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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
..., with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant , we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...flanking the centromeres with higher than average DNA methylation, and chromosome arms as the remainder of the (Supplemental Table S9). Consistent with our FTL analysis, we observed that GBS-mapped crossovers were significantly increased in the cmt3 pericentromeric regions (24.6% versus 27.8% of events...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...chromosomes, 27 chromosomes consist of one contig, 22 chromosomes have telomeres at both ends (Supplemental Table 10), and all chromosomes have a predicted centromeric region (Supplemental Table 11). The chromosome IDs of FaBen and the two haplotypes were assigned by mapping to the FaRR1 (Supplemental Fig. 10...
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Research: Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence
- Shamoni Maheshwari,
- Takayoshi Ishii,
- C. Titus Brown,
- Andreas Houben,
- and Luca Comai
Genome Res. March 2017 27: 471-478; Published in Advance February 21, 2017, doi:10.1101/gr.214619.116
...centromere regions: genetic map positions and repetitive DNA structure. Genome Res 7: 1045–1053. ↵Sanei M, Pickering R, Kumke K, Nasuda S, Houben A. 2011. Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proc Natl Acad Sci...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...of copy number increases, although transposition of elements of the ATGP3, ATCOPIA13, ATCOPIA21, and ATCOPIA51 subfamilies has also been detected under nonstressed conditions (Tsukahara et al. 2009; Quadrana et al. 2019). Differential analysis of uniquely mapped VLP DNA short sequencing reads...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...to the TATA motif. ( C ) Percentage overlap of PRs to cis -element motifs mapped to the A. thaliana for 9599 upstream regions for Bor-4 (red arrow) (for overlap in other accessions, see Supplemental Fig. S8). The overlap expected by chance was established by permuting PRs and upstream regions 1000 times (gray...
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Resource: A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
- Kaitlin U. Laverty,
- Jake M. Stout,
- Mitchell J. Sullivan,
- Hardik Shah,
- Navdeep Gill,
- Larry Holbrook,
- Gintaras Deikus,
- Robert Sebra,
- Timothy R. Hughes,
- Jonathan E. Page,
- and Harm van Bakel
Genome Res. January 2019 29: 146-156; Published in Advance November 8, 2018, doi:10.1101/gr.242594.118
...embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic...
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Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
- Sergei A. Filichkin,
- Henry D. Priest,
- Scott A. Givan,
- Rongkun Shen,
- Douglas W. Bryant,
- Samuel E. Fox,
- Weng-Keen Wong,
- and Todd C. Mockler
Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
...and that the complexity and extent of alternative splicing in plants has been significantly underestimated. Results Mapping of the Arabidopsis transcriptome To achieve a nonbiased and complete analysis of the Arabidopsis transcriptome, we utilized two approaches: cDNA libraries were prepared using either oligo...
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RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
- Stephan Ossowski,
- Korbinian Schneeberger,
- Richard M. Clark,
- Christa Lanz,
- Norman Warthmann,
- and Detlef Weigel
Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
...Supplemental Methods). These regions, which corresponded to rDNA, centromeric, and other highly repetitive sequences whose copy number is not reflected by the reference assembly, were excluded from subsequent analyses. Disregarding these regions as mapping targets is expected to significantly reduce...
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LETTER: Centromere Satellites From Arabidopsis Populations: Maintenance of Conserved and Variable Domains
- Sarah E. Hall,
- Gregory Kettler,
- and Daphne Preuss
Genome Res. February 1, 2003 13: 195-205; Published in Advance January 14, 2003, doi:10.1101/gr.593403
..., transposons, microsatellites, middle repetitive DNA, and tandemly organized satellites. The satellite repeats are not found elsewhere in the , but are restricted to the genetically defined centromere regions ( Copenhaver et al. 1999 ; The Arabidopsis Genome Initiative 2000 ). Heslop-Harrison et al. (1999...

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