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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...unknown mC binders are orange) or unmethylated probes (brown) in each context (CG, CHG, CHH). Statistically enriched proteins, often identified in mass spectrometry experiments and thus listed as contaminants in Van Leene et al. (2015), are colored purple. (B) Hierarchical clustering of the proteins (rows...
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Corrigendum: Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...and apologize for any confusion this may have caused.doi: 10.1101/gr.280860.125 Published by Cold Spring Harbor Laboratory Press Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana Jonathan Cahn , James P.B. Lloyd , Ino D. Karemaker , Pascal W.T.C. Jansen , Jahnvi Pflueger...
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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...of the five A. thaliana chromosomes (Supplemental Fig. 2A,B). Further spatial clustering tests (Roberts et al. 2012) indicated that most SNVs and indels were distributed within chromosomes in a pattern that is not significantly different from the random expectation (P-values > 0.01) (see Methods...
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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
...families are evident locally; for example, a nucleosome-dense retroelement coldspot ATCOPIA4 shows higher SPO11-1-oligo levels compared with an adjacent cluster of nucleosome-depleted Helitron hotspots (Supplemental Fig. S20). Many SPO11-1-oligo hotspot DNA transposons are short, nonautonomous fragments...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...STRs and phenotypes, summarized by the P-value from a linear mixed model, fitting STR allele as a fixed effect and kinship as a random effect. Both rows and columns are clustered, although the row dendrogram was omitted for clarity. STRs with genotype information in fewer than 25 strains...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...been recently shown that biosynthetic nonhomologous gene clusters are embedded in local 3D configurations that segregate cluster regions from the surrounding chromosome environment. Based on Hi-C and H3K27me3 distribution in Arabidopsis, it has been proposed that topology differs between shoots...
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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
...meiosis, A. thaliana centromeres and pericentromeres undergo progressive clustering during prophase-I (Fig. 3A; Armstrong et al. 2001). We observed that the heterochromatic clusters, detected by DAPI staining of DNA, stain strongly for H3K9me2 throughout leptotene, zygotene, and pachytene (Fig. 3A), which...
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Methods: Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine
- Yunhai Li,
- Kee Khoon Lee,
- Sean Walsh,
- Caroline Smith,
- Sophie Hadingham,
- Karim Sorefan,
- Gavin Cawley,
- and Michael W. Bevan
Genome Res. March 2006 16: 414-427; Published in Advance January 19, 2006, doi:10.1101/gr.4237406
...expression in a cooperative manner with the TEF motif. Discussion Dynamic transcriptional responses to glucose Glucose and ABA treatments lead to rapid dynamic changes in gene expression in Arabidopsis seedlings. Quantitative analysis of gene function and clustering of gene expression dynamics identified...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
.... thaliana certain H3K27me3-marked loci were clustered in three-dimensional Figure 2. H3K27me3 and chromatin loops. (A) Proportion of chromatin loops related to “positive strips,” defined as regions with strong Hi-C interaction with neighboring chromatin (Wang et al. 2015). Loops shorter than 6 kb...
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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
...with more than two poly(A) sites (Fig. 1A). Principle component analysis of PAT-seq data shows a good repeatability of this PAT-seq experiment (Supplemental Fig. S2B). Furthermore, the percentage of reads clustered into each poly(A) site in a gene is calculated to represent the poly(A) site usage (PSU...

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