Searching journal content for articles similar to Thomas and Schneider 21 (11): 1800.

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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 group of TFs that have coevolved to bind and repress expression of ERVs (Tadepally et al. 2008; Ecco et al. 2017; Yang et al. 2017; Bruno et al. 2019; Wolf et al. 2020; Senft and Macfarlan 2021). KZFPs bind DNA using tandem arrays of C2H2 zinc-finger domains, each recognizing two to four specific...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
....The Cys2-His2 zinc finger (ZNF) is a short nucleic acid binding domain widespread in eukaryotes. ZNFs are often arranged in tandemly repeated arrays, resulting in proteins with versatile nucleic acid binding ability (Wolfe et al. 2000; Klug 2010; Najafabadi et al. 2017). In metazoans, tandem-repeat ZNF...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...silenced by KRAB zinc finger (KZNF) proteins recruiting corepressor proteins that establish a repressive chromatin state. A number of KZNFs have been reported to bind SVAs, but their individual contribution to repressing SVAs and their roles in suppressing SVA-mediated gene-regulatory effects remains...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...-regulatory sequences responsive to both transcriptional activators as well as repressors. This is reminiscent of mammalian ERVs, which are activated by stage-specific TFs and repressed by sequence-specific KRAB-zinc finger proteins (Bruno et al. 2019; Hermant and Torres-Padilla 2021). Given the lack of the KRAB domain...
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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
...Trim28 knock-out (KO) embryos arrest shortly after implantation and fail to gastrulate (Cammas et al. 2000). TRIM28 is tethered to DNA by sequencespecific Kru¨ppel-associated box zinc finger proteins (KRAB-ZFPs) (Friedman et al. 1996; Emerson and Thomas 2009; Thomas and Schneider 2011) and induces...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...–related genes, we also included zinc-finger (ZF) and serine/threonine kinases (SER) as two non-HLAU gene families. We observed that ORs have enrichment of TEs at the promoters in all s from species of the mojavensis cluster (P-value < 0.05) (Fig. 2A). For acceptance genes, D. koepferae had enrichment of TEs...
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Research: Noncoding origins of anthropoid traits and a new null model of transposon functionalization
- Ricardo C.H. del Rosario,
- Nirmala Arul Rayan,
- and Shyam Prabhakar
Genome Res. September 2014 24: 1469-1484; Published in Advance July 20, 2014, doi:10.1101/gr.168963.113
...of nonexonic ASCs near Kr€uppel-associated box (KRAB) genes (FDR Q-value = 6 3 10#1;65) and zinc finger genes (Q = 5 3 10#1;17). Both signals derive from ASCs flanking KRAB-zinc finger (KZNF) genes (Fig. 2B; Supplemental Table S3), which direct repressive chromatin to retroviral sequences and other genomic...
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