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Research: Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division
- Yajing Hao,
- Dongpeng Wang,
- Shuheng Wu,
- Xiao Li,
- Changwei Shao,
- Peng Zhang,
- Jia-Yu Chen,
- Do-Hwan Lim,
- Xiang-Dong Fu,
- Runsheng Chen,
- and Shunmin He
Genome Res. November 2020 30: 1570-1582; Published in Advance October 15, 2020, doi:10.1101/gr.256131.119
...repeat-derived endo-siRNA mimics are sufficient to rescue Dcr-2-deficiency-induced defects in heterochromatin formation in interphase and chromosome segregation during mitosis, demonstrating that active retrotransposons are required for stable genetic inheritance.Eukaryotic s contain both gene...
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Research: The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes
- Luisa Robbez-Masson,
- Christopher H.C. Tie,
- Lucia Conde,
- Hale Tunbak,
- Connor Husovsky,
- Iva A. Tchasovnikarova,
- Richard T. Timms,
- Javier Herrero,
- Paul J. Lehner,
- and Helen M. Rowe
Genome Res. May 4, 2018 ; Published in Advance May 4, 2018, doi:10.1101/gr.228171.117
...Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom; 3Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom Retrotransposons encompass half of the human and contribute to the formation of heterochromatin, which provides...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...assessments. Our study establishes a fundamental genomic resource for future research on truffle genomics and showcases a clear example of how establishment and self-perpetuating expansion of heterochromatin can drive massive size variation owing to activity of selfish genetic elements.Transposable elements...
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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
...: arturo.mari-ordonez@gmi.oeaw.ac.atAbstractA handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24 nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...in wheat, which can be CENH3-occupied (Presting et al. 1998; Nagaki et al. 2005b; Gao et al. 2008; Neumann et al. 2011; Li et al. 2013; Sharma and Presting 2014). CRM family retrotransposons are typified by a chromodomain fusion at the C terminus of the integrase open reading frame (Gao et al. 2008...
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Research: Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- Nicole C. Riddle,
- Aki Minoda,
- Peter V. Kharchenko,
- Artyom A. Alekseyenko,
- Yuri B. Schwartz,
- Michael Y. Tolstorukov,
- Andrey A. Gorchakov,
- Jacob D. Jaffe,
- Cameron Kennedy,
- Daniela Linder-Basso,
- Sally E. Peach,
- Gregory Shanower,
- Haiyan Zheng,
- Mitzi I. Kuroda,
- Vincenzo Pirrotta,
- Peter J. Park,
- Sarah C.R. Elgin,
- and Gary H. Karpen
Genome Res. February 2011 21: 147-163; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110
...Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin Nicole C. Riddle 1 , 9 , Aki Minoda 2 , 9 , Peter V. Kharchenko 3 , 9 , Artyom A. Alekseyenko 4 , Yuri B. Schwartz 5 , 6...
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LETTER: Human heterochromatin proteins form large domains containing KRAB-ZNF genes
- Maartje J. Vogel,
- Lars Guelen,
- Elzo de Wit,
- Daniel Peric Hupkes,
- Martin Lodén,
- Wendy Talhout,
- Marike Feenstra,
- Ben Abbas,
- Anne-Kathrin Classen,
- and Bas van Steensel
Genome Res. December 2006 16: 1493-1504; Published in Advance October 12, 2006, doi:10.1101/gr.5391806
...), and Cbx5 (HP1α) in mice. Mammalian HP1 proteins are also enriched in pericentric heterochromatin ( Maison and Almouzni 2004 ). HP1 proteins contain two conserved protein domains, the N-terminal chromodomain (CD) and the C-terminal chromoshadow-domain (CSD). Both domains have been shown to contribute...
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Research: Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
- Alex de Mendoza,
- Jahnvi Pflueger,
- and Ryan Lister
Genome Res. August 2019 29: 1277-1286; Published in Advance June 25, 2019, doi:10.1101/gr.243774.118
...in the Strigamia . This strategy would be analogous to chromoviruses, a type of Gypsy retrotransposon known to use chromodomains to direct the integration of new copies to heterochromatic regions (Gao et al. 2008). Similarly, many retrotransposons encode a PHD finger domain (Kapitonov and Jurka 2003; Pérez...
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ARTICLE: Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
- Nathan J. Bowen,
- I. King Jordan,
- Jonathan A. Epstein,
- Valerie Wood,
- and Henry L. Levin
Genome Res. September 2003 13: 1984-1997; doi:10.1101/gr.1191603
...Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe Nathan J. Bowen 1 , 5 , I. King Jordan 2 , Jonathan A. Epstein 3 , Valerie...
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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
...hotspots in A. thaliana can be silenced by RNA-directed DNA methylation associated with gain of H3K9me2 and both CG and non-CG methylation (Yelina et al. 2015). Furthermore, in fission yeast, arrested recombination intermediates accumulate strongly in wild-type heterochromatin, but not in clr4 and rik1...
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