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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
..., a major group of TEs, function by a copy-and-paste mechanism using an RNA intermediate that can cause DNA damage upon integration into the , thereby leading to instability. In response to TEs, the host coevolved various defense mechanisms to silence and control retrotransposons, which include DNA...
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Research: Combinatorial DNA methylation codes at repetitive elements
- Christophe Papin,
- Abdulkhaleg Ibrahim,
- Stéphanie Le Gras,
- Amandine Velt,
- Isabelle Stoll,
- Bernard Jost,
- Hervé Menoni,
- Christian Bronner,
- Stefan Dimitrov,
- and Ali Hamiche
Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
...them independently. We first characterized the Tdg-deficient-dependent changes in DNA methylation at LTR retrotransposons (also known as endogenous retroviruses [ERVs]) in MEFs. For simplicity, we will collectively further refer to LTR retrotransposons as LTRs. The RMSK database distinguishes between...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...). In addition, DNA methylation at ICRs interacts with histone modifications, leading to a distinct histone mark signature (Henckel et al. 2009). The methylated allele displays a heterochromatic signature, enriched with repressive marks such as H3K9me3 and H4K20me3. In contrast, the nonmethylated allele...
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LETTER: Differential methylation of genes and repeats in land plants
- Pablo D. Rabinowicz,
- Robert Citek,
- Muhammad A. Budiman,
- Andrew Nunberg,
- Joseph A. Bedell,
- Nathan Lakey,
- Andrew L. O'Shaughnessy,
- Lidia U. Nascimento,
- W. Richard McCombie,
- and Robert A. Martienssen
Genome Res. October 2005 15: 1431-1440; doi:10.1101/gr.4100405
...is a common DNA modification among eukaryotes, typically in the form of cytosine methylated on carbon-5 (5-methylcytosine, 5mC). Saccharomyces cerevisiae has no 5mC, and in other fungi methylation is targeted to the scarce repeated DNA ( Selker 1990 ; Rossignol and Faugeron 1994 ). The levels and patterns...
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Research: TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
- Helen M. Rowe,
- Adamandia Kapopoulou,
- Andrea Corsinotti,
- Liana Fasching,
- Todd S. Macfarlan,
- Yara Tarabay,
- Stéphane Viville,
- Johan Jakobsson,
- Samuel L. Pfaff,
- and Didier Trono
Genome Res. March 2013 23: 452-461; Published in Advance December 10, 2012, doi:10.1101/gr.147678.112
...deletion in MEFs, it significantly decreased in their ES cell counterparts, albeit not as dramatically as in ES cells deleted for Ehmt2 (G9a), a histone methyltransferase involved in the maintenance of DNA methylation (Fig. 3C, right; Dong et al. 2008; Tachibana et al. 2008). Perhaps explaining this latter...
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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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Research: A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
- Alexandros Bousios,
- Concepcion M. Diez,
- Shohei Takuno,
- Vojtech Bystry,
- Nikos Darzentas,
- and Brandon S. Gaut
Genome Res. February 2016 26: 226-237; Published in Advance December 2, 2015, doi:10.1101/gr.193763.115
...). This chain of events is also thought to occur when a new TE invades a “naïve” (Panda and Slotkin 2013). During transcriptional silencing, the RNA-directed DNA methylation (RdDM) pathway orchestrates the deposition of DNA methylation and heterochromatic histone marks on TEs. The key steps initiate...
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Letter: Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line
- Nelson C. Lau,
- Nicolas Robine,
- Raquel Martin,
- Wei-Jen Chung,
- Yuzo Niki,
- Eugene Berezikov,
- and Eric C. Lai
Genome Res. October 2009 19: 1776-1785; Published in Advance June 18, 2009, doi:10.1101/gr.094896.109
...in somatic ovarian cells. Similar to its endogenous localization in the germarium and embryo, PIWIwas predominantly nuclear in OSS cells, as marked by the overlap with DAPI staining of DNA (Fig. 5C). However, high-magnification deconvolution microscopy revealed that PIWI was largely excluded from the highly...
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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
...of NF-Y sites are located at enhancers, many of which are tissue specific, and nearly half of the NF-Y sites are in select subclasses of HERV LTR repeats. Unlike most TFs, NF-Y can access its target DNA motif in inactive (nonmodified) or polycomb-repressed chromatin domains. Unexpectedly, NF...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...). In normal and developed tissues, TEs are often suppressed by epigenetic mechanisms such as DNA methylation, repressive histone marks, and RNA and protein products such as the PIWI-interacting RNAs (piRNA) and the Krüppel-associated box (KRAB)-containing zinc finger protein (KZFP) family proteins (Liang et...
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