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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...and Madhani 2018). Heterochromatin is generally characterized by repressive epigenetic marks, prominently DNA methylation (5′methylcytosine [5mC]), histone modifications such as histone H3 lysine-9 mono- and dimethylation (H3K9me1/H3K9me2, constitutive heterochromatin) or histone H3 lysine-27 triple...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...suppressed in oocytes (Supplemental Fig. S19G), suggesting maternal inheritance of H3K27me3 like in mouse (Inoue et al. 2017), in Drosophila (Zenk et al. 2017), and in Arabidopsis thaliana (Luo et al. 2020).DiscussionReprogramming of epigenetic modification is a critical process during early development...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
.... These patterns are examples of parent-of-origin effects (POEs), a broader class of epigenetic phenomena that manifest as phenotypic differences according to maternal or paternal inheritance (Lawson et al. 2013). The best characterized POE mechanism is genomic imprinting, an extreme case of parent...
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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
...of the detected miRNAs were shared with oocytes, suggesting their maternal inheritance. A-tailing of miRNAs peaked prominently at the zygote stage and reduced in subsequent embryonic stages. Three of five zygotes had three pronuclei, however it is unclear whether this affects global miRNA and modification levels...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
..., and hypomethylation remains uncorrected. Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the aberrant ICF1 epi. However, a small fraction of the is resilient to this rescue, highlighting the challenge of reverting disease states that are due to -wide epigenetic...
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Perspective: Transgenerational epigenetic inheritance: More questions than answers
- Lucia Daxinger and
- Emma Whitelaw
Genome Res. December 2010 20: 1623-1628; Published in Advance November 1, 2010, doi:10.1101/gr.106138.110
...of histone modifications as well as the contribution of RNA has become increasingly clear. There has always been much interest in the idea that some epigenetic marks can be inherited across generations. However, despite the fact that these marks are considered relatively stable during development (i...
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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
...generations, providing evidence for epigenetic inheritance (Cubas et al. 1999; Manning et al. 2006; Johannes et al. 2009; Martin et al. 2009; Reinders et al. 2009; Cortijo et al. 2014; Kooke et al. 2015). Epigenetic variation is widespread and heritable in nature where it maintains independently...
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Research: Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
- Anish Dattani,
- Damian Kao,
- Yuliana Mihaylova,
- Prasad Abnave,
- Samantha Hughes,
- Alvina Lai,
- Sounak Sahu,
- and A. Aziz Aboobaker
Genome Res. October 2018 28: 1543-1554; Published in Advance August 24, 2018, doi:10.1101/gr.239848.118
....aboobaker@zoo.ox.ac.ukAbstractPlanarian flatworms have an indefinite capacity to regenerate missing or damaged body parts owing to a population of pluripotent adult stems cells called neoblasts (NBs). Currently, little is known about the importance of the epigenetic status of NBs and how histone modifications regulate homeostasis and cellular...
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Perspective: The Mendelian disorders of the epigenetic machinery
- Hans Tomas Bjornsson
Genome Res. October 2015 25: 1473-1481; doi:10.1101/gr.190629.115
...to be inherited through mitosis (Russo et al. 1996). These can involve either the addition of a methyl group to a cytosine (cytosine methylation) or the addition of covalent modifications to histone tails. Here I will summarize the components that are currently known to maintain epigenetic modifications...
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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
...segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9...
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