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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
...KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and evolution Kai Otsuka1,2, Akihiko Sakashita3,4, So Maezawa2, Richard M. Schultz1,5 and Satoshi H. Namekawa1,3 1Department of Microbiology and Molecular Genetics, University of California, Davis...
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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
...(Perumal et al. 2020). As Gypsy and Copia retrotransposon families diverged ∼1 billion years ago (Llorens et al. 2009), this is further consistent with multiple LTR families convergently evolving centrophilic adaptations in different plant lineages.In the case of Arabidopsis, the majority (>90...
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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
...the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.Epigenomic modifications constitute additional regulatory layers that can alter and...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-stimulated primary aortic endothelial cells isolated from human, mouse, and cow, we find that 55 TE subfamilies are associated with RELA-bound regions, many of which reside near TNF-responsive genes. A prominent example of lineage-specific contribution of transposons comes from the bovine SINE subfamilies Bov-tA1...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
....Duplications are a major contributor to functional and divergence (Lynch and Conery 2000; Adams and Wendel 2005) especially within plant lineages (Hanada et al. 2008; Van de Peer et al. 2009). We found that duplications were highly abundant between all s, and that at smaller divergence times, duplications contributed...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...were loaded on R10.4 FLO-PRO112 flow cells and sequenced on PromethION P24 sequencer using the super accuracy model (Supplemental Table 3). See also the data release at https://www.keygene.com/newsitem/fast-contiguous-and-accurate-arabidopsis-col-0and-tomato-heinz-1706--assembly-thanks-to-new-chemistry-nano-pores-and-plant...
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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
...component of the large s of most animal and plant species (Huang et al. 2012; Wang et al. 2014). The mouse , for example, contains more than 1 million ERVs, of which only a handful are autonomous elements (Huang et al. 2012; Gagnier et al. 2019). In Arabidopsis thaliana, ancient Ty3/gypsy-type ATHILA...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger with distributed heterochromatin compared with Arabidopsis. Our results indicate the division of labor among plant...
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Research: HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses
- Rafael Contreras-Galindo,
- Mark H. Kaplan,
- Shirley He,
- Angie C. Contreras-Galindo,
- Marta J. Gonzalez-Hernandez,
- Ferdinand Kappes,
- Derek Dube,
- Susana M. Chan,
- Dan Robinson,
- Fan Meng,
- Manhong Dai,
- Scott D. Gitlin,
- Arul M. Chinnaiyan,
- Gilbert S. Omenn,
- and David M. Markovitz
Genome Res. September 2013 23: 1505-1513; Published in Advance May 8, 2013, doi:10.1101/gr.144303.112
...HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses Rafael Contreras-Galindo 1 , Mark H. Kaplan 1 , Shirley He 1 , Angie C. Contreras-Galindo 1 , Marta J. Gonzalez-Hernandez 1 , Ferdinand Kappes...
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