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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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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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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
...-associated box ZNF (KZNF) subfamily. Currently, it is unknown whether this function and coevolutionary relationship is unique to KZNFs or is a broader feature of metazoan ZNFs. Here, we present evidence that genomic conflict with TEs has been a central driver of the diversification of ZNFs in animals. Sampling...
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Resource: Multiparameter functional diversity of human C2H2 zinc finger proteins
- Frank W. Schmitges,
- Ernest Radovani,
- Hamed S. Najafabadi,
- Marjan Barazandeh,
- Laura F. Campitelli,
- Yimeng Yin,
- Arttu Jolma,
- Guoqing Zhong,
- Hongbo Guo,
- Tharsan Kanagalingam,
- Wei F. Dai,
- Jussi Taipale,
- Andrew Emili,
- Jack F. Greenblatt,
- and Timothy R. Hughes
Genome Res. December 2016 26: 1742-1752; Published in Advance November 16, 2016, doi:10.1101/gr.209643.116
...Corresponding authors: t.hughes@utoronto.ca ; jack.greenblatt@utoronto.ca ↵ 5 Present address: McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada Abstract C2H2 zinc finger proteins represent...
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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: Coevolution of retroelements and tandem zinc finger genes
- James H. Thomas and
- Sean Schneider
Genome Res. November 2011 21: 1800-1812; Published in Advance July 22, 2011, doi:10.1101/gr.121749.111
...is known about the function of these genes. Within mammals, tandem ZF genes are dominated by those with a KRAB domain, which expanded from a KRAB— tandem ZF fusion gene near the root of tetrapod vertebrates (Birtle and Ponting 2006). Most KRAB zinc finger (KZNF) proteins consist of an N-terminal KRAB...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...applied specific score thresholds to ensure accuracy: ZNF_C2H2: 0 (per domain), KRAB: 510 13, SCAN: 10, DUF3669: 21. To identify putative KZFP isoforms, we conducted proximity 511 analysis by examining genomic loci for instances where KRAB domain-containing proteins 512 were located near C2H2 zinc finger...
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LETTER: Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters
- Mark Shannon,
- Aaron T. Hamilton,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. June 2003 13: 1097-1110; Published in Advance May 12, 2003, doi:10.1101/gr.963903
...with significantly different amino acid sequences, suggesting that the related proteins probably recognize target DNA sequences that are subtly or even substantially distinct. Assignment of the 21 human and 10 mouse genes to specific positions within each cluster revealed two key features. First, the relative order...
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RESEARCH: Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12
- Evan E. Eichler,
- Susan M. Hoffman,
- Aaron A. Adamson,
- Laurie A. Gordon,
- Paula McCready,
- Jane E. Lamerdin,
- and Harvey W. Mohrenweiser
Genome Res. August 1, 1998 8: 791-808; doi:10.1101/gr.8.8.791
..., Mohrenweiser Evan Eichler Laurie A, Gordon Laurie Gordon McCready 10.1101/gr.8.8.791 1549-5469 1088-9051 genome;8/8/791 Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12 Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
..., Imbeault M, De Tribolet-Hardy J, Turelli P, Persat A, Trono D. 2022. KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. Mobile DNA 13. Jacques P-É, Jeyakani J, Bourque G. 2013. The majority of primate-specific regulatory sequences...
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