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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
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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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
.... Genome-wide distribution of SNVs in HT, ST, and MMR-deficient MA lines. Black bars show the relative distribution of Arabidopsis thaliana TAIR10 reference annotation categories (expressed as % of total ). (CDS) Coding DNA sequence, (UTRs) untranslated regions, (TE) transposable element, (Other) noncoding...
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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: 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
....DiscussionSequencing of VLP DNA detected all known functional LTR retrotransposons in Arabidopsis, as well as some nonfunctional ones. Full-length VLP DNA read coverage from ATCOPIA and ATGP families (Fig. 1B; Supplemental Fig. S3A) corresponded to relatively young and low-copy elements known to transpose. Ancient ATHILA...
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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
...acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics...
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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
...RNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes. Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis. Poly...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...transcription start sites (TSSs) has been identified in a budding yeast Saccharomyces cerevisiae (“scanning model”). Herein, we applied genomic approaches to elucidate the origin of the scanning model and its underlying genetic mechanisms. We first identified TSSs at single-nucleotide resolution for 12 yeast...
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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
...plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals...
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Research: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
- Rik Kooke,
- Lionel Morgado,
- Frank Becker,
- Henriëtte van Eekelen,
- Rashmi Hazarika,
- Qunfeng Zheng,
- Ric C.H. de Vos,
- Frank Johannes,
- and Joost J.B. Keurentjes
Genome Res. January 2019 29: 96-106; Published in Advance November 30, 2018, doi:10.1101/gr.232371.117
...and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epi...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...and dynamically regulated.The variant histone H3.3 has been linked to different steps of DNA replication. It is enriched at replication origins in Drosophila melanogaster and Arabidopsis thaliana (Deal et al. 2010; MacAlpine et al. 2010; Eaton et al. 2011; Stroud et al. 2012; Paranjape and Calvi 2016), and loss...
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