., Martienssen, R. A. (1995) Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. Science, 268 (5212). pp. 877-880. ISSN 0036-8075

Starr, T. K., Allaei, R., Silverstein, K. A. T., Staggs, R. A., Sarver, A. L., Bergemann, T. L., Gupta, M., O'Sullivan, M. G., Matise, I., Dupuy, A. J., Collier, L. S., Powers, S., Oberg, A. L., Asmann, Y. W., Thibodeau, S. N., Tessarollo, L., Copeland, N. G., Jenkins, N. A., Cormier, R. T., Largaespada, D. A. (2009) A Transposon-Based Genetic Screen in Mice Identifies Genes Altered in Colorectal Cancer. Science, 323 (5922). pp. 1747-1750. ISSN 0036-8075

Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J. D. G., Dean, C., Ma, H., Martienssen, R. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes & Development, 9 (14). pp. 1797-1810. ISSN 0890-9369

W

Weil, C., Martienssen, R. (2008) Epigenetic interactions between transposons and genes: lessons from plants. Current opinion in genetics & development, 18 (2). pp. 188-92. ISSN 0959-437X (Print)0959-437X (Linking)

Z

Zaratiegui, B. M., Vaughn, M. W., Irvine, D. V., Goto, D. , Watt, S., Bahler, J., Arcangioli, B., Martienssen, R. A. (2011) CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature, 469 (7328). pp. 112-5. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Zhou, X., Battistoni, G., El Demerdash, O., Gurtowski, J., Wunderer, J., Falciatori, I., Ladurner, P., Schatz, M. C., Hannon, G. J., Wasik, K. A. (2015) Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA, 21 (11). pp. 1885-1897. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

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