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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...families. These results are consistent with full-length elements being mostly of young age and solo LTRs being of much older origin.In the S. pombe reference strain, ∼70% of Tf2 mobilization events involve homologous recombination between newly synthesized cDNA and a pre-existing copy of Tf2; the remaining...
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Research: Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
- Xiuli Bi,
- Ying-Juan Cheng,
- Bo Hu,
- Xiaoli Ma,
- Rui Wu,
- Jia-Wei Wang,
- and Chang Liu
Genome Res. July 2017 27: 1162-1173; Published in Advance April 6, 2017, doi:10.1101/gr.215186.116
...Fig. 13). Additionally, TE genes enriched at the nuclear periphery showed a higher average level of heterochromatin marks, such as H3K9me2, H3K27me1, and DNA methylation (Supplemental Fig. 14). In terms of classes, two class-II TE genes (MuDR and CACTA-like) weremore likely to be found at the nuclear...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of Arabidopsis thaliana transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. The value of this map to study potentially intact...
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LETTER: Analysis of 5S rDNA Arrays in Arabidopsis thaliana: Physical Mapping and Chromosome-Specific Polymorphisms
- C. Cloix,
- S. Tutois,
- O. Mathieu,
- C. Cuvillier,
- M.C. Espagnol,
- G. Picard,
- and S. Tourmente
Genome Res. May 1, 2000 10: 679-690; doi:10.1101/gr.10.5.679
...of the 5S RNA gene directs specific initiation of transcription: II. The 3′ border of the region. Cell 19 : 27 – 35 . ↵ Burke D.T. , Carle G.F , Olson M.V. ( 1987 ) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236 : 806 – 812 . ↵ Camilleri C...
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Method: Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways
- Yiping Qi,
- Yong Zhang,
- Feng Zhang,
- Joshua A. Baller,
- Spencer C. Cleland,
- Yungil Ryu,
- Colby G. Starker,
- and Daniel F. Voytas
Genome Res. March 2013 23: 547-554; Published in Advance January 2, 2013, doi:10.1101/gr.145557.112
...double strand breaks in Arabidopsis thaliana is dependent on proteins involved in chromosome structure maintenance. DNA Repair (Amst) 8: 413–419. Mengiste T, Revenkova E, Bechtold N, Paszkowski J. 1999. An SMC-like protein is required for efficient homologous recombination in Arabidopsis. EMBO J 18: 4505...
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ARTICLES: A physical map of chromosome 2 of Arabidopsis thaliana.
- E A Zachgo,
- M L Wang,
- J Dewdney,
- D Bouchez,
- C Camilleri,
- S Belmonte,
- L Huang,
- M Dolan,
- and H M Goodman
Genome Res. January 1996 6: 19-25; doi:10.1101/gr.6.1.19
..., Harvard Medical School, Massachusetts General Hospital, Boston 02114, USA. Abstract A yeast artificial chromosome (YAC) physical map of chromosome 2 of Arabidopsis thaliana has been constructed by hybridization of 69 DNA markers and 61 YAC end probes to gridded arrays of YAC clones. Thirty...
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Method: Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome
- Dal-Hoe Koo,
- Fangpu Han,
- James A. Birchler,
- and Jiming Jiang
Genome Res. June 2011 21: 908-914; Published in Advance April 25, 2011, doi:10.1101/gr.116202.110
...-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9: 421–430. Gong ZY, Yu HX, Huang J, Yi CD, Gu MH. 2009. Unstable transmission of rice chromosomes without functional centromeric repeats in asexual propagation. Chromosome Res 17: 863...
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ARTICLES: An ordered yeast artificial chromosome library covering over half of rice chromosome 6.
- Y Umehara,
- H Tanoue,
- N Kurata,
- I Ashikawa,
- Y Minobe,
- and T Sasaki
Genome Res. October 1996 6: 935-942; doi:10.1101/gr.6.10.935
...of Agrobiological Resources/Society for Techno-innovation of Agriculture, Forestry and Fisheries, Ibaraki, Japan. Abstract Yeast artificial chromosome (YAC) clones carrying DNA marker sequences located on the rice genetic map of chromosome 6 were ordered for physical mapping. A total of 122 restriction...
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LETTER: Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis thaliana
- Stephen I. Wright,
- Newton Agrawal,
- and Thomas E. Bureau
Genome Res. August 2003 13: 1897-1903; doi:10.1101/gr.1281503
....org ). The sequence is in the form of pseudomolecules, the concatenated sequence of overlapping sequenced clones for each chromosome. These pseudomolecules comprise the entire sequence, with the exception of telomeres, the rDNA islands on chromosomes 2 and 4, and several small gaps denoted as N's ( Arabidopsis Genome...
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RESOURCE: A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome
- Kazutoyo Osoegawa,
- Aaron G. Mammoser,
- Chenyan Wu,
- Eirik Frengen,
- Changjiang Zeng,
- Joseph J. Catanese,
- and Pieter J. de Jong
Genome Res. March 1, 2001 11: 483-496; doi:10.1101/gr.169601
...-fold redundant human bacterial artificial chromosome (BAC) library with a large average insert size (178 kb) has been constructed to provide the intermediate substrate for the international sequencing effort. The DNA was obtained from a single anonymous volunteer, whose identity was protected through...

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