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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
...contributed equally to this work. Corresponding authors: jnw72@cornell.edu, cf458@cornell.eduAbstractCys2-His2 zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
....trono@epfl.chAbstractKrüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged...
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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: 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
...HLH transcription factors. Oncogene 24: 6729–6736. Brayer KJ, Kulshreshtha S, Segal DJ. 2008. The protein-binding potential of C2H2 zinc finger domains. Cell Biochem Biophys 51: 9–19. Burdach J, O’Connell MR, Mackay JP, Crossley M. 2012. Two-timing zinc finger transcription factors liaising with RNA. Trends Biochem...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...-associated box (KRAB) domain and a C-terminal zinc finger array, which for many mediates sequence-specific DNA recognition. The KRAB domain of a majority of KZFPs recruits the transcriptional corepressor TRIM28 (also known as KAP1), which acts as a scaffold for heterochromatin inducers such as the histone methyl...
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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
...numbers of tandem C2H2 zinc finger (tandem ZF) transcription factor proteins. In mammals, most tandem ZF genes also encode a KRAB domain (KZNF proteins). Very little is known about what forces have driven the number and diversity of tandem ZF genes. Recent studies suggest that one role of KZNF proteins...
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LETTER: Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes
- Aaron T. Hamilton,
- Stuart Huntley,
- Mary Tran-Gyamfi,
- Daniel M. Baggott,
- Laurie Gordon,
- and Lisa Stubbs
Genome Res. May 2006 16: 584-594; Published in Advance April 10, 2006, doi:10.1101/gr.4843906
..., divergence, and loss that have continued in each mammalian group. One such family encodes KRAB-zinc finger (KRAB-ZNF) proteins, which function as transcriptional repressors. One particular subfamily of KRAB-ZNF genes, including ZNF91, has expanded specifically in primates to comprise more than 110 loci...
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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
...embryos. [Supplemental material is available for this article.] TRIM28 (tripartite motif-containing protein 28, also known as KAP1, KRAB-associated protein 1, or TIF1b) is a co-repressor that is highly expressed in embryonic stem (ES) cells and is crucial to early mouse development, because homozygous...
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Research: Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells
- Ashley T. Neff,
- Ju Youn Lee,
- Jeffrey Wilusz,
- Bin Tian,
- and Carol J. Wilusz
Genome Res. August 2012 22: 1457-1467; Published in Advance April 25, 2012, doi:10.1101/gr.134312.111
...in increased stability of many histone mRNAs in iPS cells. A second pathway stabilizes a large set of zinc finger protein mRNAs, potentially through reduced levels of miRNAs that target them. Finally, a group of transcripts bearing 39 UTR C-rich sequence elements, many of which encode transcription factors...
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Research: Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs
- Michael Schnall-Levin,
- Olivia S. Rissland,
- Wendy K. Johnston,
- Norbert Perrimon,
- David P. Bartel,
- and Bonnie Berger
Genome Res. September 2011 21: 1395-1403; Published in Advance June 17, 2011, doi:10.1101/gr.121210.111
.... MicroRNA-181a modulates gene expression of zinc finger family members by directly targeting their coding regions. Nucleic Acids Res 38: 7211–7218. Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L. 2006. A comprehensive catalog of human KRAB-associated...
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